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Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study

Salt stress affects rice seed germination and seedling formation, seriously restricting rice production. Screening salt-tolerant rice varieties and analyzing the genetic mechanisms underlying salt tolerance are therefore very important to ensure rice production. In this study, 313 Oryza sativa ssp....

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Autores principales: Ju, Chunyan, Ma, Xiaoding, Han, Bing, Zhang, Wei, Zhao, Zhengwu, Geng, Leiyue, Cui, Di, Han, Longzhi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9664195/
https://www.ncbi.nlm.nih.gov/pubmed/36388603
http://dx.doi.org/10.3389/fpls.2022.1010654
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author Ju, Chunyan
Ma, Xiaoding
Han, Bing
Zhang, Wei
Zhao, Zhengwu
Geng, Leiyue
Cui, Di
Han, Longzhi
author_facet Ju, Chunyan
Ma, Xiaoding
Han, Bing
Zhang, Wei
Zhao, Zhengwu
Geng, Leiyue
Cui, Di
Han, Longzhi
author_sort Ju, Chunyan
collection PubMed
description Salt stress affects rice seed germination and seedling formation, seriously restricting rice production. Screening salt-tolerant rice varieties and analyzing the genetic mechanisms underlying salt tolerance are therefore very important to ensure rice production. In this study, 313 Oryza sativa ssp. japonica germplasm were used to conduct a genome-wide association study (GWAS) using 1% NaCl as a salt stress treatment during germination stage. The germination potential (GP) on different days and the germination index (GI) under salt stress were used as salt tolerance indicators. The results of population structure analysis showed that the 313 germplasm studied could be divided into two subpopulations, consistent with the geographical origins of the materials. There were 52 loci significantly related to salt tolerance during germination, and the phenotypic contribution rate of 29 loci was > 10%. A region on chromosome 11 (17049672–17249672 bp) was repeatedly located, and the candidate gene LOC_Os11g29490, which encodes a plasma membrane ATPase, was identified in this locus. Further haplotype analysis showed the GP of germplasm with different haplotypes at that locus significantly differed under salt stress (p < 0.05), and germplasm carrying Hap2 displayed strong salt tolerance during the germination stage. Two other promising candidate genes for salt tolerance were identified: LOC_Os01g27170 (OsHAK3), which encodes a potassium transporter, and LOC_Os10g42550 (OsITPK5), which encodes an inositol 1, 3, 4-trisphosphate 5/6-kinase. The results of this study provide a theoretical basis for salt-tolerant gene cloning and molecular design breeding in rice.
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spelling pubmed-96641952022-11-15 Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study Ju, Chunyan Ma, Xiaoding Han, Bing Zhang, Wei Zhao, Zhengwu Geng, Leiyue Cui, Di Han, Longzhi Front Plant Sci Plant Science Salt stress affects rice seed germination and seedling formation, seriously restricting rice production. Screening salt-tolerant rice varieties and analyzing the genetic mechanisms underlying salt tolerance are therefore very important to ensure rice production. In this study, 313 Oryza sativa ssp. japonica germplasm were used to conduct a genome-wide association study (GWAS) using 1% NaCl as a salt stress treatment during germination stage. The germination potential (GP) on different days and the germination index (GI) under salt stress were used as salt tolerance indicators. The results of population structure analysis showed that the 313 germplasm studied could be divided into two subpopulations, consistent with the geographical origins of the materials. There were 52 loci significantly related to salt tolerance during germination, and the phenotypic contribution rate of 29 loci was > 10%. A region on chromosome 11 (17049672–17249672 bp) was repeatedly located, and the candidate gene LOC_Os11g29490, which encodes a plasma membrane ATPase, was identified in this locus. Further haplotype analysis showed the GP of germplasm with different haplotypes at that locus significantly differed under salt stress (p < 0.05), and germplasm carrying Hap2 displayed strong salt tolerance during the germination stage. Two other promising candidate genes for salt tolerance were identified: LOC_Os01g27170 (OsHAK3), which encodes a potassium transporter, and LOC_Os10g42550 (OsITPK5), which encodes an inositol 1, 3, 4-trisphosphate 5/6-kinase. The results of this study provide a theoretical basis for salt-tolerant gene cloning and molecular design breeding in rice. Frontiers Media S.A. 2022-11-01 /pmc/articles/PMC9664195/ /pubmed/36388603 http://dx.doi.org/10.3389/fpls.2022.1010654 Text en Copyright © 2022 Ju, Ma, Han, Zhang, Zhao, Geng, Cui and Han https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Ju, Chunyan
Ma, Xiaoding
Han, Bing
Zhang, Wei
Zhao, Zhengwu
Geng, Leiyue
Cui, Di
Han, Longzhi
Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study
title Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study
title_full Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study
title_fullStr Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study
title_full_unstemmed Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study
title_short Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study
title_sort candidate gene discovery for salt tolerance in rice (oryza sativa l.) at the germination stage based on genome-wide association study
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9664195/
https://www.ncbi.nlm.nih.gov/pubmed/36388603
http://dx.doi.org/10.3389/fpls.2022.1010654
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