Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat
Abstract Background Wheat (Triticum aestivum L.) is a significant cereal crop that plays a vital role in global food production. To expedite the breeding of wheat cultivars with high protein quality, it is necessary to genetically analyze the traits related to quality. A genome-wide association stud...
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BMC
2025-02-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06171-z |
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| author | Yousheng Tian Pengpeng Liu Dezhen Kong Yingbin Nie Hongjun Xu Xinnian Han Wei Sang Weihua Li |
| author_facet | Yousheng Tian Pengpeng Liu Dezhen Kong Yingbin Nie Hongjun Xu Xinnian Han Wei Sang Weihua Li |
| author_sort | Yousheng Tian |
| collection | DOAJ |
| description | Abstract Background Wheat (Triticum aestivum L.) is a significant cereal crop that plays a vital role in global food production. To expedite the breeding of wheat cultivars with high protein quality, it is necessary to genetically analyze the traits related to quality. A genome-wide association study (GWAS) was conducted to identify the genomic regions responsible for protein quality traits in winter wheat. Results Six protein quality traits were evaluated across two locations and two years for a total of 341 wheat accessions. Utilizing the wheat 40 K SNP array, GWAS identified 97 significantly stable SNPs at 43 loci for five out of six protein quality traits using a linear mixed model. The 43 loci distribution was four for grain protein content, two for flour protein content, one for wet gluten content, four for gluten index, and thirty-two for Zeleny sedimentation value. The most significant associations were identified on chromosomes 1 A, 1B, and 1D. Haplotype analysis of loci associated with the gluten index in the 412–416 Mb interval on chromosome 1D identified three blocks. Accessions with superior haplotypes showed a significantly higher gluten index than those with inferior haplotypes. Six KASP markers were successfully developed for the gluten index, while five KASP markers were developed for the Zeleny sedimentation value. Additionally, eight candidate genes were identified that may affect protein accumulation during grain development. Conclusions Our study identified 97 SNPs significantly associated with protein quality traits; developed 6 KASP markers for gluten index, and 5 KASP markers for Zeleny sedimentation values; screened 8 candidate genes that may be related to protein quality during grain development. Thise research will offer valuable insights for wheat breeding programs in China and globally. |
| format | Article |
| id | doaj-art-d15b25e853ab46848bbf6538533d7ea5 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-d15b25e853ab46848bbf6538533d7ea52025-02-09T12:27:43ZengBMCBMC Plant Biology1471-22292025-02-0125111710.1186/s12870-025-06171-zGenome-wide association analysis and KASP markers development for protein quality traits in winter wheatYousheng Tian0Pengpeng Liu1Dezhen Kong2Yingbin Nie3Hongjun Xu4Xinnian Han5Wei Sang6Weihua Li7Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation SciencesInstitute of Crop Science, Xinjiang Academy of Agricultural and Reclamation SciencesInstitute of Crop Science, Xinjiang Academy of Agricultural and Reclamation SciencesInstitute of Crop Science, Xinjiang Academy of Agricultural and Reclamation SciencesInstitute of Crop Science, Xinjiang Academy of Agricultural and Reclamation SciencesInstitute of Crop Science, Xinjiang Academy of Agricultural and Reclamation SciencesInstitute of Crop Science, Xinjiang Academy of Agricultural and Reclamation SciencesThe Key Laboratory of the Oasis Ecological Agriculture, College of Agriculture, Shihezi UniversityAbstract Background Wheat (Triticum aestivum L.) is a significant cereal crop that plays a vital role in global food production. To expedite the breeding of wheat cultivars with high protein quality, it is necessary to genetically analyze the traits related to quality. A genome-wide association study (GWAS) was conducted to identify the genomic regions responsible for protein quality traits in winter wheat. Results Six protein quality traits were evaluated across two locations and two years for a total of 341 wheat accessions. Utilizing the wheat 40 K SNP array, GWAS identified 97 significantly stable SNPs at 43 loci for five out of six protein quality traits using a linear mixed model. The 43 loci distribution was four for grain protein content, two for flour protein content, one for wet gluten content, four for gluten index, and thirty-two for Zeleny sedimentation value. The most significant associations were identified on chromosomes 1 A, 1B, and 1D. Haplotype analysis of loci associated with the gluten index in the 412–416 Mb interval on chromosome 1D identified three blocks. Accessions with superior haplotypes showed a significantly higher gluten index than those with inferior haplotypes. Six KASP markers were successfully developed for the gluten index, while five KASP markers were developed for the Zeleny sedimentation value. Additionally, eight candidate genes were identified that may affect protein accumulation during grain development. Conclusions Our study identified 97 SNPs significantly associated with protein quality traits; developed 6 KASP markers for gluten index, and 5 KASP markers for Zeleny sedimentation values; screened 8 candidate genes that may be related to protein quality during grain development. Thise research will offer valuable insights for wheat breeding programs in China and globally.https://doi.org/10.1186/s12870-025-06171-zWheatProtein qualityGWASKASPCandidate genes |
| spellingShingle | Yousheng Tian Pengpeng Liu Dezhen Kong Yingbin Nie Hongjun Xu Xinnian Han Wei Sang Weihua Li Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat BMC Plant Biology Wheat Protein quality GWAS KASP Candidate genes |
| title | Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat |
| title_full | Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat |
| title_fullStr | Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat |
| title_full_unstemmed | Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat |
| title_short | Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat |
| title_sort | genome wide association analysis and kasp markers development for protein quality traits in winter wheat |
| topic | Wheat Protein quality GWAS KASP Candidate genes |
| url | https://doi.org/10.1186/s12870-025-06171-z |
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