Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis
Introduction Maize (Zea mays L.) is one of the most important crops worldwide, the kernel size-related traits are the major components of maize grain yield.Methods To dissect the genetic architecture of four kernel-related traits of 100-kernel weight, kernel length, kernel width, and kernel diameter...
| Autores principales: | , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
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Frontiers Media
2024
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| Acceso en línea: | https://hdl.handle.net/10568/162557 |
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| author | Jingtao Qu Diansi Yu Wei Gu Muhammad Hayder Bin Khalid Huiyun Kuang Dongdong Dang Hui Wang Prasanna, Boddupalli M. Xuecai Zhang Ao Zhang Hongjian Zheng Yuan Guan |
| author_browse | Ao Zhang Diansi Yu Dongdong Dang Hongjian Zheng Hui Wang Huiyun Kuang Jingtao Qu Muhammad Hayder Bin Khalid Prasanna, Boddupalli M. Wei Gu Xuecai Zhang Yuan Guan |
| author_facet | Jingtao Qu Diansi Yu Wei Gu Muhammad Hayder Bin Khalid Huiyun Kuang Dongdong Dang Hui Wang Prasanna, Boddupalli M. Xuecai Zhang Ao Zhang Hongjian Zheng Yuan Guan |
| author_sort | Jingtao Qu |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Introduction Maize (Zea mays L.) is one of the most important crops worldwide, the kernel size-related traits are the major components of maize grain yield.Methods To dissect the genetic architecture of four kernel-related traits of 100-kernel weight, kernel length, kernel width, and kernel diameter, a genome-wide association study (GWAS) was conducted in the waxy and sweet maize panel comprising of 447 maize inbred lines re-sequenced at the 5x coverage depth. GWAS analysis was carried out with the mixed linear model using 1,684,029 high-quality SNP markers.Results In total, 49 SNPs significantly associated with the four kernel-related traits were identified, including 46 SNPs on chromosome 3, two SNPs on chromosome 4, and one SNP on chromosome 7. Haplotype regression analysis identified 338 haplotypes that significantly affected these four kernel-related traits. Genomic selection (GS) results revealed that a set of 10,000 SNPs and a training population size of 30% are sufficient for the application of GS in waxy and sweet maize breeding for kernel weight and kernel size. Forty candidate genes associated with the four kernel-related traits were identified, including both Zm00001d000707 and Zm00001d044139 expressed in the kernel development tissues and stages with unknown functions.Discussion These significant SNPs and important haplotypes provide valuable information for developing functional markers for the implementation of marker-assisted selection in breeding. The molecular mechanism of Zm00001d000707 and Zm00001d044139 regulating these kernel-related traits needs to be investigated further. |
| format | Journal Article |
| id | CGSpace162557 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1625572025-12-08T10:29:22Z Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis Jingtao Qu Diansi Yu Wei Gu Muhammad Hayder Bin Khalid Huiyun Kuang Dongdong Dang Hui Wang Prasanna, Boddupalli M. Xuecai Zhang Ao Zhang Hongjian Zheng Yuan Guan kernels high-throughput sequencing genome-wide association studies marker-assisted selection maize Introduction Maize (Zea mays L.) is one of the most important crops worldwide, the kernel size-related traits are the major components of maize grain yield.Methods To dissect the genetic architecture of four kernel-related traits of 100-kernel weight, kernel length, kernel width, and kernel diameter, a genome-wide association study (GWAS) was conducted in the waxy and sweet maize panel comprising of 447 maize inbred lines re-sequenced at the 5x coverage depth. GWAS analysis was carried out with the mixed linear model using 1,684,029 high-quality SNP markers.Results In total, 49 SNPs significantly associated with the four kernel-related traits were identified, including 46 SNPs on chromosome 3, two SNPs on chromosome 4, and one SNP on chromosome 7. Haplotype regression analysis identified 338 haplotypes that significantly affected these four kernel-related traits. Genomic selection (GS) results revealed that a set of 10,000 SNPs and a training population size of 30% are sufficient for the application of GS in waxy and sweet maize breeding for kernel weight and kernel size. Forty candidate genes associated with the four kernel-related traits were identified, including both Zm00001d000707 and Zm00001d044139 expressed in the kernel development tissues and stages with unknown functions.Discussion These significant SNPs and important haplotypes provide valuable information for developing functional markers for the implementation of marker-assisted selection in breeding. The molecular mechanism of Zm00001d000707 and Zm00001d044139 regulating these kernel-related traits needs to be investigated further. 2024-09-27 2024-11-21T17:36:05Z 2024-11-21T17:36:05Z Journal Article https://hdl.handle.net/10568/162557 en Open Access application/pdf Frontiers Media Qu, J., Yu, D., Gu, W., Khalid, M. H. B., Kuang, H., Dang, D., Wang, H., Prasanna, B., Zhang, X., Zhang, A., Zheng, H., & Guan, Y. (2024). Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis. Frontiers in Genetics, 15, art 1431043. https://doi.org/10.3389/fgene.2024.1431043 |
| spellingShingle | kernels high-throughput sequencing genome-wide association studies marker-assisted selection maize Jingtao Qu Diansi Yu Wei Gu Muhammad Hayder Bin Khalid Huiyun Kuang Dongdong Dang Hui Wang Prasanna, Boddupalli M. Xuecai Zhang Ao Zhang Hongjian Zheng Yuan Guan Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis |
| title | Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis |
| title_full | Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis |
| title_fullStr | Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis |
| title_full_unstemmed | Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis |
| title_short | Genetic architecture of kernel-related traits in sweet and waxy maize revealed by genome-wide association analysis |
| title_sort | genetic architecture of kernel related traits in sweet and waxy maize revealed by genome wide association analysis |
| topic | kernels high-throughput sequencing genome-wide association studies marker-assisted selection maize |
| url | https://hdl.handle.net/10568/162557 |
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