The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose
Li, Shubin1; Yang, Guoqian2,6,7; Yang, Shuhua3; Just, Jeremy4; Yan, Huijun1; Zhou, Ningning1; Jian, Hongying1; Wang, Qigang1; Chen, Min1; Qiu, Xianqin1; Zhang, Hao1; Dong, Xue2; Jiang, Xiaodong2,6; Sun, Yibo2,6; Zhong, Micai2,6; Bendahmane, Mohammed4; Ning, Guogui5; Ge, Hong3; Hu, Jin-Yong2; Tang, Kaixue1
Corresponding AuthorGe, Hong(gehong@caas.cn) ; Hu, Jin-Yong(hujinyong@mail.kib.ac.cn) ; Tang, Kaixue(kxtang@hotmail.com)
2019-04-12
Source PublicationSCIENTIFIC REPORTS
ISSN2045-2322
Volume9Pages:13
AbstractRoses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis 'Old Blush' (OB) and R. wichuraiana 'Basyes' Thornless' (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.
DOI10.1038/s41598-019-42428-y
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000464342700010
Citation statistics
Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/66159
Collection中国科学院东亚植物多样性与生物地理学重点实验室
Corresponding AuthorGe, Hong; Hu, Jin-Yong; Tang, Kaixue
Affiliation1.Yunnan Acad Agr Sci, Flower Res Inst, Natl Engn Res Ctr Ornamental Hort, Yunnan Flower Breeding Key Lab, Kunming 650231, Yunnan, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China
3.Chinese Acad Agr Sci, Inst Vegetables & Flowers, Beijing 100081, Peoples R China
4.UCB Lyon 1, Univ Lyon, INRA, CNRS,Lab Reprod & Dev Plantes,ENS Lyon, F-69364 Lyon, France
5.Huazhong Agr Univ, Coll Hort & Forestry Sci, Key Lab Hort Plant Biol, Minist Educ, Wuhan 430070, Hubei, Peoples R China
6.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
7.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
Recommended Citation
GB/T 7714
Li, Shubin,Yang, Guoqian,Yang, Shuhua,et al. The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose[J]. SCIENTIFIC REPORTS,2019,9:13.
APA Li, Shubin.,Yang, Guoqian.,Yang, Shuhua.,Just, Jeremy.,Yan, Huijun.,...&Tang, Kaixue.(2019).The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose.SCIENTIFIC REPORTS,9,13.
MLA Li, Shubin,et al."The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose".SCIENTIFIC REPORTS 9(2019):13.
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