Molecular dissection of maize seedling salt tolerance using a genome‐wide association analysis method

Summary Salt stress is a major devastating abiotic factor that affects the yield and quality of maize. However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome‐wide association study was perf...

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Veröffentlicht in:Plant biotechnology journal 2021-10, Vol.19 (10), p.1937-1951
Hauptverfasser: Luo, Meijie, Zhang, Yunxia, Li, Jingna, Zhang, Panpan, Chen, Kuan, Song, Wei, Wang, Xiaqing, Yang, Jinxiao, Lu, Xiaoduo, Lu, Baishan, Zhao, Yanxin, Zhao, Jiuran
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container_end_page 1951
container_issue 10
container_start_page 1937
container_title Plant biotechnology journal
container_volume 19
creator Luo, Meijie
Zhang, Yunxia
Li, Jingna
Zhang, Panpan
Chen, Kuan
Song, Wei
Wang, Xiaqing
Yang, Jinxiao
Lu, Xiaoduo
Lu, Baishan
Zhao, Yanxin
Zhao, Jiuran
description Summary Salt stress is a major devastating abiotic factor that affects the yield and quality of maize. However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome‐wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs). The phenotypic data for 27 traits revealed coefficients of variation of >25%. In total, 149 significant SNPs explaining 6.6%–11.2% of the phenotypic variation for each SNP were identified. Of the 104 identified quantitative trait loci (QTLs), 83 were related to salt tolerance and 21 to normal traits. Additionally, 13 QTLs were associated with two to five traits. Eleven and six QTLs controlling salt tolerance traits and normal root growth, respectively, co‐localized with QTL intervals reported previously. Based on functional annotations, 13 candidate genes were predicted. Expression levels analysis of 12 candidate genes revealed that they were all responsive to salt stress. The CRISPR/Cas9 technology targeting three sites was applied in maize, and its editing efficiency reached 70%. By comparing the biomass of three CRISPR/Cas9 mutants of ZmCLCg and one zmpmp3 EMS mutant with their wild‐type plants under salt stress, the salt tolerance function of candidate genes ZmCLCg and ZmPMP3 were confirmed. Chloride content analysis revealed that ZmCLCg regulated chloride transport under sodium chloride stress. These results help to explain genetic variations in salt tolerance and provide novel loci for generating salt‐tolerant maize lines.
doi_str_mv 10.1111/pbi.13607
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However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome‐wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs). The phenotypic data for 27 traits revealed coefficients of variation of &gt;25%. In total, 149 significant SNPs explaining 6.6%–11.2% of the phenotypic variation for each SNP were identified. Of the 104 identified quantitative trait loci (QTLs), 83 were related to salt tolerance and 21 to normal traits. Additionally, 13 QTLs were associated with two to five traits. Eleven and six QTLs controlling salt tolerance traits and normal root growth, respectively, co‐localized with QTL intervals reported previously. Based on functional annotations, 13 candidate genes were predicted. Expression levels analysis of 12 candidate genes revealed that they were all responsive to salt stress. The CRISPR/Cas9 technology targeting three sites was applied in maize, and its editing efficiency reached 70%. By comparing the biomass of three CRISPR/Cas9 mutants of ZmCLCg and one zmpmp3 EMS mutant with their wild‐type plants under salt stress, the salt tolerance function of candidate genes ZmCLCg and ZmPMP3 were confirmed. Chloride content analysis revealed that ZmCLCg regulated chloride transport under sodium chloride stress. These results help to explain genetic variations in salt tolerance and provide novel loci for generating salt‐tolerant maize lines.</description><identifier>ISSN: 1467-7644</identifier><identifier>EISSN: 1467-7652</identifier><identifier>DOI: 10.1111/pbi.13607</identifier><identifier>PMID: 33934485</identifier><language>eng</language><publisher>England: John Wiley &amp; Sons, Inc</publisher><subject>Abiotic factors ; Abiotic stress ; Annotations ; Association analysis ; association mapping ; Chloride transport ; Coefficient of variation ; Content analysis ; Corn ; CRISPR ; Crops ; Gene expression ; Gene mapping ; Genes ; Genetic diversity ; genetic loci ; Genome-wide association studies ; Genomes ; Homeostasis ; Inbreeding ; maize ; Metabolism ; Metabolites ; Molecular modelling ; Mutants ; Nucleotides ; Phenotypic variations ; Plant growth ; Quantitative trait loci ; Rice ; Salinity ; Salinity tolerance ; Salt ; Salt tolerance ; Seedlings ; Single-nucleotide polymorphism ; Sodium chloride ; Stress</subject><ispartof>Plant biotechnology journal, 2021-10, Vol.19 (10), p.1937-1951</ispartof><rights>2021 The Authors. 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However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome‐wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs). The phenotypic data for 27 traits revealed coefficients of variation of &gt;25%. In total, 149 significant SNPs explaining 6.6%–11.2% of the phenotypic variation for each SNP were identified. Of the 104 identified quantitative trait loci (QTLs), 83 were related to salt tolerance and 21 to normal traits. Additionally, 13 QTLs were associated with two to five traits. Eleven and six QTLs controlling salt tolerance traits and normal root growth, respectively, co‐localized with QTL intervals reported previously. Based on functional annotations, 13 candidate genes were predicted. 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Zhang, Yunxia ; Li, Jingna ; Zhang, Panpan ; Chen, Kuan ; Song, Wei ; Wang, Xiaqing ; Yang, Jinxiao ; Lu, Xiaoduo ; Lu, Baishan ; Zhao, Yanxin ; Zhao, Jiuran</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4437-dde9bdd5c4a4a594ab2bb64b4e7f7d7190154a6c883f8067bed46b999ea622023</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Abiotic factors</topic><topic>Abiotic stress</topic><topic>Annotations</topic><topic>Association analysis</topic><topic>association mapping</topic><topic>Chloride transport</topic><topic>Coefficient of variation</topic><topic>Content analysis</topic><topic>Corn</topic><topic>CRISPR</topic><topic>Crops</topic><topic>Gene expression</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genetic diversity</topic><topic>genetic loci</topic><topic>Genome-wide association studies</topic><topic>Genomes</topic><topic>Homeostasis</topic><topic>Inbreeding</topic><topic>maize</topic><topic>Metabolism</topic><topic>Metabolites</topic><topic>Molecular modelling</topic><topic>Mutants</topic><topic>Nucleotides</topic><topic>Phenotypic variations</topic><topic>Plant growth</topic><topic>Quantitative trait loci</topic><topic>Rice</topic><topic>Salinity</topic><topic>Salinity tolerance</topic><topic>Salt</topic><topic>Salt tolerance</topic><topic>Seedlings</topic><topic>Single-nucleotide polymorphism</topic><topic>Sodium chloride</topic><topic>Stress</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Luo, Meijie</creatorcontrib><creatorcontrib>Zhang, Yunxia</creatorcontrib><creatorcontrib>Li, Jingna</creatorcontrib><creatorcontrib>Zhang, Panpan</creatorcontrib><creatorcontrib>Chen, Kuan</creatorcontrib><creatorcontrib>Song, Wei</creatorcontrib><creatorcontrib>Wang, Xiaqing</creatorcontrib><creatorcontrib>Yang, Jinxiao</creatorcontrib><creatorcontrib>Lu, Xiaoduo</creatorcontrib><creatorcontrib>Lu, Baishan</creatorcontrib><creatorcontrib>Zhao, Yanxin</creatorcontrib><creatorcontrib>Zhao, Jiuran</creatorcontrib><collection>Wiley-Blackwell Open Access Titles</collection><collection>Wiley Free Content</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Materials Science &amp; 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However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome‐wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs). The phenotypic data for 27 traits revealed coefficients of variation of &gt;25%. In total, 149 significant SNPs explaining 6.6%–11.2% of the phenotypic variation for each SNP were identified. Of the 104 identified quantitative trait loci (QTLs), 83 were related to salt tolerance and 21 to normal traits. Additionally, 13 QTLs were associated with two to five traits. Eleven and six QTLs controlling salt tolerance traits and normal root growth, respectively, co‐localized with QTL intervals reported previously. Based on functional annotations, 13 candidate genes were predicted. Expression levels analysis of 12 candidate genes revealed that they were all responsive to salt stress. The CRISPR/Cas9 technology targeting three sites was applied in maize, and its editing efficiency reached 70%. By comparing the biomass of three CRISPR/Cas9 mutants of ZmCLCg and one zmpmp3 EMS mutant with their wild‐type plants under salt stress, the salt tolerance function of candidate genes ZmCLCg and ZmPMP3 were confirmed. Chloride content analysis revealed that ZmCLCg regulated chloride transport under sodium chloride stress. These results help to explain genetic variations in salt tolerance and provide novel loci for generating salt‐tolerant maize lines.</abstract><cop>England</cop><pub>John Wiley &amp; Sons, Inc</pub><pmid>33934485</pmid><doi>10.1111/pbi.13607</doi><tpages>15</tpages><orcidid>https://orcid.org/0000-0003-0694-016X</orcidid><orcidid>https://orcid.org/0000-0003-2044-6846</orcidid><orcidid>https://orcid.org/0000-0001-5737-2583</orcidid><oa>free_for_read</oa></addata></record>
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subjects Abiotic factors
Abiotic stress
Annotations
Association analysis
association mapping
Chloride transport
Coefficient of variation
Content analysis
Corn
CRISPR
Crops
Gene expression
Gene mapping
Genes
Genetic diversity
genetic loci
Genome-wide association studies
Genomes
Homeostasis
Inbreeding
maize
Metabolism
Metabolites
Molecular modelling
Mutants
Nucleotides
Phenotypic variations
Plant growth
Quantitative trait loci
Rice
Salinity
Salinity tolerance
Salt
Salt tolerance
Seedlings
Single-nucleotide polymorphism
Sodium chloride
Stress
title Molecular dissection of maize seedling salt tolerance using a genome‐wide association analysis method
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