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Evolution of different rice ecotypes and genetic basis of flooding adaptability in Deepwater rice by GWAS

文献类型： 外文期刊

作者： Wang, Xueqiang 1 ; Zhao, Yan 4 ; Jiang, Conghui 5 ; Wang, Libing 2 ; Chen, Lei 6 ; Li, Fengmei 2 ; Zhang, Yanhong 7 ; Pan, Yinghua 6 ; Zhang, Tianzhen 1 ;

作者机构： 1.Zhejiang Univ, Coll Agr & Biotechnol, Agron Dept, Hangzhou 310058, Peoples R China

2.Hainan Yazhou Bay Seed Lab, Sanya 572025, Hainan, Peoples R China

3.Zhejiang Univ, Hainan Inst, Sanya 572025, Hainan, Peoples R China

4.Shandong Agr Univ, Coll Agron, State Key Lab Crop Biol, Shandong Key Lab Crop Biol, Jinan 271018, Shandong, Peoples R China

5.Shandong Acad Agr Sci, Shandong Rice Res Inst, Jinan 250100, Peoples R China

6.Guangxi Acad Agr Sci, Rice Res Inst, Guangxi Key Lab Rice Genet & Breeding, Nanning 530007, Peoples R China

7.Xinjiang Acad Agr Sci, Inst Nucl & Biol Technol, Urumqi 830091, Peoples R China

关键词： Rice ecotype; Evolution; Genomic analysis; Deepwater rice; GWAS

期刊名称：BMC PLANT BIOLOGY （ 影响因子：5.26； 五年影响因子：5.761 ）

ISSN： 1471-2229

年卷期： 2022 年 22 卷 1 期

页码：

收录情况： SCI

摘要： Background Rice is the world's second largest food crop and accelerated global climate change due to the intensification of human activities has a huge impact on rice. Research on the evolution of different rice ecotypes is essential for enhancing the adaptation of rice to the unpredictable environments. Results The sequencing data of 868 cultivated and 140 wild rice accessions were used to study the domestication history and signatures of adaptation in the distinct rice ecotypes genome. The different populations had formed distinct rice ecotypes by phylogenetic analyses and were domesticated independently in the two subspecies of rice, especially deepwater and upland rice. The domestication history of distinct rice ecotypes was confirmed and the four predicted admixture events mainly involved gene flow between wild rice and cultivated rice. Importantly, we identified numerous selective sweeps that have occurred during the domestication of different rice ecotypes and one candidate gene (LOC_Os11g21804) for deepwater based on transcriptomic evidence. In addition, many regions of genomic differentiation between the different rice ecotypes were identified. Furthermore, the main reason for the increase in genetic diversity in the ecotypes of xian (indica) rice was the high proportion of alternative allele frequency in new mutations. Genome-wide association analysis revealed 28 QTLs associated with flood tolerance which contained 12 related cloned genes, and 20 candidate genes within 13 deepwater QTLs were identified by transcriptomic and haplotype analyses. Conclusions These results enhanced our understanding of domestication history in different rice ecotypes and provided valuable insights for genetic improvement and breeding of rice in the current changing environments.

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