Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize
Ear diameter (ED) is a critical component of grain yield (GY) in maize (<i>Zea mays</i> L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and...
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MDPI AG
2023-06-01
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| Online Access: | https://www.mdpi.com/2073-4425/14/6/1305 |
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| author | Fuyan Jiang Li Liu Ziwei Li Yaqi Bi Xingfu Yin Ruijia Guo Jing Wang Yudong Zhang Ranjan Kumar Shaw Xingming Fan |
| author_facet | Fuyan Jiang Li Liu Ziwei Li Yaqi Bi Xingfu Yin Ruijia Guo Jing Wang Yudong Zhang Ranjan Kumar Shaw Xingming Fan |
| author_sort | Fuyan Jiang |
| collection | DOAJ |
| description | Ear diameter (ED) is a critical component of grain yield (GY) in maize (<i>Zea mays</i> L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and SNPs associated with ED; and (2) identify putative functional genes that may affect ED in maize. To accomplish this, an elite maize inbred line, Ye107, which belongs to the Reid heterotic group, was used as a common parent and crossed with seven elite inbred lines from three different heterotic groups (Suwan1, Reid, and nonReid) that exhibited abundant genetic variation in ED. This led to the construction of a multi-parent population consisting of 1215 F<sub>7</sub> recombinant inbred lines (F<sub>7</sub>RILs). A genome-wide association study (GWAS) and linkage analysis were then conducted for the multi-parent population using 264,694 high-quality SNPs generated via the genotyping-by-sequencing method. Our study identified a total of 11 SNPs that were significantly associated with ED through the GWAS, and three QTLs were revealed by the linkage analysis for ED. The major QTL on chromosome 1 was co-identified in the region by the GWAS at SNP_143985532. SNP_143985532, located upstream of the <i>Zm00001d030559</i> gene, encodes a callose synthase that is expressed in various tissues, with the highest expression level in the maize ear primordium. Haplotype analysis indicated that the haplotype B (allele AA) of <i>Zm00001d030559</i> was positively correlated with ED. The candidate genes and SNPs identified in this study provide crucial insights for future studies on the genetic mechanism of maize ED formation, cloning of ED-related genes, and genetic improvement of ED. These results may help develop important genetic resources for enhancing maize yield through marker-assisted breeding. |
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| spelling | doaj.art-01ebd06cda73479189918287e788e58b2023-11-18T10:35:59ZengMDPI AGGenes2073-44252023-06-01146130510.3390/genes14061305Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in MaizeFuyan Jiang0Li Liu1Ziwei Li2Yaqi Bi3Xingfu Yin4Ruijia Guo5Jing Wang6Yudong Zhang7Ranjan Kumar Shaw8Xingming Fan9Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, ChinaYunnan Dehong Dai and Jingpo Nationality Institute of Agricultural Sciences, Mangshi 678400, 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 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, ChinaEar diameter (ED) is a critical component of grain yield (GY) in maize (<i>Zea mays</i> L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and SNPs associated with ED; and (2) identify putative functional genes that may affect ED in maize. To accomplish this, an elite maize inbred line, Ye107, which belongs to the Reid heterotic group, was used as a common parent and crossed with seven elite inbred lines from three different heterotic groups (Suwan1, Reid, and nonReid) that exhibited abundant genetic variation in ED. This led to the construction of a multi-parent population consisting of 1215 F<sub>7</sub> recombinant inbred lines (F<sub>7</sub>RILs). A genome-wide association study (GWAS) and linkage analysis were then conducted for the multi-parent population using 264,694 high-quality SNPs generated via the genotyping-by-sequencing method. Our study identified a total of 11 SNPs that were significantly associated with ED through the GWAS, and three QTLs were revealed by the linkage analysis for ED. The major QTL on chromosome 1 was co-identified in the region by the GWAS at SNP_143985532. SNP_143985532, located upstream of the <i>Zm00001d030559</i> gene, encodes a callose synthase that is expressed in various tissues, with the highest expression level in the maize ear primordium. Haplotype analysis indicated that the haplotype B (allele AA) of <i>Zm00001d030559</i> was positively correlated with ED. The candidate genes and SNPs identified in this study provide crucial insights for future studies on the genetic mechanism of maize ED formation, cloning of ED-related genes, and genetic improvement of ED. These results may help develop important genetic resources for enhancing maize yield through marker-assisted breeding.https://www.mdpi.com/2073-4425/14/6/1305maizeear diametercandidate geneGWASQTL |
| spellingShingle | Fuyan Jiang Li Liu Ziwei Li Yaqi Bi Xingfu Yin Ruijia Guo Jing Wang Yudong Zhang Ranjan Kumar Shaw Xingming Fan Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize Genes maize ear diameter candidate gene GWAS QTL |
| title | Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize |
| title_full | Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize |
| title_fullStr | Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize |
| title_full_unstemmed | Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize |
| title_short | Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize |
| title_sort | identification of candidate qtls and genes for ear diameter by multi parent population in maize |
| topic | maize ear diameter candidate gene GWAS QTL |
| url | https://www.mdpi.com/2073-4425/14/6/1305 |
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