An integrated peach genome structural variation map uncovers genes associated with fruit traits

被引:85
|
作者
Guo, Jian [1 ,2 ]
Cao, Ke [1 ]
Deng, Cecilia [3 ]
Li, Yong [1 ]
Zhu, Gengrui [1 ]
Fang, Weichao [1 ]
Chen, Changwen [1 ]
Wang, Xinwei [1 ]
Wu, Jinlong [1 ]
Guan, Liping [1 ]
Wu, Shan [4 ]
Guo, Wenwu [2 ]
Yao, Jia-Long [3 ]
Fei, Zhangjun [4 ,5 ]
Wang, Lirong [1 ]
机构
[1] Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Zhengzhou, Peoples R China
[2] Huazhong Agr Univ, Coll Hort & Forestry Sci, Wuhan, Peoples R China
[3] New Zealand Inst Plant & Food Res Ltd, Private Bag 92169, Auckland 1142, New Zealand
[4] Cornell Univ, Boyce Thompson Inst Plant Res, Tower Rd, Ithaca, NY 14853 USA
[5] USDA ARS, Robert W Holley Ctr Agr & Hlth, Ithaca, NY 14853 USA
基金
美国国家科学基金会; 中国国家自然科学基金;
关键词
SVs; GWAS; Peach; Fruit; Fruit shape; COPY NUMBER VARIATION; WIDE ASSOCIATION; AGRONOMIC TRAITS; PAIRED-END; REVEALS; DOMESTICATION; DISCOVERY; INSIGHTS; VARIANT; WILD;
D O I
10.1186/s13059-020-02169-y
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
BackgroundGenome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.ResultsHere, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation.ConclusionsThe integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.
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页数:19
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