Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.)
Kernel row number (KRN) is one of the key traits that significantly affect maize yield and productivity. Therefore, investigating the candidate genes and their functions in regulating KRN provides a theoretical basis and practical direction for genetic improvement in maize breeding, which is vital f...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/13/23/3308 |
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| author | Jiao Kong Fuyan Jiang Ranjan K. Shaw Yaqi Bi Xingfu Yin Yanhui Pan Xiaodong Gong Haiyang Zong Babar Ijaz Xingming Fan |
| author_facet | Jiao Kong Fuyan Jiang Ranjan K. Shaw Yaqi Bi Xingfu Yin Yanhui Pan Xiaodong Gong Haiyang Zong Babar Ijaz Xingming Fan |
| author_sort | Jiao Kong |
| collection | DOAJ |
| description | Kernel row number (KRN) is one of the key traits that significantly affect maize yield and productivity. Therefore, investigating the candidate genes and their functions in regulating KRN provides a theoretical basis and practical direction for genetic improvement in maize breeding, which is vital for increasing maize yield and understanding domestication. In this study, three recombinant inbred line (RIL) populations were developed using the parental lines AN20, YML1218, CM395, and Ye107, resulting in a multiparent population comprising a total of 490 F9 RILs. Phenotypic evaluation of the RILs for KRN was performed in three distinct environments. The heritability estimates of the RILs ranged from 81.40% to 84.16%. Genotyping-by-sequencing (GBS) of RILs identified 569,529 high-quality single nucleotide polymorphisms (SNPs). Combined genome-wide association study (GWAS) and linkage analyses revealed 120 SNPs and 22 quantitative trait loci (QTLs) which were significantly associated with KRN in maize. Furthermore, two novel candidate genes, <i>Zm00001d042733</i> and <i>Zm00001d042735</i>, regulating KRN in maize were identified, which were located in close proximity to the significant SNP3-178,487,003 and overlapping the interval of QTL <i>qKRN3-1</i>. <i>Zm00001d042733</i> encodes ubiquitin carboxyl-terminal hydrolase and <i>Zm00001d042735</i> encodes the Arabidopsis Tóxicos en Levadura family of proteins. This study identified novel candidate loci and established a theoretical foundation for further functional validation of candidate genes. These findings deepen our comprehension of the genetic mechanisms that underpin KRN and offer potential applications of KRN-related strategies in developing maize varieties with higher yield. |
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| language | English |
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| publishDate | 2024-11-01 |
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| series | Plants |
| spelling | doaj.art-1db4850a57594599b6b65b6f6e5e11752024-12-13T16:29:54ZengMDPI AGPlants2223-77472024-11-011323330810.3390/plants13233308Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.)Jiao Kong0Fuyan Jiang1Ranjan K. Shaw2Yaqi Bi3Xingfu Yin4Yanhui Pan5Xiaodong Gong6Haiyang Zong7Babar Ijaz8Xingming Fan9College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaInstitute of Resource Plants, Yunnan University, Kunming 650500, ChinaInstitute of Resource Plants, Yunnan University, Kunming 650500, ChinaInstitute of Resource Plants, Yunnan University, Kunming 650500, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaKernel row number (KRN) is one of the key traits that significantly affect maize yield and productivity. Therefore, investigating the candidate genes and their functions in regulating KRN provides a theoretical basis and practical direction for genetic improvement in maize breeding, which is vital for increasing maize yield and understanding domestication. In this study, three recombinant inbred line (RIL) populations were developed using the parental lines AN20, YML1218, CM395, and Ye107, resulting in a multiparent population comprising a total of 490 F9 RILs. Phenotypic evaluation of the RILs for KRN was performed in three distinct environments. The heritability estimates of the RILs ranged from 81.40% to 84.16%. Genotyping-by-sequencing (GBS) of RILs identified 569,529 high-quality single nucleotide polymorphisms (SNPs). Combined genome-wide association study (GWAS) and linkage analyses revealed 120 SNPs and 22 quantitative trait loci (QTLs) which were significantly associated with KRN in maize. Furthermore, two novel candidate genes, <i>Zm00001d042733</i> and <i>Zm00001d042735</i>, regulating KRN in maize were identified, which were located in close proximity to the significant SNP3-178,487,003 and overlapping the interval of QTL <i>qKRN3-1</i>. <i>Zm00001d042733</i> encodes ubiquitin carboxyl-terminal hydrolase and <i>Zm00001d042735</i> encodes the Arabidopsis Tóxicos en Levadura family of proteins. This study identified novel candidate loci and established a theoretical foundation for further functional validation of candidate genes. These findings deepen our comprehension of the genetic mechanisms that underpin KRN and offer potential applications of KRN-related strategies in developing maize varieties with higher yield.https://www.mdpi.com/2223-7747/13/23/3308maizekernel row numberGWASQTL mappingcandidate genes |
| spellingShingle | Jiao Kong Fuyan Jiang Ranjan K. Shaw Yaqi Bi Xingfu Yin Yanhui Pan Xiaodong Gong Haiyang Zong Babar Ijaz Xingming Fan Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.) Plants maize kernel row number GWAS QTL mapping candidate genes |
| title | Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.) |
| title_full | Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.) |
| title_fullStr | Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.) |
| title_full_unstemmed | Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.) |
| title_short | Combined Genome-Wide Association Study and Linkage Analysis for Mining Candidate Genes for the Kernel Row Number in Maize (<i>Zea mays</i> L.) |
| title_sort | combined genome wide association study and linkage analysis for mining candidate genes for the kernel row number in maize i zea mays i l |
| topic | maize kernel row number GWAS QTL mapping candidate genes |
| url | https://www.mdpi.com/2223-7747/13/23/3308 |
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