Genome-Wide Association Analysis for Salt–Induced Phenotypic and Physiologic Responses in Rice at Seedling and Reproductive Stages

Gang Chen,Keming Hu,Jianhua Zhao,Shengwei Zhang,Zhiming Feng,Feifei Guo,Wenfeng Shan,Zilong Guo,Xiaoxia Wu,Jinqiao Zhang,Zongxiang Chen,Qiuqing Jiang,Shimin Zuo

doi:10.3389/fpls.2022.822618

Abstract

Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. In this study, the salt tolerance of 220 rice accessions from rice diversity panel l (RDP1), representing five subpopulations, were evaluated based on 16 ST indices at both seedling and reproductive stages under salt stress. An apparent inconsistency was found for ST between the two stages. Through a gene-based/tightly linked genome-wide association study with 201,332 single nucleotide polymorphisms (SNPs) located within genes and their flanking regions were used, a total of 214 SNPs related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-quantitative trait locus (QTL) for ST and the response patterns of differential expression genes to salt stress, thirty-eight candidate genes were suggested to be involved in the regulation of rice ST. In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).

Highlights

Rice (Oryza Sativa L.) is one of the most important food crops that feeds more than half of the population of the world
According to the phenotypic distribution, we found that sRV-Chl6 and sRVDR6 presented an apparently skewed distribution, while the rest four salt tolerance (ST)-related indices displayed a more scattered distribution (Supplementary Figure 1), demonstrating a significant variance of ST among accessions tested at the seedling stage
Only a few attempts have been made to discover loci associated with ST across developmental stages and, especially, at the reproductive stage (Ganie et al, 2019; Haque et al, 2020)

Summary

Introduction

Rice (Oryza Sativa L.) is one of the most important food crops that feeds more than half of the population of the world. Improving rice tolerance to various biotic and abiotic stresses is an important strategy to increase rice yield. Very few rice varieties could grow on highly salinized land, and rice in seedling and reproductive stages is generally most sensitive to salt stress (Khan et al, 2008; Ali et al, 2014; Emon et al, 2015; Rohila et al, 2019). Developing rice varieties with salt tolerance (ST) is considered as the most promising, less resource-consuming, and socially acceptable approach to cope with salinity stress and to take full advantage of marginal lands

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Results

Conclusion