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Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae)
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; .ORCID iD: 0000-0001-9437-3198
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2019 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 11, p. 3663-3672Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
The Genetics Society of America , 2019. Vol. 9, no 11, p. 3663-3672
Keywords [en]
RADseq, linkage map, marker distribution, segregation, genome organization
National Category
Genetics
Identifiers
URN: urn:nbn:se:umu:diva-165769DOI: 10.1534/g3.119.400684ISI: 000495646300017PubMedID: 31506321OAI: oai:DiVA.org:umu-165769DiVA, id: diva2:1375534
Available from: 2019-12-05 Created: 2019-12-05 Last updated: 2019-12-05Bibliographically approved

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Zhao, WeiWang, Xiao-Ru

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Zhao, WeiWang, Xiao-RuMao, Jian-Feng
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Department of Ecology and Environmental SciencesUmeå Plant Science Centre (UPSC)
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G3: Genes, Genomes, Genetics
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