Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize
Maize is an important food crop, and 100-kernel weight (HKW) is one of the three key components of yield. In this study, 200 maize inbred lines were used as the material, and HKW was evaluated over three consecutive years in two environments. A genome-wide association study (GWAS) was conducted usin...
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2024-12-01
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| author | Meixia Wang Danyang Cheng Haojie Ren Haoyang Li Ruiyu Wang Chunlin Dong Jianzhong Chang |
| author_facet | Meixia Wang Danyang Cheng Haojie Ren Haoyang Li Ruiyu Wang Chunlin Dong Jianzhong Chang |
| author_sort | Meixia Wang |
| collection | DOAJ |
| description | Maize is an important food crop, and 100-kernel weight (HKW) is one of the three key components of yield. In this study, 200 maize inbred lines were used as the material, and HKW was evaluated over three consecutive years in two environments. A genome-wide association study (GWAS) was conducted using the Blink and FarmCPU models with 44,935 SNP markers evenly distributed across the maize genome. A total of 25 SNPs significantly associated with HKW were identified, with three SNPs detected in both models. Six significant SNPs were located within previously mapped QTL bins associated with grain weight. In the linkage disequilibrium (LD) regions of the significant SNP loci, 198 candidate genes were identified, of which 74 had annotation information. Further analysis revealed 21 candidate genes related to HKW, such as <i>GRMZM2G010555</i> (alternative oxidase), <i>GRMZM2G102471</i> (ubiquitin-conjugating enzyme), <i>GRMZM2G060669</i> (histone deacetylase), <i>GRMZM2G090156</i> (methyltransferase), <i>GRMZM2G002075</i> (BZIP transcription factor), and <i>GRMZM2G138454</i> (bHLH transcription factor). The SNP loci and candidate genes identified in this study provide important references for marker-assisted selection, fine mapping, and gene cloning related to HKW in maize. |
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| institution | DOAJ |
| issn | 2073-4395 |
| language | English |
| publishDate | 2024-12-01 |
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| spelling | doaj-art-547f0ecffa5941e58fa748e4fd628dac2025-08-20T02:53:18ZengMDPI AGAgronomy2073-43952024-12-011412295410.3390/agronomy14122954Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in MaizeMeixia Wang0Danyang Cheng1Haojie Ren2Haoyang Li3Ruiyu Wang4Chunlin Dong5Jianzhong Chang6College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Agronomy, Shanxi Agricultural University, Jinzhong 030801, ChinaCollege of Agronomy, Shanxi Agricultural University, Jinzhong 030801, ChinaShanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan 030031, ChinaShanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan 030031, ChinaShanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan 030031, ChinaShanxi Institute of Organic Dryland Farming, Shanxi Agricultural University, Taiyuan 030031, ChinaMaize is an important food crop, and 100-kernel weight (HKW) is one of the three key components of yield. In this study, 200 maize inbred lines were used as the material, and HKW was evaluated over three consecutive years in two environments. A genome-wide association study (GWAS) was conducted using the Blink and FarmCPU models with 44,935 SNP markers evenly distributed across the maize genome. A total of 25 SNPs significantly associated with HKW were identified, with three SNPs detected in both models. Six significant SNPs were located within previously mapped QTL bins associated with grain weight. In the linkage disequilibrium (LD) regions of the significant SNP loci, 198 candidate genes were identified, of which 74 had annotation information. Further analysis revealed 21 candidate genes related to HKW, such as <i>GRMZM2G010555</i> (alternative oxidase), <i>GRMZM2G102471</i> (ubiquitin-conjugating enzyme), <i>GRMZM2G060669</i> (histone deacetylase), <i>GRMZM2G090156</i> (methyltransferase), <i>GRMZM2G002075</i> (BZIP transcription factor), and <i>GRMZM2G138454</i> (bHLH transcription factor). The SNP loci and candidate genes identified in this study provide important references for marker-assisted selection, fine mapping, and gene cloning related to HKW in maize.https://www.mdpi.com/2073-4395/14/12/2954maize100-kernel weightgenome-wide association studycandidate gene identification |
| spellingShingle | Meixia Wang Danyang Cheng Haojie Ren Haoyang Li Ruiyu Wang Chunlin Dong Jianzhong Chang Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize Agronomy maize 100-kernel weight genome-wide association study candidate gene identification |
| title | Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize |
| title_full | Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize |
| title_fullStr | Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize |
| title_full_unstemmed | Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize |
| title_short | Genome-Wide Association Analysis Identifies Loci and Candidate Genes for 100-Kernel Weight in Maize |
| title_sort | genome wide association analysis identifies loci and candidate genes for 100 kernel weight in maize |
| topic | maize 100-kernel weight genome-wide association study candidate gene identification |
| url | https://www.mdpi.com/2073-4395/14/12/2954 |
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