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Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

文献类型：期刊论文

作者Tan, Qiuping3,4,5,6; Li, Sen3,4,5; Zhang, Yuzheng3,4,5; Chen, Min2; Wen, Binbin3,4,5; Jiang, Shan3,4,5; Chen, Xiude3,4,5; Fu, Xiling3,4,5; Li, Dongmei3,4,5; Wu, Hongyu1,5
刊名HORTICULTURE RESEARCH
出版日期2021-12-01
卷号8期号:1页码:18
ISSN号2662-6810
DOI10.1038/s41438-021-00648-2
通讯作者Xiao, Wei(gulight986918@163.com) ; Li, Ling(lilingsdau@163.com)
英文摘要Prunus species include many important perennial fruit crops, such as peach, plum, apricot, and related wild species. Here, we report de novo genome assemblies for five species, including the cultivated species peach (Prunus persica), plum (Prunus salicina), and apricot (Prunus armeniaca), and the wild peach species Tibetan peach (Prunus mira) and Chinese wild peach (Prunus davidiana). The genomes ranged from 240 to 276 Mb in size, with contig N50 values of 2.27-8.30 Mb and 25,333-27,826 protein-coding gene models. As the phylogenetic tree shows, plum diverged from its common ancestor with peach, wild peach species, and apricot similar to 7 million years ago (MYA). We analyzed whole-genome resequencing data of 417 peach accessions, called 3,749,618 high-quality SNPs, 577,154 small indels, 31,800 deletions, duplications, and inversions, and 32,338 insertions, and performed a structural variant-based genome-wide association study (GWAS) of key agricultural traits. From our GWAS data, we identified a locus associated with a fruit shape corresponding to the OVATE transcription factor, where a large inversion event correlates with higher OVATE expression in flat-shaped accessions. Furthermore, a GWAS revealed a NAC transcription factor associated with fruit developmental timing that is linked to a tandem repeat variant and elevated NAC expression in early-ripening accessions. We also identified a locus encoding microRNA172d, where insertion of a transposable element into its promoter was found in double-flower accessions. Thus, our efforts have suggested roles for OVATE, a NAC transcription factor, and microRNA172d in fruit shape, fruit development period, and floral morphology, respectively, that can be connected to traits in other crops, thereby demonstrating the importance of parallel evolution in the diversification of several commercially important domesticated species. In general, these genomic resources will facilitate functional genomics, evolutionary research, and agronomic improvement of these five and other Prunus species. We believe that structural variant-based GWASs can also be used in other plants, animal species, and humans and be combined with deep sequencing GWASs to precisely identify candidate genes and genetic architecture components.
WOS关键词PERSICA L. BATSCH ; LINKAGE DISEQUILIBRIUM ; STRUCTURAL VARIANTS ; GENETIC-VARIATION ; QUALITY ; TOMATO ; IDENTIFICATION ; DOMESTICATION ; TRANSPORTER ; ANNOTATION
WOS研究方向Plant Sciences ; Genetics & Heredity ; Agriculture
语种英语
WOS记录号WOS:000702471000010
资助机构National Key Research and Development Plan ; National Natural Science Foundation of China ; Provincial Natural Science Foundation of Shandong ; Shandong Province Agricultural Good Seed Project ; Funding for major agricultural application technology innovation projects in Shandong Province
源URL[http://ir.yic.ac.cn/handle/133337/30756]  
专题烟台海岸带研究所_近岸生态与环境实验室
烟台海岸带研究所_海岸带信息集成与综合管理实验室
通讯作者Xiao, Wei; Li, Ling
作者单位1.Shandong Agr Univ, Coll Forestry, Tai An 271018, Shandong, Peoples R China
2.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China
3.Shandong Collaborat Innovat Ctr Fruit & Vegetable, Tai An 271018, Shandong, Peoples R China
4.Shandong Agr Univ, Coll Hort Sci & Engn, Tai An 271018, Shandong, Peoples R China
5.Shandong Agr Univ, State Key Lab Crop Biol, Tai An 271018, Shandong, Peoples R China
6.Shandong Agr Univ, Coll Life Sci, Tai An 271018, Shandong, Peoples R China
推荐引用方式
GB/T 7714		 Tan, Qiuping,Li, Sen,Zhang, Yuzheng,et al. Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach[J]. HORTICULTURE RESEARCH,2021,8(1):18.
APA Tan, Qiuping.,Li, Sen.,Zhang, Yuzheng.,Chen, Min.,Wen, Binbin.,...&Li, Ling.(2021).Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach.HORTICULTURE RESEARCH,8(1),18.
MLA Tan, Qiuping,et al."Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach".HORTICULTURE RESEARCH 8.1(2021):18.

入库方式： OAI收割

来源：烟台海岸带研究所

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