Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

Rice - Tập 12 Số 1 - 2019
Chen Liu1, Kai Chen2, Xiuqin Zhao2,2,1, Xiaoqian Wang3, Congcong Shen1, Yajun Zhu1, Mingli Dai4, Xianjin Qiu4, Rongwei Yang4, Danying Xing4, Yunlong Pang3, Jianlong Xu2
1Laboratory of Lingnan Modern Agriculture/ Agricultural Genomics Institute at Shenzhen, Shenzhen, 518120, China
2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
3State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian 271018, China
4College of Agriculture, Yangtze University, Jingzhou, 434025, China

Tóm tắt

Abstract Background Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. Results Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms “biological processes” and “molecular function” with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. Conclusions Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

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Tập 12 Số 1

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