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  • 1. Al Azzawi, Tiba Nazar Ibrahim
    et al.
    Khan, Murtaza
    Hussain, Adil
    Shahid, Muhammad
    Imran, Qari Muhammad
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik. School of Applied Biosciences, Kyungpook National University, Korea.
    Mun, Bong-Gyu
    Lee, Sang-Uk
    Yun, Byung-Wook
    Evaluation of Iraqi Rice Cultivars for Their Tolerance to Drought Stress2020Inngår i: Agronomy, E-ISSN 2073-4395, Vol. 10, nr 11, artikkel-id 1782Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Drought stress is a serious problem around the globe and particularly in the Republic of Iraq. Rice is the third most consumed crop for the Iraqi people; however, its cultivation and production is very low due to several challenges including drought. The current study was performed to evaluate five Iraqi rice cultivars along with relevant (drought-tolerant and drought-susceptible) controls under drought stress, either by treatment with 10% PEG (polyethylene glycol) or through water withholding to induce natural drought stress. The phenotypes of all the cultivars were evaluated and the transcriptional responses of key drought-responsive candidate genes, identified through the EST-SSR marker-based approach, were studied. We also studied transcript accumulation of drought-related transcriptional factors, such as OsGRASS23, OsbZIP12, and OsDREB2A. Moreover, the reference cultivars also included a drought-tolerant inter-specific cultivar Nerica 7 (a cross between Oryza sativa ssp. indica X O. glaberrima). Among the cultivars, the more drought-tolerant phenotypic characteristics and higher transcript accumulation of drought-related marker genes OsE647 and OsE1899 and transcriptional factors OsGRASS23, OsbZIP12, and OsDREB2A were observed in four (out of five) significantly drought-tolerant Iraqi cultivars; Mashkab, followed by Furat, Yasmen, and Amber 33. On another note, Amber Barka was found to be significantly drought susceptible. Mashkab and Amber Barka were found to be the most drought-tolerant and-susceptible cultivars, respectively. The identified tolerant cultivars may potentially serve as a genetic source for the incorporation of drought-tolerant phenotypes in rice.

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  • 2. Almeida, Pedro
    et al.
    Proux-Wera, Estelle
    Churcher, Allison M
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Soler, Lucile
    Dainat, Jacques
    Pucholt, Pascal
    Nordlund, Jessica
    Martin, Tom
    Ronnberg-Wastljung, Ann-Christin
    Nystedt, Bjorn
    Berlin, Sofia
    Mank, Judith E.
    Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion2020Inngår i: BMC Biology, E-ISSN 1741-7007, Vol. 18, nr 1, artikkel-id 78Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.

    Results: Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.

    Conclusions: Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

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  • 3.
    Androsiuk, P.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. University of Warmia & Mazury, Poland.
    Shimono, A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Westin, J.
    Lindgren, D.
    Fries, A.
    Wang, X. -R
    Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden2013Inngår i: Silvae Genetica, ISSN 0037-5349, Vol. 62, nr 3, s. 127-136Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 4. Capovilla, Giovanna
    et al.
    Symeonidi, Efthymia
    Wu, Rui
    Schmid, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, 72076 Tübingen, Germany.
    Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana2017Inngår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, nr 18, s. 5117-5127Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    FLOWERING LOCUS M (FLM), a component of the thermosensory flowering time pathway in Arabidopsis thaliana, is regulated by temperature-dependent alternative splicing (AS). The main splicing variant, FLM-beta, is a well-documented floral repressor that is down-regulated in response to increasing ambient growth temperature. Two hypotheses have been formulated to explain how flowering time is modulated by AS of FLM. In the first model a second splice variant, FLM-delta, acts as a dominant negative isoform that competes with FLM-beta at elevated ambient temperatures, thereby indirectly promoting flowering. Alternatively, it has been suggested that the induction of flowering at elevated temperatures is caused only by reduced FLM-beta expression. To better understand the role of the two FLM splice forms, we employed CRISPR/Cas9 technology to specifically delete the exons that characterize each splice variant. Lines that produced repressive FLM-beta but were incapable of producing FLM-delta were late flowering. In contrast, FLM-beta knockout lines that still produced FLM-delta flowered early, but not earlier than the flm-3 loss of function mutant, as would be expected if FLM-delta had a dominant-negative effect on flowering. Our data support the role of FLM-beta as a flower repressor and provide evidence that a contribution of FLM-delta to the regulation of flowering time in wild-type A. thaliana seems unlikely.

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  • 5.
    Garkava-Gustavsson, L.
    et al.
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Sätra, J. Skytte af
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Odilbekov, F.
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Abreu, I.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Johansson, Annika I.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    van de Weg, E.
    Plant Breeding, Wageningen University & Research, Wageningen, Netherlands.
    Zhebentyayeva, T.
    Department of Ecosystem Science and Management, University Park, The Pennsylvania State University, PA, United States.
    Resistance to Neonectria ditissima in apple: insights from metabolomics and lipidomics analyses2023Inngår i: Xxxi international horticultural congress (ihc2022): International symposium on breeding and effective use of biotechnology and molecular tools in horticultural crops / [ed] V. Bus; M. Causse, International Society for Horticultural Science , 2023, s. 329-335Konferansepaper (Fagfellevurdert)
    Abstract [en]

    European canker, caused by the necrotrophic fungus Neonectria ditissima, is the most serious disease in apple production in Sweden. The disease is favored by a relatively cool and rainy climate. The canker damages have a significant economic impact due to reduced bearing surface and increased orchard management costs. The possibilities for chemical and biological control are very limited. Therefore, directed breeding for new resistant cultivars is urgently needed. Knowledge of inheritance of canker resistance and understanding of molecular mechanisms involved in resistant and susceptible responses to fungal attacks would facilitate breeding. In this study, we evaluated the tempo-spatial differences in plant-pathogen interactions in a set of partially resistant and susceptible cultivars by conducting metabolomic and lipidomic analyses. The major trends in metabolomics and lipidomic profiles were common among cultivars, irrespective of the degree of susceptibility. Several metabolites and lipids varied with time point and cultivar under N. ditissima infection. Putative key metabolites such as suberic acid and jasmonic acid were upregulated in all cultivars upon infection. Additionally, several lipids exhibited changes 30 to 45 days post-inoculation. Thus, the approach used seems to have resulted in a rich data set to be further analyzed in light of ongoing QTL-mapping efforts.

  • 6. Hjalten, Joakim
    et al.
    Axelsson, E. Petter
    Julkunen-Tiitto, Riitta
    Wennström, Anders
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Pilate, Gilles
    Innate and Introduced Resistance Traits in Genetically Modified Aspen Trees and Their Effect on Leaf Beetle Feeding2013Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 8, nr 9, s. e73819-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genetic modifications of trees may provide many benefits, e. g. increase production, and mitigate climate change and herbivore impacts on forests. However, genetic modifications sometimes result in unintended effects on innate traits involved in plant-herbivore interactions. The importance of intentional changes in plant defence relative to unintentional changes and the natural variation among clones used in forestry has not been evaluated. By a combination of biochemical measurements and bioassays we investigated if insect feeding on GM aspens is more affected by intentional (induction Bt toxins) than of unintentional, non-target changes or clonal differences in innate plant defence. We used two hybrid wildtype clones (Populus tremula x P. tremuloides and Populus tremula x P. alba) of aspen that have been genetically modified for 1) insect resistance (two Bt lines) or 2) reduced lignin properties (two lines COMT and CAD), respectively. Our measurements of biochemical properties suggest that unintended changes by GM modifications (occurring due to events in the transformation process) in innate plant defence (phenolic compounds) were generally smaller but fundamentally different than differences seen among different wildtype clones (e. g. quantitative and qualitative, respectively). However, neither clonal differences between the two wildtype clones nor unintended changes in phytochemistry influenced consumption by the leaf beetle (Phratora vitellinae). By contrast, Bt induction had a strong direct intended effect as well as a post experiment effect on leaf beetle consumption. The latter suggested lasting reduction of beetle fitness following Bt exposure that is likely due to intestinal damage suffered by the initial Bt exposure. We conclude that Bt induction clearly have intended effects on a target species. Furthermore, the effect of unintended changes in innate plant defence traits, when they occur, are context dependent and have in comparison to Bt induction probably less pronounced effect on targeted herbivores.

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  • 7.
    Mahawar, Lovely
    et al.
    Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India.
    Ramasamy, Kesava Priyan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Pandey, Aparna
    Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India.
    Prasad, Sheo Mohan
    Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India.
    Iron deficiency in plants: an update on homeostasis and its regulation by nitric oxide and phytohormones2023Inngår i: Plant growth regulation (Print), ISSN 0167-6903, E-ISSN 1573-5087, Vol. 100, s. 283-299Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Iron is an essential micronutrient for plants as it involves in several important physiological processes. Understanding iron homeostasis in plants is pivotal, not only for improving their growth and development but also for enhancing human nutrition as plants are the principal dietary source of iron. This calls for the need to enrich bioavailable iron in crops to resolve iron starvation issue especially in low income and rural populations who have limited access to food markets and proper health facilities. The uptake of iron from rhizosphere, its transporters and transcription factors that regulate iron acquisition are well characterized. Here, the present review emphasizes on the role of signalling molecules particularly phytohormones and nitric oxide and their interactive co-ordination in iron homeostasis in agriculturally important crops that grow at pH 6.0-7.5 and have limited access to Fe2+. The involvement of these signalling molecules in up-regulating iron acquisition genes (FRO2 and IRT1), iron translocation to the cellular compartments and accessibility of iron storage which are important for proper iron homeostasis hence can be considered as vital biofortification strategy for crop plants to address hidden hunger.

  • 8.
    Ren, Keni
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för tillämpad fysik och elektronik.
    Zoom in on the precision livestock farming2021Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Global attention to the welfare of zoo animals and livestock results in stronger legislation and higher pressure for achieving higher standards of animal welfare. Monitoring and understanding animal behaviour can assist in optimising the welfare of zoo and livestock animals. Precision livestock farming solutions open the door to increase automation of behaviour monitoring and welfare management. The overall purpose of the thesis was to investigate the possibilities of using computer vision and sensor technology for studying animal behaviour in zoo and production environments. To fulfil this overall purpose, two main research questions were addressed: How can we identify and track individual animals using computer vision and sensor technology? Combining the identity and position information, how well animal behaviour can be monitored and analysed?

    First, we developed and justified methods for identifying and tracking individual animals in different livestock environments: zoo outdoor environment, sheep barn and free-stall dairy cattle barn's indoor production environment. Three methods were developed to identify and track individual animals: a combination of radio frequency identification and camera sensor, a deep learning method based on visual biometrics and behaviour features and an ultra-wideband based real-time location system method. The data quality, in terms of missing data, in one commercially available ultra-wideband system was examined. The choice of method was justified according to different species' natural appearance, breeding strategy and housing conditions. We found that the computer vision system can perform as good as an expert in identifying individual bears based on images. The real-time location system can provide the position of individual animals inside barns with a mean error under 0.4 m. No major obstacles were found to interfere with the ultra-wideband based real-time location system. The between-cow variation was statistically significant.

    Second, two animal behaviour monitoring systems that assist activity registration and analysing social interactions were proposed. To detect sheep's standing and lying behaviour in sheep barn environments, infrared radiation cameras, and three-dimensional computer vision technology were used. Dairy cows' negative and positive social interactions were analysed using a Long-term Recurrent Convolution Networks model. Both systems integrated the real-time location system and computer vision system to perform identification, tracking and analysing animal behaviour tasks. Working with real systems in a real-world application setting made the study more credible and valuable for the related research. The result showed that the system was able to understand animal standing lying activity and social behaviour.

    The developed technologies and the results of the experiments added value for the animal behaviour monitoring by focusing on individual or sub-group in a herd and analysing individual activity and social behaviour continuously. By understanding animal behaviour, it can push the continuous surveillance system towards a welfare decision support system.

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  • 9.
    Sullivan, Alexis R.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. School of Forest Resources and Environmental Science, Michigan Technological Universi ty, 1400 Townsend Drive, Houghton, MI 49931, USA.
    Owusu, Sandra A.
    Weber, Jaime A.
    Hipp, Andrew L.
    Gailing, Oliver
    Hybridization and divergence in multi-species oak (Quercus) communities2016Inngår i: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 181, nr 1, s. 99-114Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oaks (Quercus: Fagaceae) commonly interbreed yet retain their morphological, genetic and ecological distinctiveness. Post-zygotic isolation mechanisms, such as ecologically dependent selection on adaptive loci, may therefore limit introgression. To test this hypothesis, we quantified hybridization and genetic divergence across the contact zone of four red oaks (Quercus section Lobatae) in the Great Lakes region of North America using a suite of 259 amplified fragment length polymorphisms and 27 genic and genomic microsatellite markers. First, we identified hybrids using genetic structure analysis and confirmed the reliability of our assignments via simulations. Then, we identified candidate loci for species maintenance with three complementary tests for selection and obtained partial gene sequences linked to an outlier locus and three other loci. We detected evidence of recent hybridization among all species and considerable gene flow between Q.ellipsoidalis and Q.velutina. Overall, c.20% of Q.velutina had recent ancestry from Q.ellipsoidalis, whereas nearly 30% of Q.ellipsoidalis had a Q.velutina ancestor. Most loci were negligibly to weakly differentiated among species, but two gene-linked microsatellites deviated significantly from neutral expectations in multiple, complementary outlier tests. Both outlier loci were located in the same 15-cM bin on an existing Q.robur linkage map, a region under divergent selection in other oak species. Adaptive loci in this highly differentiated genomic region may contribute to ecological divergence among species and limit introgression.

  • 10.
    Wang, Wen‐Bo
    et al.
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China; 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.
    He, Xiang‐Feng
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China.
    Yan, Xue‐Mei
    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.
    Ma, Bo
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China; 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.
    Lu, Cun‐Fu
    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.
    Wu, Jing
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China.
    Zheng, Yi
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China.
    Wang, Wen‐He
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China.
    Xue, Wen‐Bo
    BGI Genomics, BGI-Shenzhen, Shenzhen, China.
    Tian, Xue-Chan
    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.
    Guo, Jing-Fang
    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.
    El‐Kassaby, Yousry A.
    Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada.
    Porth, Ilga
    Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, Canada.
    Leng, Ping‐Sheng
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China.
    Hu, Zeng‐Hui
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, College of Landscape Architecture, Bioinformatics Center, Beijing University of Agriculture, Beijing, China.
    Mao, Jian-Feng
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. 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.
    Chromosome‐scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata2023Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 238, nr 5, s. 2016-2032Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated.

    First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation.

    Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays.

    Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

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  • 11.
    Wang, Xi
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bernhardsson, Carolina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Ingvarsson, Pär K.
    Linnean Centre for Plant Biology, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)2020Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 12, nr 2, s. 3803-3817Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (π = 0.0049 in Central-Europe, π = 0.0063 in Sweden-Norway, π = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

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