Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.)
Abstract Background Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only par...
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| Format: | Article |
| Language: | English |
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BMC
2022-05-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-022-03602-z |
| _version_ | 1817985349373132800 |
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| author | Xia Shi Zhengfu Zhou Wenxu Li Maomao Qin Pan Yang Jinna Hou Fangfang Huang Zhensheng Lei Zhengqing Wu Jiansheng Wang |
| author_facet | Xia Shi Zhengfu Zhou Wenxu Li Maomao Qin Pan Yang Jinna Hou Fangfang Huang Zhensheng Lei Zhengqing Wu Jiansheng Wang |
| author_sort | Xia Shi |
| collection | DOAJ |
| description | Abstract Background Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood. Results Here, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61–26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain. Conclusion To identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding. |
| first_indexed | 2024-04-13T23:56:58Z |
| format | Article |
| id | doaj.art-d49b2cedd8244d18b840aa1fbd8bcf44 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-13T23:56:58Z |
| publishDate | 2022-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-d49b2cedd8244d18b840aa1fbd8bcf442022-12-22T02:23:51ZengBMCBMC Plant Biology1471-22292022-05-0122111410.1186/s12870-022-03602-zGenome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.)Xia Shi0Zhengfu Zhou1Wenxu Li2Maomao Qin3Pan Yang4Jinna Hou5Fangfang Huang6Zhensheng Lei7Zhengqing Wu8Jiansheng Wang9Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesHenan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesHenan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesHenan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesHenan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesHenan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesCollege of Life Sciences, Henan Agricultural UniversityHenan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesHenan Institute of Crop Molecular Breeding, Henan Academy of Agricultural SciencesCollege of Chemistry and Environment Engineering, Pingdingshan UniversityAbstract Background Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood. Results Here, a genome-wide association study (GWAS) was performed to dissect the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations. In total, 11 non-redundant genetic loci associated with Ca concentration were identified and they explained, on average, 9.61–26.93% of the phenotypic variation. Cultivars containing more superior alleles had increased grain Ca concentrations. Notably, four non-redundant loci were mutually verified by different statistical models in at least two environments, indicating their stability across different environments. Four putative candidate genes linked to Ca accumulation were revealed from the stable genetic loci. Among them, two genes, associated with the stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), encode the subunits of V-type Proton ATPase (TraesCS4A02G428900 and TraesCS3B02G241000), which annotated as the typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain. Conclusion To identify genetic loci associated with Ca accumulation, we conducted GWAS on Ca concentrations and detected 11 genetic loci; whereas four genetic loci were stable across different environments. A genetic loci hot spot exists at the end of chromosome 4A and associated with the putative candidate gene TraesCS4A02G428900. The candidate gene TraesCS4A02G428900 encodes V-type proton ATPase subunit e and highly expressed in wheat grains, and it possibly involved in Ca accumulation. This study increases our understanding of the genetic architecture of Ca accumulation in wheat grains, which is potentially helpful for wheat Ca biofortification pyramid breeding.https://doi.org/10.1186/s12870-022-03602-zHexaploid wheat (Triticum aestivum L.)Ca accumulationsuperior allelespyramid breedinggenome-wide association analysis |
| spellingShingle | Xia Shi Zhengfu Zhou Wenxu Li Maomao Qin Pan Yang Jinna Hou Fangfang Huang Zhensheng Lei Zhengqing Wu Jiansheng Wang Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.) BMC Plant Biology Hexaploid wheat (Triticum aestivum L.) Ca accumulation superior alleles pyramid breeding genome-wide association analysis |
| title | Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.) |
| title_full | Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.) |
| title_fullStr | Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.) |
| title_full_unstemmed | Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.) |
| title_short | Genome-wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat (Triticum aestivum L.) |
| title_sort | genome wide association study reveals the genetic architecture for calcium accumulation in grains of hexaploid wheat triticum aestivum l |
| topic | Hexaploid wheat (Triticum aestivum L.) Ca accumulation superior alleles pyramid breeding genome-wide association analysis |
| url | https://doi.org/10.1186/s12870-022-03602-z |
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