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Volume 12
Issue 11
10.3390/plants12112163
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Article

Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis

by
Rui Wang
†,
Zhenzhen Zhou
†,
Mengyuan Xiong
,
Mingyu Du
,
Xingxing Lin
,
Cuiping Liu
,
Mingwei Lu
,
Zhengbo Liu
,
Yinping Chang
and
Erbao Liu
*
College of Agronomy, Anhui Agricultural University, Hefei 230036, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2023, 12(11), 2163; https://doi.org/10.3390/plants12112163
Submission received: 2 May 2023 / Revised: 18 May 2023 / Accepted: 27 May 2023 / Published: 30 May 2023
(This article belongs to the Topic Tolerance to Drought and Salt Stress in Plants)
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Abstract

Mining salt tolerance genes is significant for breeding high-quality salt-tolerant rice varieties in order to improve the utilization of saline–alkaline land. In this study, 173 rice accessions were measured for their germination potential (GP), germination rate (GR), seedling length (SL), root length (RL), germination potential relative to salt damage rate (GPR), germination rate relative to salt damage rate (GRR), seedling length relative to salt damage rate (SLR), relative salt damage rate at the germination stage (RSD) and comprehensive relative salt damage rate in the early seedling stage (CRS) under normal and salt stress conditions. Genome-wide association analysis was performed with 1,322,884 high-quality SNPs obtained by resequencing. Eight quantitative trait loci (QTLs) related to salt tolerance traits at the germination stage were detected in 2020 and 2021. They were related to the GPR (qGPR2) and SLR (qSLR9), which were newly discovered in this study. Three genes were predicted as salt tolerance candidate genes: LOC_Os02g40664, LOC_Os02g40810, and LOC_Os09g28310. At present, marker-assisted selection (MAS) and gene-edited breeding are becoming more widespread. Our discovery of candidate genes provides a reference for research in this field. The elite alleles identified in this study may provide a molecular basis for cultivating salt-tolerant rice varieties.
Keywords: rice; germination stage; salt tolerance; SNP loci; genome-wide association analysis rice; germination stage; salt tolerance; SNP loci; genome-wide association analysis

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MDPI and ACS Style

Wang, R.; Zhou, Z.; Xiong, M.; Du, M.; Lin, X.; Liu, C.; Lu, M.; Liu, Z.; Chang, Y.; Liu, E. Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis. Plants 2023, 12, 2163. https://doi.org/10.3390/plants12112163

AMA Style

Wang R, Zhou Z, Xiong M, Du M, Lin X, Liu C, Lu M, Liu Z, Chang Y, Liu E. Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis. Plants. 2023; 12(11):2163. https://doi.org/10.3390/plants12112163

Chicago/Turabian Style

Wang, Rui, Zhenzhen Zhou, Mengyuan Xiong, Mingyu Du, Xingxing Lin, Cuiping Liu, Mingwei Lu, Zhengbo Liu, Yinping Chang, and Erbao Liu. 2023. "Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis" Plants 12, no. 11: 2163. https://doi.org/10.3390/plants12112163

APA Style

Wang, R., Zhou, Z., Xiong, M., Du, M., Lin, X., Liu, C., Lu, M., Liu, Z., Chang, Y., & Liu, E. (2023). Mining Salt Tolerance SNP Loci and Prediction of Candidate Genes in the Rice Bud Stage by Genome-Wide Association Analysis. Plants, 12(11), 2163. https://doi.org/10.3390/plants12112163

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