Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean
Powdery mildew disease (PMD) is caused by the obligate biotrophic fungus Microsphaera diffusa Cooke & Peck (M. diffusa) and results in significant yield losses in soybean (Glycine max (L.) Merr.) crops. By identifying disease-resistant genes and breeding soybean accessions with enhanced resi...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1369650/full |
| _version_ | 1797229383662960640 |
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| author | Guoqiang Liu Guoqiang Liu Yuan Fang Xueling Liu Xueling Liu Jiacan Jiang Jiacan Jiang Guangquan Ding Guangquan Ding Yongzhen Wang Yongzhen Wang Xueqian Zhao Xueqian Zhao Xiaomin Xu Xiaomin Xu Mengshi Liu Mengshi Liu Yingxiang Wang Yingxiang Wang Cunyi Yang Cunyi Yang |
| author_facet | Guoqiang Liu Guoqiang Liu Yuan Fang Xueling Liu Xueling Liu Jiacan Jiang Jiacan Jiang Guangquan Ding Guangquan Ding Yongzhen Wang Yongzhen Wang Xueqian Zhao Xueqian Zhao Xiaomin Xu Xiaomin Xu Mengshi Liu Mengshi Liu Yingxiang Wang Yingxiang Wang Cunyi Yang Cunyi Yang |
| author_sort | Guoqiang Liu |
| collection | DOAJ |
| description | Powdery mildew disease (PMD) is caused by the obligate biotrophic fungus Microsphaera diffusa Cooke & Peck (M. diffusa) and results in significant yield losses in soybean (Glycine max (L.) Merr.) crops. By identifying disease-resistant genes and breeding soybean accessions with enhanced resistance, we can effectively mitigate the detrimental impact of PMD on soybeans. We analyzed PMD resistance in a diversity panel of 315 soybean accessions in two locations over 3 years, and candidate genes associated with PMD resistance were identified through genome-wide association studies (GWAS), haplotype analysis, qRT-PCR, and EMS mutant analysis. Based on the GWAS approach, we identified a region on chromosome 16 (Chr16) in which 21 genes form a gene cluster that is highly correlated with PMD resistance. In order to validate and refine these findings, we conducted haplotype analysis of 21 candidate genes and indicated there are single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) variations of Glyma.16G214000, Glyma.16G214200, Glyma.16G215100 and Glyma.16G215300 within the coding and promoter regions that exhibit a strong association with resistance against PMD. Subsequent structural analysis of candidate genes within this cluster revealed that in 315 accessions, the majority of accessions exhibited resistance to PMD when Glyma.16G214300, Glyma.16G214800 and Glyma.16G215000 were complete; however, they demonstrated susceptibility to PMD when these genes were incomplete. Quantitative real-time PCR assays (qRT-PCR) of possible candidate genes showed that 14 candidate genes (Glyma.16G213700, Glyma.16G213800, Glyma.16G213900, Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214500, Glyma.16G214585, Glyma.16G214669, Glyma.16G214700, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300) were involved in PMD resistance. Finally, we evaluated the PMD resistance of mutant lines from the Williams 82 EMS mutations library, which revealed that mutants of Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300, exhibited sensitivity to PMD. Combined with the analysis results of GWAS, haplotypes, qRT-PCR and mutants, the genes Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300 were identified as highly correlated with PMD resistance. The candidate genes identified above are all NLR family genes, and these discoveries deepen our understanding of the molecular basis of PMD resistance in soybeans and will be useful for guiding breeding strategies. |
| first_indexed | 2024-04-24T15:11:43Z |
| format | Article |
| id | doaj.art-7427e692846e42be9e25f53f2047bd31 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-24T15:11:43Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-7427e692846e42be9e25f53f2047bd312024-04-02T11:00:38ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-03-011510.3389/fpls.2024.13696501369650Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybeanGuoqiang Liu0Guoqiang Liu1Yuan Fang2Xueling Liu3Xueling Liu4Jiacan Jiang5Jiacan Jiang6Guangquan Ding7Guangquan Ding8Yongzhen Wang9Yongzhen Wang10Xueqian Zhao11Xueqian Zhao12Xiaomin Xu13Xiaomin Xu14Mengshi Liu15Mengshi Liu16Yingxiang Wang17Yingxiang Wang18Cunyi Yang19Cunyi Yang20Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaGuangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, ChinaKey Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, ChinaPowdery mildew disease (PMD) is caused by the obligate biotrophic fungus Microsphaera diffusa Cooke & Peck (M. diffusa) and results in significant yield losses in soybean (Glycine max (L.) Merr.) crops. By identifying disease-resistant genes and breeding soybean accessions with enhanced resistance, we can effectively mitigate the detrimental impact of PMD on soybeans. We analyzed PMD resistance in a diversity panel of 315 soybean accessions in two locations over 3 years, and candidate genes associated with PMD resistance were identified through genome-wide association studies (GWAS), haplotype analysis, qRT-PCR, and EMS mutant analysis. Based on the GWAS approach, we identified a region on chromosome 16 (Chr16) in which 21 genes form a gene cluster that is highly correlated with PMD resistance. In order to validate and refine these findings, we conducted haplotype analysis of 21 candidate genes and indicated there are single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) variations of Glyma.16G214000, Glyma.16G214200, Glyma.16G215100 and Glyma.16G215300 within the coding and promoter regions that exhibit a strong association with resistance against PMD. Subsequent structural analysis of candidate genes within this cluster revealed that in 315 accessions, the majority of accessions exhibited resistance to PMD when Glyma.16G214300, Glyma.16G214800 and Glyma.16G215000 were complete; however, they demonstrated susceptibility to PMD when these genes were incomplete. Quantitative real-time PCR assays (qRT-PCR) of possible candidate genes showed that 14 candidate genes (Glyma.16G213700, Glyma.16G213800, Glyma.16G213900, Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214500, Glyma.16G214585, Glyma.16G214669, Glyma.16G214700, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300) were involved in PMD resistance. Finally, we evaluated the PMD resistance of mutant lines from the Williams 82 EMS mutations library, which revealed that mutants of Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300, exhibited sensitivity to PMD. Combined with the analysis results of GWAS, haplotypes, qRT-PCR and mutants, the genes Glyma.16G214000, Glyma.16G214200, Glyma.16G214300, Glyma.16G214800, Glyma.16G215000, Glyma.16G215100 and Glyma.16G215300 were identified as highly correlated with PMD resistance. The candidate genes identified above are all NLR family genes, and these discoveries deepen our understanding of the molecular basis of PMD resistance in soybeans and will be useful for guiding breeding strategies.https://www.frontiersin.org/articles/10.3389/fpls.2024.1369650/fullGWASPMDhaplotypesqRT-PCREMS mutationsNLR |
| spellingShingle | Guoqiang Liu Guoqiang Liu Yuan Fang Xueling Liu Xueling Liu Jiacan Jiang Jiacan Jiang Guangquan Ding Guangquan Ding Yongzhen Wang Yongzhen Wang Xueqian Zhao Xueqian Zhao Xiaomin Xu Xiaomin Xu Mengshi Liu Mengshi Liu Yingxiang Wang Yingxiang Wang Cunyi Yang Cunyi Yang Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean Frontiers in Plant Science GWAS PMD haplotypes qRT-PCR EMS mutations NLR |
| title | Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean |
| title_full | Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean |
| title_fullStr | Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean |
| title_full_unstemmed | Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean |
| title_short | Genome-wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean |
| title_sort | genome wide association study and haplotype analysis reveal novel candidate genes for resistance to powdery mildew in soybean |
| topic | GWAS PMD haplotypes qRT-PCR EMS mutations NLR |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1369650/full |
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