The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet
Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related...
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/23/14735 |
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| author | Xiaodong Liu Yang Yang Siyou Hou Yihan Men Yuanhuai Han |
| author_facet | Xiaodong Liu Yang Yang Siyou Hou Yihan Men Yuanhuai Han |
| author_sort | Xiaodong Liu |
| collection | DOAJ |
| description | Panicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice–foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as <i>Si3g11200</i> (<i>OsDER1</i>), <i>Si1g27910</i> (<i>OsMADS6</i>), <i>Si7g27560</i> (<i>GS5</i>), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as <i>Si3g11200</i> affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding. |
| first_indexed | 2024-03-09T17:46:58Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T17:46:58Z |
| publishDate | 2022-11-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-ed0b7a8a07364f05b026dd4f1fe59a872023-11-24T11:07:01ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123231473510.3390/ijms232314735The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail MilletXiaodong Liu0Yang Yang1Siyou Hou2Yihan Men3Yuanhuai Han4Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, ChinaShanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, ChinaShanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, ChinaShanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, ChinaShanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Taiyuan 030031, ChinaPanicle traits are important factors affecting yield, and their improvement has long been a critical goal in foxtail millet breeding. In order to understand the genetic basis of panicle formation, a large-scale genome-wide association study (GWAS) was performed in this study for six panicle-related traits based on 706,646 high-polymorphism SNP loci in 407 accessions. As a result, 87 quantitative trait loci (QTL) regions with a physical distance of less than 100 kb were detected to be associated with these traits in three environments. Among them, 27 core regions were stably detected in at least two environments. Based on rice–foxtail millet homologous comparison, expression, and haplotype analysis, 27 high-confidence candidate genes in the QTL regions, such as <i>Si3g11200</i> (<i>OsDER1</i>), <i>Si1g27910</i> (<i>OsMADS6</i>), <i>Si7g27560</i> (<i>GS5</i>), etc., affected panicle-related traits by involving multiple plant growth regulator pathways, a photoperiod response, as well as panicle and grain development. Most of these genes showed multiple effects on different panicle-related traits, such as <i>Si3g11200</i> affecting all six traits. In summary, this study clarified a strategy based on the integration of GWAS, a homologous comparison, and haplotype analysis to discover the genomic regions and candidate genes for important traits in foxtail millet. The detected QTL regions and candidate genes could be further used for gene clone and marker-assisted selection in foxtail millet breeding.https://www.mdpi.com/1422-0067/23/23/14735foxtail milletpanicle-related traitsgenome-wide association studyhomology analysishaplotype analysis |
| spellingShingle | Xiaodong Liu Yang Yang Siyou Hou Yihan Men Yuanhuai Han The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet International Journal of Molecular Sciences foxtail millet panicle-related traits genome-wide association study homology analysis haplotype analysis |
| title | The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet |
| title_full | The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet |
| title_fullStr | The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet |
| title_full_unstemmed | The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet |
| title_short | The Integration of Genome-Wide Association Study and Homology Analysis to Explore the Genomic Regions and Candidate Genes for Panicle-Related Traits in Foxtail Millet |
| title_sort | integration of genome wide association study and homology analysis to explore the genomic regions and candidate genes for panicle related traits in foxtail millet |
| topic | foxtail millet panicle-related traits genome-wide association study homology analysis haplotype analysis |
| url | https://www.mdpi.com/1422-0067/23/23/14735 |
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