Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice
IntroductionSaline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve rice saline-alkali tolerance at the germination stage. MethodsTo understand the genetic b...
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Frontiers Media S.A.
2023-05-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1170641/full |
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| author | Guogen Zhang Guogen Zhang Zhiyuan Bi Jing Jiang Jingbing Lu Keyang Li Di Bai Xinchen Wang Xueyu Zhao Min Li Xiuqin Zhao Wensheng Wang Wensheng Wang Jianlong Xu Zhikang Li Zhikang Li Fan Zhang Fan Zhang Yingyao Shi |
| author_facet | Guogen Zhang Guogen Zhang Zhiyuan Bi Jing Jiang Jingbing Lu Keyang Li Di Bai Xinchen Wang Xueyu Zhao Min Li Xiuqin Zhao Wensheng Wang Wensheng Wang Jianlong Xu Zhikang Li Zhikang Li Fan Zhang Fan Zhang Yingyao Shi |
| author_sort | Guogen Zhang |
| collection | DOAJ |
| description | IntroductionSaline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve rice saline-alkali tolerance at the germination stage. MethodsTo understand the genetic basis of saline-alkali tolerance and facilitate breeding efforts for developing saline-alkali tolerant rice varieties, the genetic basis of rice saline-alkali tolerance was dissected by phenotyping seven germination-related traits of 736 diverse rice accessions under the saline-alkali stress and control conditions using genome-wide association and epistasis analysis (GWAES).ResultsTotally, 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified as significantly associated with saline-alkali tolerance, which explained a significant portion of the total phenotypic variation of the saline-alkali tolerance traits in the 736 rice accessions. Most of these QTNs were located in genomic regions either harboring saline-alkali tolerance QTNs or known genes for saline-alkali tolerance reported previously. Epistasis as an important genetic basis of rice saline-alkali tolerance was validated by genomic best linear unbiased prediction in which inclusion of both main-effect and epistatic QTNs showed a consistently better prediction accuracy than either main-effect or epistatic QTNs alone. Candidate genes for two pairs of important epistatic QTNs were suggested based on combined evidence from the high-resolution mapping plus their reported molecular functions. The first pair included a glycosyltransferase gene LOC_Os02g51900 (UGT85E1) and an E3 ligase gene LOC_Os04g01490 (OsSIRP4), while the second pair comprised an ethylene-responsive transcriptional factor, AP59 (LOC_Os02g43790), and a Bcl-2-associated athanogene gene, OsBAG1 (LOC_Os09g35630) for salt tolerance. Detailed haplotype analyses at both gene promoter and CDS regions of these candidate genes for important QTNs identified favorable haplotype combinations with large effects on saline-alkali tolerance, which can be used to improve rice saline-alkali tolerance by selective introgression. DiscussionOur findings provided saline-alkali tolerant germplasm resources and valuable genetic information to be used in future functional genomic and breeding efforts of rice saline-alkali tolerance at the germination stage. |
| first_indexed | 2024-04-09T13:11:25Z |
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| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-09T13:11:25Z |
| publishDate | 2023-05-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-90caf59a11df40e2a16a9a3670eb90d42023-05-12T07:07:39ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-05-011410.3389/fpls.2023.11706411170641Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in riceGuogen Zhang0Guogen Zhang1Zhiyuan Bi2Jing Jiang3Jingbing Lu4Keyang Li5Di Bai6Xinchen Wang7Xueyu Zhao8Min Li9Xiuqin Zhao10Wensheng Wang11Wensheng Wang12Jianlong Xu13Zhikang Li14Zhikang Li15Fan Zhang16Fan Zhang17Yingyao Shi18College of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, ChinaCollege of Agronomy, Anhui Agricultural University, Hefei, Anhui, ChinaIntroductionSaline-alkali stress is one of the main abiotic factors limiting rice production worldwide. With the widespread use of rice direct seeding technology, it has become increasingly important to improve rice saline-alkali tolerance at the germination stage. MethodsTo understand the genetic basis of saline-alkali tolerance and facilitate breeding efforts for developing saline-alkali tolerant rice varieties, the genetic basis of rice saline-alkali tolerance was dissected by phenotyping seven germination-related traits of 736 diverse rice accessions under the saline-alkali stress and control conditions using genome-wide association and epistasis analysis (GWAES).ResultsTotally, 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified as significantly associated with saline-alkali tolerance, which explained a significant portion of the total phenotypic variation of the saline-alkali tolerance traits in the 736 rice accessions. Most of these QTNs were located in genomic regions either harboring saline-alkali tolerance QTNs or known genes for saline-alkali tolerance reported previously. Epistasis as an important genetic basis of rice saline-alkali tolerance was validated by genomic best linear unbiased prediction in which inclusion of both main-effect and epistatic QTNs showed a consistently better prediction accuracy than either main-effect or epistatic QTNs alone. Candidate genes for two pairs of important epistatic QTNs were suggested based on combined evidence from the high-resolution mapping plus their reported molecular functions. The first pair included a glycosyltransferase gene LOC_Os02g51900 (UGT85E1) and an E3 ligase gene LOC_Os04g01490 (OsSIRP4), while the second pair comprised an ethylene-responsive transcriptional factor, AP59 (LOC_Os02g43790), and a Bcl-2-associated athanogene gene, OsBAG1 (LOC_Os09g35630) for salt tolerance. Detailed haplotype analyses at both gene promoter and CDS regions of these candidate genes for important QTNs identified favorable haplotype combinations with large effects on saline-alkali tolerance, which can be used to improve rice saline-alkali tolerance by selective introgression. DiscussionOur findings provided saline-alkali tolerant germplasm resources and valuable genetic information to be used in future functional genomic and breeding efforts of rice saline-alkali tolerance at the germination stage.https://www.frontiersin.org/articles/10.3389/fpls.2023.1170641/fullgermination stagegenome-wide association studyepistasisricesaline-alkali tolerance |
| spellingShingle | Guogen Zhang Guogen Zhang Zhiyuan Bi Jing Jiang Jingbing Lu Keyang Li Di Bai Xinchen Wang Xueyu Zhao Min Li Xiuqin Zhao Wensheng Wang Wensheng Wang Jianlong Xu Zhikang Li Zhikang Li Fan Zhang Fan Zhang Yingyao Shi Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice Frontiers in Plant Science germination stage genome-wide association study epistasis rice saline-alkali tolerance |
| title | Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice |
| title_full | Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice |
| title_fullStr | Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice |
| title_full_unstemmed | Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice |
| title_short | Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice |
| title_sort | genome wide association and epistasis studies reveal the genetic basis of saline alkali tolerance at the germination stage in rice |
| topic | germination stage genome-wide association study epistasis rice saline-alkali tolerance |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1170641/full |
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