Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses
Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adapt...
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| Format: | Article |
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.822516/full |
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| author | Mohammad Rafiqul Islam Shahzad Amir Naveed Yue Zhang Zhikang Li Zhikang Li Zhikang Li Xiuqin Zhao Sajid Fiaz Fan Zhang Fan Zhang Zhichao Wu Zhiqing Hu Binying Fu Yingyao Shi Shahid Masood Shah Jianlong Xu Jianlong Xu Wensheng Wang Wensheng Wang Wensheng Wang |
| author_facet | Mohammad Rafiqul Islam Shahzad Amir Naveed Yue Zhang Zhikang Li Zhikang Li Zhikang Li Xiuqin Zhao Sajid Fiaz Fan Zhang Fan Zhang Zhichao Wu Zhiqing Hu Binying Fu Yingyao Shi Shahid Masood Shah Jianlong Xu Jianlong Xu Wensheng Wang Wensheng Wang Wensheng Wang |
| author_sort | Mohammad Rafiqul Islam |
| collection | DOAJ |
| description | Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing. |
| first_indexed | 2024-12-24T00:28:53Z |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-24T00:28:53Z |
| publishDate | 2022-02-01 |
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| spelling | doaj.art-f26d63eab09f4fb3902f9967dba382a62022-12-21T17:24:21ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-02-011310.3389/fgene.2022.822516822516Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association AnalysesMohammad Rafiqul Islam0Shahzad Amir Naveed1Yue Zhang2Zhikang Li3Zhikang Li4Zhikang Li5Xiuqin Zhao6Sajid Fiaz7Fan Zhang8Fan Zhang9Zhichao Wu10Zhiqing Hu11Binying Fu12Yingyao Shi13Shahid Masood Shah14Jianlong Xu15Jianlong Xu16Wensheng Wang17Wensheng Wang18Wensheng Wang19Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaDepartment of Plant Breeding and Genetics, The University of Haripur, Haripur, PakistanInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaDepartment of Biotechnology, COMSATS University Islamabad-Abbottabad Campus, Abbottabad, PakistanInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaInstitute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, ChinaNational Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, ChinaMultiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.https://www.frontiersin.org/articles/10.3389/fgene.2022.822516/fulldirect seedingQTL mappingsalinityanaerobicGWAS |
| spellingShingle | Mohammad Rafiqul Islam Shahzad Amir Naveed Yue Zhang Zhikang Li Zhikang Li Zhikang Li Xiuqin Zhao Sajid Fiaz Fan Zhang Fan Zhang Zhichao Wu Zhiqing Hu Binying Fu Yingyao Shi Shahid Masood Shah Jianlong Xu Jianlong Xu Wensheng Wang Wensheng Wang Wensheng Wang Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses Frontiers in Genetics direct seeding QTL mapping salinity anaerobic GWAS |
| title | Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses |
| title_full | Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses |
| title_fullStr | Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses |
| title_full_unstemmed | Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses |
| title_short | Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses |
| title_sort | identification of candidate genes for salinity and anaerobic tolerance at the germination stage in rice by genome wide association analyses |
| topic | direct seeding QTL mapping salinity anaerobic GWAS |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.822516/full |
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