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  • 1.
    Androsiuk, P.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. University of Warmia & Mazury, Poland.
    Shimono, A.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Westin, J.
    Lindgren, D.
    Fries, A.
    Wang, X. -R
    Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden2013In: Silvae Genetica, ISSN 0037-5349, Vol. 62, no 3, p. 127-136Article in journal (Refereed)
    Abstract [en]

    Efficient use of any breeding resources requires a good understanding of the genetic value of the founder breeding materials for predicting the gain and diversity in future generations. This study evaluates the distribution of genetic variation and level of relatedness among and within nine breeding populations of Norway spruce for Northern Sweden using nuclear microsatellite markers. A sample set of 456 individuals selected from 140 stands were genotyped with, 15 SSR loci. Over all loci each individual was identified with unique multilocus genotype. High genetic diversity (average H-e=0.820) and low population differentiation (F-ST = 0.0087) characterized this material. Although low in F-ST, the two northernmost populations were clustered as a distinct group diverged from the central populations. The population differentiation pattern corresponds well with the post glacial migration history of Norway spruce and the current gene flow and human activity in the region. The average inbreeding coefficient was 0.084 after removal loci with high frequency of null alleles. The estimated relatedness of the trees gathered in the breeding populations was very low (average kinship coefficient 0.0077) and not structured. The high genetic variation and low and not structured relatedness between individuals found in the breeding populations confirm that the Norway spruce breeding stock for northern Sweden represent valuable genetic resources for both long-term breeding and conservation programs.

  • 2. Araki, N.H.T.
    et al.
    Khatab, I.A.
    Hemamali, K.K.G.U.
    Inomata,, N.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Szmidt, A.E.
    Phylogeography of Larix sukaczewii Dyl. and Larix sibirica L. inferred from nucleotide variation of nuclear genes2008In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 4, p. 611-623Article in journal (Refereed)
    Abstract [en]

    We investigated phylogeography of Larix sukaczewii and Larix sibirica using nucleotide variation at three following nuclear gene regions: 5.8 S rDNA including two internal transcribed spacers (ITS), cinnamyl alcohol dehydrogenase (CAD), and phytochrome-O (PHYO). We also included sequences of the 4-coumarate: coenzyme A ligase (4CL) gene region obtained in our recent study. CAD and PHYO showed very low nucleotide variation, but ITS and 4CL had levels of variation similar to those reported for other conifers. Pleistocene refugia have been hypothesized to exist in the Southern Urals and South Central Siberia, where four out of nine of the investigated populations occur. We found moderate to high levels of population differentiation (FST=0.115–0.531) in some pairwise comparisons suggesting limited gene flow and independent evolution of some refugial populations. In L. sukaczewii, low levels of differentiation were found among populations from areas glaciated during the Pleistocene, indicating their recent origin. Our results also suggest these populations were created by migrants from multiple, genetically distinct refugia. Furthermore, some haplotypes observed in populations from previously glaciated areas were not found in putative refugial populations, suggesting these populations might have contributed little to the extant populations created after the Last Glacial Maximum. Some authors regard L. sukaczewii and L. sibirica as a single species, while others consider them as separate species. The observed conspicuous differences in haplotype composition and distribution between L. sukaczewii and L. sibirica, together with high values of FST between populations of the two species, appear to support the latter classification.

  • 3. Chen, Xinyu
    et al.
    Yuan, Huwei
    Hu, Xiange
    Meng, Jingxiang
    Zhou, Xianqing
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. National Engineering Laboratory for Forest Tree Breeding, Key Laboratory of Genetic and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People’s Republic of China.
    Li, Yue
    Variations in electrical impedance and phase angle among seedlings of Pinus densata and parental species in Pinus tabuliformis habitat environment2015In: Journal of Forestry Research, ISSN 1007-662X, E-ISSN 1993-0607, Vol. 26, no 3, p. 777-783Article in journal (Refereed)
    Abstract [en]

    Electrical impedance (EI) and phase angle (PHI) parameters in AC impedance spectroscopy are important electrical parameters in the study of medical pathology. However, little is known about their application in variation and genetic relationship studies of forest trees. In order to test whether impedance parameters could be used in genetic relationship analysis among conifer species, EI and PHI were measured in a seedling experiment test composed of Pinus tabuliformis, Pinus yunnanensis, and Pinus densata in a habitat of Pinus tabuliformis. The results showed that variations in both EI and PHI among species were significant in different electric frequencies, and the EI and PHI values measured in the two populations of P. densata were between the two parental species, P. yunnanensis and P. tabuliformis. These results show that these two impedance parameters could reflect the genetic relationship among pine species. This was the first time using the two AC impedance spectroscopy parameters to test the genetic relationship analysis between tree species, and would be a hopeful novel reference methodology for future studies in evolution and genetic variation of tree species.

  • 4.
    Funda, Tomas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wennstrom, Ulfstand
    Almqvist, Curt
    Torimaru, Takeshi
    Gull, Bengt Andersson
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Low rates of pollen contamination in a Scots pine seed orchard in Sweden: the exception or the norm?2015In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 30, no 7, p. 573-586Article in journal (Refereed)
    Abstract [en]

    We investigated mating structure and gene flow in a clonal seed orchard of Scots pine (Pinus sylvestris L.) over three consecutive pollination seasons (2010-2012) with nine nuclear microsatellite markers. The paternity of 1991 offspring from four maternal parents was assigned to 28 candidate fathers using an exclusion procedure and a likelihood-based method implemented in the program CERVUS. Relative reproductive success was highly variable among pollen parents but consistent across years and ranged from 0.1% to 18.3%. Consequently, the seed crops' effective number of fathers was reduced to 52.9%, 48.8%, and 45.7% of the census in the three seasons, respectively. Self-fertilization fluctuated around the orchard's expected value of 5.1%, reaching 4.05%, 7.71%, and 6.61%, respectively. Pollen contamination was estimated to be 5.64%, 7.29%, and 4.89%, respectively, after correction for cryptic gene flow. CERVUS provided similar results as the exclusion method, but estimates greatly varied depending on the input parameters, mainly the proportion of fathers sampled. These results indicate the studied seed orchard is a well-functioning production population with only minor negative effects of self-fertilization and pollen contamination on the quality of seed crops. Genotyping issues associated with microsatellites as a potential source of false paternity assignment and exclusion are discussed.

  • 5.
    Funda, Tomas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Forest Genetics and Plant Physiology, UPSCSwedish University of Agricultural Sciences, Umeå, Sweden.
    Wennström, Ulfstand
    Almqvist, Curt
    Andersson Gull, Bengt
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Mating dynamics of Scots pine in isolation tents2016In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 12, no 6, article id 112Article in journal (Refereed)
    Abstract [en]

    Seed orchards are forest tree production populations for supplying the forest industry with consistent and abundant seed crops of superior genetic quality. However, genetic quality can be severely affected by non-random mating among parents and the occurrence of background pollination. This study analyzed mating structure and background pollination in six large isolation tents established in a clonal Scots pine seed orchard in northern Sweden. The isolation tents were intended to form a physical barrier against background pollen and induce earlier flowering relative to the surrounding trees. We scored flowering phenology inside and outside the tents and tracked airborne pollen density inside and outside the seed orchard in three consecutive pollination seasons. We genotyped 5683 offspring collected from the tents and open controls using nine microsatellite loci, and assigned paternity using simple exclusion method. We found that tent trees shed pollen and exhibited maximum female receptivity approximately 1 week earlier than trees in open control. The majority of matings in tents (78.3 %) occurred at distances within two trees apart (about 5 m). Self-fertilization was relatively high (average 21.8 %) in tents without supplemental pollination (SP), but it was substantially reduced in tents with SP (average 7.7 %). Pollen contamination was low in open controls (4.8-7.1 %), and all tents remained entirely free of foreign pollen. Our study demonstrates that tent isolation is effective in blocking pollen immigration and in manipulating flowering phenology. When complimented with supplemental pollination, it could become a useful seed orchard management practice to optimize the gain and diversity of seed orchard crops.

  • 6.
    Gao, Jie
    et al.
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Wang, Baosheng
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Mao, Ian-Feng
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zeng, Qing-Yin
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 19, p. 4811-4827Article in journal (Refereed)
    Abstract [en]

    Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.

  • 7.
    Hall, David
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Advanced Innovation Center for Tree Breeding by MolecularDesign; College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Wennström, Ulfstand
    Andersson Gull, Bengt
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing2020In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540Article in journal (Refereed)
    Abstract [en]

    Estimating kinship is fundamental for studies of evolution, conservation, and breeding. Genotyping-by-sequencing (GBS) and other restriction based genotyping methods have become widely applied in these applications in non-model organisms. However, sequencing errors, depth, and reproducibility between library preps could potentially hinder accurate genetic inferences. In this study, we tested different sets of parameters in data filtering, different reference populations and eight estimation methods to obtain a robust procedure for relatedness estimation in Scots pine (Pinus sylvestris L.). We used a seed orchard as our study system, where candidate parents are known and pedigree reconstruction can be compared with theoretical expectations. We found that relatedness estimates were lower than expected for all categories of kinship estimated if the proportion of shared SNPs was low. However, estimates reached expected values if loci showing an excess of heterozygotes were removed and genotyping error rates were considered. The genetic variance-covariance matrix (G-matrix) estimation, however, performed poorly in kinship estimation. The reduced relatedness estimates are likely due to false heterozygosity calls. We analyzed the mating structure in the seed orchard and identified a selfing rate of 3% (including crosses between clone mates) and external pollen contamination of 33.6%. Little genetic structure was observed in the sampled Scots pine natural populations, and the degree of inbreeding in the orchard seed crop is comparable to natural stands. We illustrate that under our optimized data processing procedure, relatedness, and genetic composition, including level of pollen contamination within a seed orchard crop, can be established consistently by different estimators.

  • 8. Hu, Xian-Ge
    et al.
    Jin, Yuqing
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mao, Jian-Feng
    Li, Yue
    Predicting Impacts of Future Climate Change on the Distribution of the Widespread Conifer Platycladus orientalis2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 7, article id e0132326Article in journal (Refereed)
    Abstract [en]

    Chinese thuja (Platycladus orientalis) has a wide but fragmented distribution in China. It is an important conifer tree in reforestation and plays important roles in ecological restoration in the arid mountains of northern China. Based on high-resolution environmental data for current and future scenarios, we modeled the present and future suitable habitat for P. orientalis, evaluated the importance of environmental factors in shaping the species' distribution, and identified regions of high risk under climate change scenarios. The niche models showed that P. orientalis has suitable habitat of ca. 4.2x10(6) km(2) across most of eastern China and identified annual temperature, monthly minimum and maximum ultraviolet-B radiation and wet-day frequency as the critical factors shaping habitat availability for P. orientalis. Under the low concentration greenhouse gas emissions scenario, the range of the species may increase as global warming intensifies; however, under the higher concentrations of emissions scenario, we predicted a slight expansion followed by contraction in distribution. Overall, the range shift to higher latitudes and elevations would become gradually more significant. The information gained from this study should be an useful reference for implementing long-term conservation and management strategies for the species.

  • 9. Hu, Xian-Ge
    et al.
    Liu, Hui
    Jin, YuQing
    Sun, Yan-Qiang
    Li, Yue
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Beijing Forestry Univ, Natl Engn Lab Tree Breeding, Key Lab Genet & Breeding Forest Trees & Ornamenta, Beijing, China.
    El-Kassaby, Yousry A.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Beijing Forestry Univ, Natl Engn Lab Tree Breeding, Key Lab Genet & Breeding Forest Trees & Ornamenta, Beijing, China.
    Mao, Jian-Feng
    De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 2, article id e0148985Article in journal (Refereed)
    Abstract [en]

    Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.

  • 10. Hu, Xian-Ge
    et al.
    Liu, Hui
    Zhang, Jia-Qing
    Sun, Yan-Qiang
    Jin, YuQing
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    El-Kassaby, Yousry A.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Mao, Jian-Feng
    Global transcriptome analysis of Sabina chinensis (Cupressaceae), a valuable reforestation conifer2016In: Molecular breeding, ISSN 1380-3743, E-ISSN 1572-9788, Vol. 36, no 7, article id 99Article in journal (Refereed)
    Abstract [en]

    Sabina chinensis has broad distribution in China and is widely used in the reforestation and as an urban tree. The species is frost resistant and grows well on contaminated soils and is becoming valuable for soil remediation and protection against air pollution. Breeding programs aimed at exploiting the species' unique properties were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from five different tissues using RNA-Seq to gain insight on the functional genes and the development of molecular markers for breeding and conservation purposes. In total 90,382,108 high-quality sequence reads (similar to 9.0 bp) were obtained, and 116,814 unigenes (>= 200 nt) were assembled. Of which, 45,026 and 15,589 unigenes were mapped to the Nr and KOG databases, 31,288 (26.78 %) and 17,596 (15.06 %) were annotated to GO and KEGG database, respectively. Additionally, 28,843 (24.68 %) and 43,033 (36.84 %) S. chinensis unigenes were aligned to the Pinus taeda draft genome and PLAZA2.5 database, respectively. A total of 4570 simple sequence repeat (SSR) motifs were identified in the unigenes. Furthermore, we obtained 6 (12.5 %) polymorphic and 21 (43.75 %) monomorphic loci in the verification of 48 randomly selected SSR loci. This study represents the first transcriptome data of S. chinensis and confirms that the transcriptome assembly data of S. chinensis are a useful resource for EST-SSR loci development. The substantial number of transcripts obtained will aid our understanding of the species adaptation mechanisms and provide valuable genomic information for conservation and breeding applications.

  • 11. Inomata, Nobuyuki
    et al.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Changtragoon, Suchitra
    Szmidt, Alfred E
    Levels and patterns of DNA variation in two sympatric mangrove species, Rhizophora apiculata and R. mucronata from Thailand2009In: Genes & Genetic Systems, ISSN 1341-7568, E-ISSN 1880-5779, Vol. 84, no 4, p. 277-86Article in journal (Refereed)
    Abstract [en]

    In mangrove species the past geomorphic changes in coastal regions and reproductive systems are important factors of their distribution and genetic structure of populations. However, very little is known about the levels of genetic variation of Rhiozophora species in Southeast Asia. In this study, we surveyed levels and patterns of genetic variation as well as population structure of two sympatric mangrove species, Rhizophora apiculata and R. mucronata in Thailand, using five nuclear genes and two cpDNA regions. In all investigated DNA regions, nucleotide variation within species was low, while nucleotide divergence between the two species was considerable. The nuclear genes evolved 10 times faster than the cpDNA regions. In both R. apiculata and R. mucronata, significant positive F(IS) values were found, indicating deviation from Hardy-Weinberg proportions and a deficiency of heterozygotes. In both species, we found significant genetic differentiation between populations. However, the pattern of population differentiation (F(ST)) of R. apiculata differed from that of R. mucronata. Our results suggest that the two investigated species have different demographic history, even though they are sympatric and have similar reproductive systems.

  • 12. Jia, Kai-Hua
    et al.
    Zhao, Wei
    Maier, Paul Andrew
    Hu, Xian-Ge
    Jin, Yuqing
    Zhou, Shan-Shan
    Jiao, Si-Qian
    El-Kassaby, Yousry A.
    Wang, Tongli
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Mao, Jian-Feng
    Landscape genomics predicts climate change-related genetic offset for the widespread Platycladus orientalis (Cupressaceae)2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571Article in journal (Refereed)
    Abstract [en]

    Understanding and quantifying populations' adaptive genetic variation and their response to climate change are critical to reforestation's seed source selection, forest management decisions, and gene conservation. Landscape genomics combined with geographic and environmental information provide an opportunity to interrogate forest populations' genome-wide variation for understanding the extent to which evolutionary forces shape past and contemporary populations' genetic structure, and identify those populations that may be most at risk under future climate change. Here, we used genotyping by sequencing to generate over 11,000 high-quality variants from Platycladus orientalis range-wide collection to evaluate its diversity and to predict genetic offset under future climate scenarios. Platycladus orientalis is a widespread conifer in China with significant ecological, timber, and medicinal values. We found population structure and evidences of isolation by environment, indicative of adaptation to local conditions. Gradient forest modeling identified temperature-related variables as the most important environmental factors influencing genetic variation and predicted areas with higher risk under future climate change. This study provides an important reference for forest resource management and conservation for P. orientalis.

  • 13. Jin, Yuqing
    et al.
    Ma, Yongpeng
    Wang, Shun
    Hu, Xian-Ge
    Huang, Li-Sha
    Li, Yue
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). 1National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Mao, Jian-Feng
    Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 34821Article in journal (Refereed)
    Abstract [en]

    Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average H-e = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

  • 14. Jin, Yuqing
    et al.
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; .
    Nie, Shuai
    Liu, Si-Si
    El-Kassaby, Yousry A.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
    Mao, Jian-Feng
    Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae)2019In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 11, p. 3663-3672Article in journal (Refereed)
    Abstract [en]

    Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species' genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species' 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.

  • 15. Khatab, Ismael A
    et al.
    Ishiyama, Hiroko
    Inomata, Nobuyuki
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Szmidt, Alfred E
    Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes.2008In: Genes & Genetic Systems, ISSN 1341-7568, Vol. 83, no 1, p. 55-66Article in journal (Refereed)
    Abstract [en]

    Larch (Larix Mill.) is one of the most widely distributed tree genera in Eurasia. To determine population structure and to verify classification of five species and three varieties of the Eurasian Larix species, we investigated levels and patterns of nucleotide variation of two nuclear gene regions: the 4-coumarate coenzyme A ligase (4CL) and the coumarate 3-hydroxylase (C3H). In the 4CL region nucleotide diversity at silent sites (πsil) varied between 0.0020 in L. gmelinii to 0.0116 in L. gmelinii var. japonica and in the C3H region between 0.0019 in L. kaempferi to 0.0066 in L. gmelinii var. japonica. In both gene regions statistically significant population differentiation (FST) was detected among adjacent refugial populations of some species suggesting limited gene flow and/or long time isolation of some refugial populations. On the other hand, populations of L. sukaczewii from northwestern Russia, which was glaciated 20,000 years ago showed no differentiation. This result is consistent with recent postglacial origin of these populations. Haplotype composition of some of the investigated Eurasian Larix species suggested that they are considerably diverged. Some haplotypes were unique to individual species. Our results indicate that more intensive sampling especially from known refugial regions is necessary for inferring correct classification of Eurasian Larix species and inferring their postglacial migration.

  • 16. Lan, Ting
    et al.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zeng, Qing-Yin
    Structural and Functional Evolution of Positively Selected Sites in Pine Glutathione S-Transferase Enzyme Family2013In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 288, no 34, p. 24441-24451Article in journal (Refereed)
    Abstract [en]

    Phylogenetic analyses have identified positive selection as an important driver of protein evolution, both structural and functional. However, the lack of appropriate combined functional and structural assays has generally hindered attempts to elucidate patterns of positively selected sites and their effects on enzyme activity and substrate specificity. In this study we investigated the evolutionary divergence of the glutathione S-transferase (GST) family in Pinus tabuliformis, a pine that is widely distributed from northern to central China, including cold temperate and drought-stressed regions. GSTs play important roles in plant stress tolerance and detoxification. We cloned 44 GST genes from P. tabuliformis and found that 26 of the 44 belong to the largest (Tau) class of GSTs and are differentially expressed across tissues and developmental stages. Substitution models identified five positively selected sites in the Tau GSTs. To examine the functional significance of these positively selected sites, we applied protein structural modeling and site-directed mutagenesis. We found that four of the five positively selected sites significantly affect the enzyme activity and specificity; thus their variation broadens the GST family substrate spectrum. In addition, positive selection has mainly acted on secondary substrate binding sites or sites close to (but not directly at) the primary substrate binding site; thus their variation enables the acquisition of new catalytic functions without compromising the protein primary biochemical properties. Our study sheds light on selective aspects of the functional and structural divergence of the GST family in pine and other organisms.

  • 17. Lan, Ting
    et al.
    Yang, Zhi-Ling
    Yang, Xue
    Liu, Yan-Jing
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zeng, Qing-Yin
    Extensive functional diversification of the Populus glutathione S-transferase supergene family2009In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 21, no 12, p. 3749-3766Article in journal (Refereed)
    Abstract [en]

    Identifying how genes and their functions evolve after duplication is central to understanding gene family radiation. In this study, we systematically examined the functional diversification of the glutathione S-transferase (GST) gene family in Populus trichocarpa by integrating phylogeny, expression, substrate specificity, and enzyme kinetic data. GSTs are ubiquitous proteins in plants that play important roles in stress tolerance and detoxification metabolism. Genome annotation identified 81 GST genes in Populus that were divided into eight classes with distinct divergence in their evolutionary rate, gene structure, expression responses to abiotic stressors, and enzymatic properties of encoded proteins. In addition, when all the functional parameters were examined, clear divergence was observed within tandem clusters and between paralogous gene pairs, suggesting that subfunctionalization has taken place among duplicate genes. The two domains of GST proteins appear to have evolved under differential selective pressures. The C-terminal domain seems to have been subject to more relaxed functional constraints or divergent directional selection, which may have allowed rapid changes in substrate specificity, affinity, and activity, while maintaining the primary function of the enzyme. Our findings shed light on mechanisms that facilitate the retention of duplicate genes, which can result in a large gene family with a broad substrate spectrum and a wide range of reactivity toward different substrates.

  • 18. Li, Wei
    et al.
    Wang, Xiaoru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Li, Yue
    Variation in floral phenological synchronization in a clonal seed orchard of pinus tabuliformis in northeast of China2012In: Silvae Genetica, ISSN 0037-5349, Vol. 61, no 4-5, p. 133-142Article in journal (Refereed)
    Abstract [en]

    Flowering phenology in an orchard is a crucial factor affecting the gene exchange among clones and consequently changing genetic composition of the seed crop. Pinus tabuliformis is now at the crucial period from first generation clonal seed orchards to advanced generation seed orchards in China. In this study, variation and stability in floral phenological synchronization of all the clones and possible mating pairs, in terms of an index of phenological overlap, were observed in a first generation clonal seed orchard which located in northeast of China. Results showed that significant variations occurred in the clones and mating pairs. This kind of variation was apparently related with temperature and humidity of the research site. With increasing age, levels of flowering synchronization were likely to rise in the clones and mating pairs. In general, the average flowering synchronization of male parents was slightly higher than that of female parents, female management in a seed orchard should be paied more attention. Flowering time was under strong genetic control and this genetic control was stronger in the female flowering process than of the males in terms of board sense heritability and year to year correlation analysis. Flowering synchronization of female parents was positively correlated between most years and can be a reliable reference for early and late predication in Pinus tabuliformis seed orchard during stage of initial seed harvest to stable seed production. According to their average levels of flowering synchronization, 49 clones in the first generation clonal seed orchard were divided into 11 different groups. Results of this paper provided the basic information for first generation seed orchard management and advanced seed orchard establishment of Pinus tabuliformis.

  • 19. Liu, Yan-Jing
    et al.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zeng, Qing-Yin
    De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China2019In: Science China Life Sciences, ISSN 1674-7305, E-ISSN 1869-1889, Vol. 62, no 5, p. 609-618Article in journal (Refereed)
    Abstract [en]

    The white poplar (Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa (black cottonwood) occurred similar to 5.0 Mya (3.0, 7.1). Fourfold synonymous third-codon transversion (4DTV) and synonymous substitution rate (ks) distributions supported the occurrence of the salicoid WGD event (similar to 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170 +/- 0.014, which was lower than that in Italy (0.271 +/- 0.051) and Hungary (0.264 +/- 0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P. alba populations examined.

  • 20. Mao Li , J.-F.
    et al.
    Li., Y.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Empirical assessment of the reproductive fitness components of the hybrid pine Pinus densata on the Tibetan Plateau2009In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 23, no 3, p. 447-462Article in journal (Refereed)
    Abstract [en]

    Pinus densata is distributed on the Tibetan Plateau, where it forms extensive forests at high elevations. Genetic studies have provided evidence that P. densata originated through hybridization between P. yunnanensis and P. tabuliformis. To clarify the relationships among these pines, and assess their reproductive fitness in their respective habitats, we conducted a comparative analysis of eight cone and seed morphometric traits and six reproductive traits in them. Among the eight morphometric traits examined, six appeared to be intermediate in P. densata between those of P. yunnanensis and P. tabuliformis. There were significant differences among the three pines in all of the morphometric traits, and P. densata showed greater variability in these traits than the other two pines. In contrast to the morphometric traits, the reproductive traits (including the proportions of filled and empty seeds, ovule abortion rate, seed efficiency, meiotic abnormalities during microsporogenesis and pollen viability) differed little among the three pines, indicating that they have similar overall rates of effective pollination and fertilization in their respective natural environments. Despite their location on the high plateau, natural populations of P. densata appeared to have normal levels of reproductive success, comparable to those of the two parental species in their natural habitats. This study provides empirical data characterizing the reproductive success and adaptation of a stabilized homoploid hybrid in a novel habitat that is ecologically and spatially inaccessible to its parental species.

  • 21. Mao, Jian-Feng
    et al.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Distinct niche divergence characterizes the homoploid hybrid speciation of Pinus densata on the Tibetan Plateau2011In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 177, no 4, p. 424-439Article in journal (Refereed)
    Abstract [en]

    Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system-based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.

  • 22. Meng, Jingxiang
    et al.
    Mao, Jian-Feng
    Zhao, Wei
    Xing, Fangqian
    Chen, Xinyu
    Liu, Hao
    Xing, Zhen
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Li, Yue
    Adaptive Differentiation in Seedling Traits in a Hybrid Pine Species Complex, Pinus densata and Its Parental Species, on the Tibetan Plateau2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 3, article id e0118501Article in journal (Refereed)
    Abstract [en]

    Evidence from molecular genetics demonstrates that Pinus densata is a natural homoploid hybrid originating from the parent species Pinus tabuliformis and Pinus yunnanensis, and ecological selection may have played a role in the speciation of Pinus densata. However, data on differentiation in adaptive traits in the species complex are scarce. In this study, we performed a common garden test on 16 seedling traits to examine the differences between Pinus densata and its parental species in a high altitude environment. We found that among the 16 analyzed traits, 15 were significantly different among the species. Pinus tabuliformis had much earlier bud set and a relatively higher bud set ratio but poorer seedling growth, and Pinus yunnanensis had opposite responses for the same traits. Pinus densata had the greatest fitness with higher viability and growth rates than the parents. The relatively high genetic contribution of seedling traits among populations suggested that within each species the evolutionary background is complex. The correlations between the seedling traits of a population within a species and the environmental factors indicated different impacts of the environment on species evolution. The winter temperature is among the most important climate factors that affected the fitness of the three pine species. Our investigation provides empirical evidence on adaptive differentiation among this pine species complex at seedling stages.

  • 23.
    Olajos, Fredrik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bokma, Folmer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bartels, Pia
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Myrstener, Erik
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rydberg, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Öhlund, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bindler, Richard
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zale, Rolf
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Estimating species colonization dates using DNA in lake sediment2018In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 9, no 3, p. 535-543Article in journal (Refereed)
    Abstract [en]
    1. Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives.
    2. We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files.
    3. In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post-glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization.
    4. Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
  • 24.
    Pan, Jin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wang, Baosheng
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
    Pei, Zhi-Yong
    Zhao, Wei
    Gao, Jie
    Mao, Jian-Feng
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers2015In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 15, no 4, p. 711-722Article in journal (Refereed)
    Abstract [en]

    Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11000 and 14751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking.

  • 25. Qian, Chaoju
    et al.
    Yin, Hengxia
    Shi, Yong
    Zhao, Jiecai
    Yin, Chengliang
    Luo, Wanyin
    Dong, Zhibao
    Chen, Guoxiong
    Yan, Xia
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ma, Xiao-Fei
    Population dynamics of Agriophyllum squarrosum, a pioneer annual plant endemic to mobile sand dunes, in response to global climate change2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 26613Article in journal (Refereed)
    Abstract [en]

    Climate change plays an important role in the transition of ecosystems. Stratigraphic investigations have suggested that the Asian interior experienced frequent transitions between grassland and desert ecosystems as a consequence of global climate change. Using maternally and bi-parentally inherited markers, we investigated the population dynamics of Agriophyllum squarrosum (Chenopodiaceae), an annual pioneer plant endemic to mobile sand dunes. Phylogeographic analysis revealed that A. squarrosum could originate from Gurbantunggut desert since similar to 1.6 Ma, and subsequently underwent three waves of colonisation into other deserts and sandy lands corresponding to several glaciations. The rapid population expansion and distribution range shifts of A. squarrosum from monsoonal climate zones suggested that the development of the monsoonal climate significantly enhanced the population growth and gene flow of A. squarrosum. These data also suggested that desertification of the fragile grassland ecosystems in the Qinghai-Tibetan Plateau was more ancient than previously suggested and will be aggravated under global warming in the future. This study provides new molecular phylogeographic insights into how pioneer annual plant species in desert ecosystems respond to global climate change, and facilitates evaluation of the ecological potential and genetic resources of future crops for non-arable dry lands to mitigate climate change.

  • 26. Ren, Lin-Ling
    et al.
    Liu, Yan-Jing
    Liu, Hai-Jing
    Qian, Ting-Ting
    Qi, Li-Wang
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zeng, Qing-Yin
    Subcellular relocalization and positive selection play key Roles in the retention of duplicate genes of populus class III peroxidase family2014In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 26, no 6, p. 2404-2419Article in journal (Refereed)
    Abstract [en]

    Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families.

  • 27.
    Shimono, Ayako
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Torimaru, Takeshi
    Lindgren, Dag
    Karlsson, Bo
    Spatial variation in local pollen flow and mating success in a Picea abies clone archive and their implications for a novel “breeding without breeding” strategy2011In: Tree Genetics & Genomes, ISSN 1614-2942, Vol. 7, p. 499-509Article in journal (Refereed)
    Abstract [en]

    Currently, Norway spruce (Picea abies) breeding in Sweden is based on crosses between the best clones followed by clonal testing of the progenies to select for the long-term breeding population. An alternative breeding strategy called “Breeding without Breeding” (BwB) is proposed, which, in principle, relies on the DNA markerbased pedigree reconstruction from wind-pollinated progenies instead of controlled crosses. To test whether the pedigree structure could be established from progenies of clonal trials, we investigated the spatial pattern of local pollen flow and paternity assignment in a clone archive of Norway spruce. The results showed that 42% of the progeny can be assigned to fathers within 30-m distance with high confidence. Effective pollen dispersal decreased rapidly with distance and followed exponential distribution on local scale. The extent of close-neighbor (within 6 m) mating ranged from 0% to 48% among grafts with an average of 13%. Distance explained 25% deviance in mating success, and other factors such as phenology and spatial configuration of the clones should have contributed the rest. The success of parentage assignment in clone archive opens up the possibility to apply BwB in clonal trials of species that are easy to propagate vegetatively. This procedure could substantially shorten the breeding cycle and still give similar gain per year as the conventional breeding.

  • 28.
    Sullivan, Alexis R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Eldfjell, Yrin
    Schiffthaler, Bastian
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Delhomme, Nicolas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Asp, Torben
    Hebelstrup, Kim H.
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Öber, Lisa
    Møller, Max
    Arvestad, Lars
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants2020In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 12, no 1, p. 3586-3598Article in journal (Refereed)
    Abstract [en]

    Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

  • 29.
    Sullivan, Alexis R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schiffthaler, Bastian
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Thompson, Stacey Lee
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Biology, Dalhousie University, Halifax, NS, Canada.
    Street, Nathaniel R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)2017In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 7, p. 1689-1701Article in journal (Refereed)
    Abstract [en]

    Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of similar to 35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.

  • 30.
    Torimaru, Takeshi
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Fries, A
    Andersson, B
    Lindgren, D
    Evaluation of pollen contamination in an advanced Scots pine seed orchard in Sweden2009In: Silvae Genetica, ISSN 0037-5349, Vol. 58, no 5-6, p. 262-269Article in journal (Refereed)
    Abstract [en]

    The pollination pattern in a Scots pine (Pinus sylvestris L.) seed orchard consisting of 28 clones was studied using nine microsatellite (SSR) loci. The nine SSR loci produced unique multilocus genotypes for each of the orchard's 28 clones and allowed paternal assignment of the studied 305 seed using paternity exclusion probability of 99.9%. Fifty two percent of the studied seeds were sired by outside the orchard pollen sources (i.e., pollen contamination) and as expected, low selfing (2.3%) was detected. These results are valuable for the evaluation of the seed orchard function and the impact of contamination on the expected genetic gain.

  • 31.
    Torimaru, Takeshi
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wennstrom, U.
    Lindgren, D.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Effects of male fecundity, interindividual distance and anisotropic pollen dispersal on mating success in a Scots pine (Pinus sylvestris) seed orchard2012In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 108, no 3, p. 312-321Article in journal (Refereed)
    Abstract [en]

    Quantifying the effect of pollen dispersal and flowering traits on mating success is essential for understanding evolutionary responses to changing environments and establishing strategies for forest tree breeding. This study examined, quantitatively, the effects of male fecundity, interindividual distance and anisotropic pollen dispersal on the mating success of Scots pine (Pious sylvestris), utilizing a well-mapped Scots pine seed orchard. Paternity analysis of 1021 seeds sampled from 87 trees representing 28 clones showed that 53% of the seeds had at least one potential pollen parent within the orchard. Pronounced variation in paternal contribution was observed among clones. Variations in pollen production explained up to 78% of the variation in mating success, which was 11.2 times greater for clones producing the largest amount of pollen than for clones producing the least pollen. Mating success also varied with intertree distance and direction, which explained up to 28% of the variance. Fertilization between neighboring trees 2.3 m apart was 2.4 times more frequent than between trees 4.6 m apart, and up to 12.4 times higher for trees downwind of the presumed prevailing wind direction than for upwind trees. The effective number of pollen donors recorded in the seed orchard (12.2) was smaller than the theoretical expectation (19.7). Based on the empirical observations, a mating model that best describes the gene dispersal pattern in clonal seed orchards was constructed.

  • 32.
    Torimaru, Takeshi
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Hirosaki University, Hirosaki, Japan.
    Wennstrom, Ulfstand
    Andersson, Bengt
    Almqvist, Curt
    Wang, Xiao-Ru
    Reduction of pollen contamination in Scots pine seed orchard crop by tent isolation2013In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 28, no 8, p. 715-723Article in journal (Refereed)
    Abstract [en]

    This study examined the differences in mating system between indoor versus outdoor Scots pine (Pinus sylvestris L.) seed orchard using DNA markers. By analyzing the paternities in seed crops from isolation tents, we found a significant reduction in contamination rate, from 23% in the outdoor open blocks to 0% inside the tents. Increase in selfing rate and a decrease in genetic diversity in the crops were also observed inside the tents. These undesirable effects can be mitigated to some extent by the supplementation of extra pollen genotypes, e.g. selfing rate decreased from 14.4% to 6.6% and the effective number of fathers increased from 6 to 11.4 in the tents without and with supplemental mass pollination, respectively. Our study showed that tent isolation may become an effective rescuer for seed orchards where pollen contamination is severe.

  • 33.
    Wang, B.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Climent, J.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch)2015In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 114, no 4, p. 413-418Article in journal (Refereed)
    Abstract [en]

    Horizontal gene transfer (HGT) is viewed as very common in the plant mitochondrial (mt) genome, but, to date, only one case of HGT has been found in gymnosperms. Here we report a new case of HGT, in which a mt nad5-1 fragment was transferred from an angiosperm to Pinus canariensis. Quantitative assay and sequence analyses showed that the foreign nad5-1 is located in the mt genome of P. canariensis and is nonfunctional. An extensive survey in the genus Pinus revealed that the angiosperm-derived nad5-1 is restricted to P. canariensis and present across the species' range. Molecular dating based on chloroplast DNA suggested that the HGT event occurred in the late Miocene after P. canariensis split from its closest relatives, and that the foreign copy became fixed in P. canariensis owing to drift during its colonization of the Canary Islands. The mechanism of this HGT is unclear but it was probably achieved through either direct cell-cell contact or external vectors. Our discovery provides evidence for an important role of HGT in plant mt genome evolution.

  • 34.
    Wang, Baosheng
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mahani, Marjan Khalili
    Ng, Wei Lun
    Kusumi, Junko
    Phi, Hai Hong
    Inomata, Nobuyuki
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Szmidt, Alfred E.
    Extremely low nucleotide polymorphism in Pinus krempfii Lecomte, a unique flat needle pine endemic to Vietnam2014In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 11, p. 2228-2238Article in journal (Refereed)
    Abstract [en]

    Pinus krempfii Lecomte is a morphologically and ecologically unique pine, endemic to Vietnam. It is regarded as vulnerable species with distribution limited to just two provinces: Khanh Hoa and Lam Dong. Although a few phylogenetic studies have included this species, almost nothing is known about its genetic features. In particular, there are no studies addressing the levels and patterns of genetic variation in natural populations of P.krempfii. In this study, we sampled 57 individuals from six natural populations of P.krempfii and analyzed their sequence variation in ten nuclear gene regions (approximately 9kb) and 14 mitochondrial (mt) DNA regions (approximately 10kb). We also analyzed variation at seven chloroplast (cp) microsatellite (SSR) loci. We found very low haplotype and nucleotide diversity at nuclear loci compared with other pine species. Furthermore, all investigated populations were monomorphic across all mitochondrial DNA (mtDNA) regions included in our study, which are polymorphic in other pine species. Population differentiation at nuclear loci was low (5.2%) but significant. However, structure analysis of nuclear loci did not detect genetically differentiated groups of populations. Approximate Bayesian computation (ABC) using nuclear sequence data and mismatch distribution analysis for cpSSR loci suggested recent expansion of the species. The implications of these findings for the management and conservation of P.krempfii genetic resources were discussed.

  • 35.
    Wang, Baosheng
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mao, Jian-Feng
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Gao, Jie
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Zhao, Wei
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Colonization of the Tibetan Plateau by the homoploid hybrid pine Pinus densata2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 18, p. 3796-3811Article in journal (Refereed)
    Abstract [en]

    Pinus densata is an intriguingly successful homoploid hybrid species that occupies vast areas of the southeastern Tibetan Plateau in which neither of its parental species are present, but the colonization processes involved are poorly understood. To shed light on how this species colonized and became established on the plateau, we surveyed paternally inherited chloroplast (cp) and maternally inherited mitochondrial (mt) DNA variation within and among 54 populations of P. densata and its putative parental species throughout their respective ranges. Strong spatial genetic structure of both cp and mtDNA were detected in P. densata populations. Mitotypes specific to P. densata were likely generated by complex recombination events. A putative ancestral hybrid zone in the northeastern periphery of P. densata was identified, and we propose that the species then colonized the plateau by migrating westwards. Along the colonization route, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. The direction and intensity of introgression from parental species varied among geographic regions. In western parts of its range, the species seems to have been isolated from seed and pollen flow from its parent species for a long time. The observed spatial distribution of genetic diversity in P. densata also appears to reflect the persistence of this species on the plateau during the last glaciation. Our results indicate that both ancient and contemporary population dynamics have contributed to the spatial distribution of genetic diversity in P. densata, which accordingly reflects its evolutionary history.

  • 36.
    Wang, Baosheng
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mao, Jian-Feng
    National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China.
    Zhao, Wei
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Impact of Geography and Climate on the Genetic Differentiation of the Subtropical Pine Pinus yunnanensis2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 6, p. e67345-Article in journal (Refereed)
    Abstract [en]

    Southwest China is a biodiversity hotspot characterized by complex topography, heterogeneous regional climates and rich flora. The processes and driving factors underlying this hotspot remain to be explicitly tested across taxa to gain a general understanding of the evolution of biodiversity and speciation in the region. In this study, we examined the role played by historically neutral processes, geography and environment in producing the current genetic diversity of the subtropical pine Pinus yunnanensis. We used genetic and ecological methods to investigate the patterns of genetic differentiation and ecological niche divergence across the distribution range of this species. We found both continuous genetic differentiation over the majority of its range, and discrete isolated local clusters. The discrete differentiation between two genetic groups in the west and east peripheries is consistent with niche divergence and geographical isolation of these groups. In the central area of the species' range, population structure was shaped mainly by neutral processes and geography rather than by ecological selection. These results show that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, and illustrate the importance of ecological factors in forming or maintaining genetic divergence across a complex landscape. Our findings differ from other phylogenetic studies that identified the historical drainage system in the region as the primary factor shaping population structure, and highlight the heterogeneous contributions that geography and environment have made to genetic diversity among taxa in southwest China.

  • 37.
    Wang, Baosheng
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 80, p. 20-30Article in journal (Refereed)
    Abstract [en]

    The evolution of the mitochondrial (mt) genome is far from being fully understood. Systematic investigations into the modes of inheritance, rates and patterns of recombination, nucleotide substitution, and structural changes in the mt genome are still lacking in many groups of plants. In this study, we sequenced >11 kbp mtDNA segments from multiple accessions of 36 pine species to characterize the evolutionary patterns of mtDNA in the genus Pious. We found extremely low substitution rates and complex repetitive sequences scattered across different genome regions, as well as chimeric structures that were probably generated by multiple intergenomic recombinations. The mtDNA-based phylogeny of the genus differed from that based on chloroplast and nuclear DNA in the placement of several groups of species. Such discordances suggest a series of mtDNA capture events during past range shifts of the pine species and that both vertical and horizontal inheritance are implicated in the evolution of mtDNA in Pinus. MtDNA dating revealed that most extant lineages of the genus originated during Oligocene-Miocene radiation and subgenus Strobus diversified earlier than subgenus Pinus. Our findings illustrate a reticular evolutionary pathway for the mt genome through capture and recombination in the genus Pinus, and provide new insights into the evolution of the genus.

  • 38.
    Wang, Xiao-Ru
    et al.
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Torimaru, Takeshi
    Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
    Lindgren, Dag
    Fries, Anders
    Marker-based parentage analysis facilitates low input ‘breeding without breeding’ strategies for forest trees2010In: Tree Genetics and Genomes, ISSN 1614-2942, Vol. 6, no 2, p. 227-235Article in journal (Refereed)
    Abstract [en]

    Controlled crosses and progeny testing are important components of tree breeding programs. Recently, a new approach, ‘breeding without breeding’ (BWB), has been proposed to obtain structured pedigrees for the breeding and testing from wind-pollinated progenies; the technique uses high-resolution markers instead of conventional approaches. The BWB approach is attractive for outcrossing conifers where the breeding cycle is long and reproductive maturity is often delayed. For the application of the BWB approach, the accurate assignment of parents is essential. The first step in the application of the BWB approach is to conduct tests into the reliability of paternity and parent-pair exclusion procedures in complex situations. In this study we conducted multi-locus-based empirical and simulation analyses for a Scots pine seed orchard crop, in order to develop the appropriate parentage assignment techniques for BWB and to investigate whether pedigrees from a seed orchard crop can be determined with sufficient accuracy. The results were promising, as 93–97% of the seeds generated by mating among the seed orchard clones were correctly assigned to a parent-pair. When mating occurred with foreign pollen, the success rate of identifying mother clones was 60–78%. Based on these results, we propose three novel low input breeding strategies for forest trees. The principles of the different options and their potential benefits and costs are described and discussed using Scots pine as a case study.

  • 39. Wei, Tao
    et al.
    Wang, Cai-Ling
    Kao, Hong-Na
    Yang, Hai-Ling
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zeng, Qing-Yin
    Molecular and catalytic characterization of a phi class glutathione transferase from Cathaya argyrophylla2012In: Biochemical Systematics and Ecology, ISSN 0305-1978, E-ISSN 1873-2925, Vol. 40, p. 75-85Article in journal (Refereed)
    Abstract [en]

    Plant phi class glutathione transferases (GSTs) play important roles in stress tolerance and detoxification metabolism. This study reports the cloning, expression and biochemical characteristics of a phi GST gene (CaGSTF) from the endemic and endangered conifer Cathaya argyrophylla. The recombinant CaGSTF showed GSH-conjugating activity towards the substrate NED-Cl and CDNB. Kinetic analysis revealed low catalytic efficiency with a k(cat)/K-m(GSH) value of 9.82 mM(-1)S(-1). The CaGSTF proved to be a thermolabile enzyme, at 40 degrees C the enzyme's activity was nearly abolished. Site-directed mutagenesis revealed that Ser12, Lys42, Ile55, Glu67 and Ser68 of CaGSTF are critical components of glutathione-binding sites that contribute to the enzyme's catalytic activity. Compared to other plant phi GSTs and conifer tau GSTs, CaGSTF showed a narrow substrate spectrum, low catalytic efficiency and thermolability. These atypical properties suggest the enzyme may have a limited functional role in the organism's adaptation to environmental stresses in the subtropical regions. (C) 2011 Elsevier Ltd. All rights reserved.

  • 40. Xia, Hanhan
    et al.
    Wang, Baosheng
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Pan, Jin
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Mao, Jian-Feng
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis2018In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, no 10, p. 1931-1945Article in journal (Refereed)
    Abstract [en]

    The phylogeographic histories of plants in East Asia are complex and shaped by both past large‐scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping‐by‐sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among‐population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

  • 41. Xing, Fangqian
    et al.
    Mao, Jian-Feng
    Meng, Jingxiang
    Dai, Jianfeng
    Zhao, Wei
    Liu, Hao
    Xing, Zhen
    Zhang, Hua
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Li, Yue
    Needle morphological evidence of the homoploid hybrid origin of Pinus densata based on analysis of artificial hybrids and the putative parents, Pinus tabuliformis and Pinus yunnanensis2014In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 10, p. 1890-1902Article in journal (Refereed)
    Abstract [en]

    Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P.densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P.densata were seeded in a high-altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P.densata and between the two parental species, P.tabuliformis and P.yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92%, which was very similar to P.densata. The eight needle traits (needle length, the mean number of stomata in sections 2mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P.densata. The similar needle features between the artificial hybrids and P.densata could be used to verify the homoploid hybrid origin of P.densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.

  • 42. Xu, Chao-Qun
    et al.
    Liu, Hui
    Zhou, Shan-Shan
    Zhang, Dong-Xu
    Zhao, Wei
    Wang, Sihai
    Chen, Fu
    Sun, Yan-Qiang
    Nie, Shuai
    Jia, Kai-Hua
    Jiao, Si-Qian
    Zhang, Ren-Gang
    Yun, Quan-Zheng
    Guan, Wenbin
    Wang, Xuewen
    Gao, Qiong
    Bennetzen, Jeffrey L.
    Maghuly, Fatemeh
    Porth, Ilga
    Van de Peer, Yves
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
    Ma, Yongpeng
    Mao, Jian-Feng
    Genome sequence of Malania oleifera, a tree with great value for nervonic acid production2019In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 8, no 2, article id giy164Article in journal (Refereed)
    Abstract [en]

    Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.

  • 43. Yang, Zhi-Ling
    et al.
    Liu, Hai-Jing
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zeng, Qing-Yin
    Molecular evolution and expression divergence of the Populus polygalacturonase supergene family shed light on the evolution of increasingly complex organs in plants2013In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 197, no 4, p. 1353-1365Article in journal (Refereed)
    Abstract [en]

    Plant polygalacturonases (PGs) are involved in cell separation processes during many stages of plant development. Investigation into the diversification of this large gene family in land plants could shed light on the evolution of structural development. We conducted whole-genome annotation, molecular evolution and gene expression analyses of PG genes in five species of land plant: Populus, Arabidopsis, rice, Selaginella and Physcomitrella. We identified 75, 44, 16 and 11 PG genes from Populus, rice, Selaginella and Physcomitrella genomes, respectively, which were divided into three classes. We inferred rapid expansion of class I PG genes in Populus, Arabidopsis and rice, while copy numbers of classes II and III PG genes were relatively conserved in all five species. Populus, Arabidopsis and rice class I PG genes were under more relaxed selection constraints than class II PG genes, while this selective pressure divergence was not observed in Selaginella and Physcomitrella PG families. In addition, class I PG genes underwent marked expression divergence in Populus, rice and Selaginella. Our results suggest that PG gene expansion occurred after the divergence of the lycophytes and euphyllophytes, and this expansion was likely paralleled by the evolution of increasingly complex organs in land plants.

  • 44.
    Zale, Rolf
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Huang, Y. -T
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bigler, Christian
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wood, J. R.
    Dalén, L.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Segerström, U.
    Klaminder, Jonatan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Growth of plants on the Late Weichselian ice-sheet during Greenland interstadial-1?2018In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 185, p. 222-229Article in journal (Refereed)
    Abstract [en]

    Unglaciated forelands and summits protruding from ice-sheets are commonly portrayed as areas where plants first establish at the end of glacial cycles. But is this prevailing view of ice-free refugia too simplistic? Here, we present findings suggesting that surface debris supported plant communities far beyond the rim of the Late Weichselian Ice-sheet during Greenland interstadial 1 (GI-1 or Bolling-Altered interstadial). We base our interpretations upon findings from terrigenous sediments largely resembling 'plant-trash' deposits in North America (known to form as vegetation established on stagnant ice became buried along with glacial debris during the deglaciation). In our studied deposit, we found macrofossils (N = 10) overlapping with the deglaciation period of the area (9.5-10 cal kyr BP) as well as samples (N = 2) with ages ranging between 12.9 and 13.3 cal kyr BP. The latter ages indicate growth of at least graminoids during the GI-1 interstadial when the site was near the geographic center of the degrading ice-sheet. We suggest that exposure of englacial material during GI-1 created patches of supraglacial debris capable of supporting vascular plants three millennia before deglaciation. The composition and resilience of this early plant community remain uncertain. Yet, the younger group of macrofossils, in combination with pollen and ancient DNA analyses of inclusions, imply that shrubs (Salix sp., Betula sp. and Ericaceae sp) and even tree species (Larix) were present in the debris during the final deglaciation stage. 

  • 45.
    Zeng, Qing-Yin
    et al.
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Rasmuson-Lestander, Åsa
    Umeå University, Faculty of Science and Technology, Molecular Biology (Faculty of Science and Technology).
    Wang, Xiao-Ru
    Extensive set of mitochondrial LSU rDNA-based oligonucleotide probes for the detection of common airborne fungi.2004In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 237, no 1, p. 79-87Article in journal (Refereed)
    Abstract [en]

    Fungi exist in every indoor and outdoor environment. Many fungi are toxigenic or pathogens that may cause various public health concerns. Rapid and accurate detection and identification of fungi require specific markers. In this study, partial mitochondrial large subunit rDNA was amplified and sequenced from 32 fungal strains representing 31 species from 14 genera. Based on the sequence variation pattern, 26 oligonucleotide probes were designed for their discrimination. The specificity of the probes was evaluated through homology search against GenBank database and hybridization examination on 38 fungal strains. The 26 probes were verified as highly specific to 20 fungal species. A two-step detection procedure through PCR followed by probe hybridization gave ten-fold increase in detection sensitivity than single-step PCR assay and would be a practical approach for environmental sample screening. The probes developed in this study can be applied in clinical diagnosis and environmental monitoring of fungal agents.

  • 46. Zhao, Wei
    et al.
    Meng, Jingxiang
    Wang, Baosheng
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zhang, Lisha
    Xu, Yulan
    Zeng, Qing-Yin
    Li, Yue
    Mao, Jian-Feng
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Weak Crossability Barrier but Strong Juvenile Selection Supports Ecological Speciation of the Hybrid Pine Pinus Densata on the Tibetan Plateau2014In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, no 11, p. 3120-3133Article in journal (Refereed)
    Abstract [en]

    Determining how a new hybrid lineage can achieve reproductive isolation is a key to understanding the process and mechanisms of homoploid hybrid speciation. Here, we evaluated the degree and nature of reproductive isolation between the ecologically successful hybrid species Pinus densata and its parental species P. tabuliformis and P. yunnanensis. We performed interspecific crosses among the three species to assess their crossability. We then conducted reciprocal transplantation experiments to evaluate their fitness differentiation, and to examine how natural populations representing different directions of introgression differ in adaptation. The crossing experiments revealed weak genetic barriers among the species. The transplantation trials showed manifest evidence of local adaptation as the three species all performed best in their native habitats. Pinus densata populations from the western edge of its distribution have evolved a strong local adaptation to the specific habitat in that range; populations representing different directions of introgressants with the two parental species all showed fitness disadvantages in this P. densata habitat. These observations illustrate that premating isolation through selection against immigrants from other habitat types or postzygotic isolation through selection against backcrosses between the three species is strong. Thus, ecological selection in combination with endogenous components and geographic isolation has likely played a significant role in the speciation of P. densata.

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