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Deciphering variation of 239 elite japonica rice genomes for whole genome sequences-enabled breeding

文献类型： 外文期刊

作者： Liu, Chuanxue 1 ; Peng, Pei 2 ; Li, Weiguo 2 ; Ye, Changrong 2 ; Zhang, Shuhua 1 ; Wang, Ruiying 1 ; Li, Dong 2 ; Guan, S 1 ;

作者机构： 1.Heilongjiang Acad Agr Sci, Rice Res Inst, Zhongyang Ave, Jiamusi 164026, Heilongjiang, Peoples R China

2.Huazhi Biotech Co Ltd, 618 Heping Rd, Changsha 410125, Hunan, Peoples R China

3.Hunan Agr Univ, Coll Agr, China Southern Reg Collaborat Innovat Ctr Cereal, Changsha 410125, Hunan, Peoples R China

关键词： japonica; Rice; Genome; Sequencing; Variation

期刊名称：GENOMICS （ 影响因子：5.736； 五年影响因子：4.939 ）

ISSN： 0888-7543

年卷期： 2021 年 113 卷 5 期

页码：

收录情况： SCI

摘要： Revealing genomic variation of representative and diverse germplasm is the cornerstone of deploying genomics information into genetic improvement programs of species of agricultural importance. Here we report the resequencing of 239 japonica rice elites representing the genetic diversity of japonica germplasm in China, Japan and Korea. A total of 4.8 million SNPs and PAV of 35,634 genes were identified. The elites from Japan and Korea are closely related and relatively less diverse than those from China. A japonica rice pan-genome was constructed, and 35 Mb non-redundant novel sequences were identified, from which 1131 novel genes were predicted. Strong selection signals of genomic regions were detected on most of the chromosomes. The heading date genes Hd1 and Hd3a have been artificially selected during the breeding process. The results from this study lay the foundation for future whole genome sequences-enabled breeding in rice and provide a paradigm for other species.

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