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Genome-Wide Scan for Genetic Signatures Based on the Whole-Genome Resequencing of Salt- and Drought-Tolerant Rice Varieties

文献类型： 外文期刊

作者： Jiang, Conghui 1 ; Wang, Yulong 2 ; Zhou, Jinjun 3 ; Rashid, Muhammad Abdul Rehman 4 ; Li, Yaping 1 ; Peng, Yongbin 1 ; Xie, Lixia 1 ; Zhou, Guanhua 1 ; He, Yanan 1 ; Sun, Wei 1 ; Zheng, Chongke 1 ; Xie, Xianzhi 1 ;

作者机构： 1.Shandong Acad Agr Sci, Inst Wetland Agr & Ecol, Jinan 250100, Peoples R China

2.China Agr Univ, Coll Agron & Biotechnol, State Key Lab Agrobiotechnol, Beijing Key Lab Crop Genet Improvement, Beijing 100193, Peoples R China

3.Shandong Acad Agr Sci, Inst Crop Germplasm Resources, Jinan 250100, Peoples R China

4.Govt Coll Univ Faisalabad, Dept Agr Sci Bioinformat & Biotechnol, Faisalabad 38000, Pakistan

关键词： rice; resequencing; salt tolerance; drought tolerance; genomic variation

期刊名称：AGRONOMY-BASEL （ 影响因子：3.7； 五年影响因子：4.0 ）

ISSN：

年卷期： 2023 年 13 卷 7 期

页码：

收录情况： SCI

摘要： Identifying elite stress-tolerant varieties and elucidating the genetic mechanisms mediating stress resistance can help breeders develop and exploit new rice germplasm resources. In this study, we identified five salt-tolerant varieties and five drought-tolerant upland rice varieties by survival rate and drought tolerance grade and constructed variation maps of the resistance using a deep-sequencing approach. Using 116 rice accessions from the 3000 Rice Genomes Project, we characterized the population structure of sequenced varieties. Through comparative genomics and transcriptome analysis, we screened 39 salt-response candidate genes. Natural variation analysis on root length-related drought candidate gene showed that Hap1 and Hap4 were the predominant haplotypes in indica, while Hap5 was the predominant haplotype in japonica. Gene Ontology (GO) analysis showed that carbohydrate metabolic process, defense response, and response to stimulus were the common GO terms associated with salt and drought tolerance. Selective signatures in elite stress-tolerant varieties indicated that multiple important stress tolerance genes, namely OsRac1, Pikp-2, Xa26, OsSIRP4, and wsl1, were selected and utilized in these sequenced rice varieties. These findings may be useful for clarifying the genetic variations among elite stress-tolerant varieties, while also laying the foundation for a more comprehensive investigation of the genetic basis of salt and drought tolerance.

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