An Integration of Linkage Mapping and GWAS Reveals the Key Genes for Ear Shank Length in Maize

Abstract

Ear shank length (ESL) has significant effects on grain yield and kernel dehydration rate in maize. Herein, linkage mapping and genome-wide association study were combined to reveal the genetic architecture of maize ESL. Sixteen quantitative trait loci (QTL) were identified in the segregation population, among which five were repeatedly detected across multiple environments. Meanwhile, 23 single nucleotide polymorphisms were associated with the ESL in the association panel, of which four were located in the QTL identified by linkage mapping and were designated as the population-common loci. A total of 42 genes residing in the linkage disequilibrium regions of these common variants and 12 of them were responsive to ear shank elongation. Of the 12 genes, five encode leucine-rich repeat receptor-like protein kinases, proline-rich proteins, and cyclin11, respectively, which were previously shown to regulate cell division, expansion, and elongation. Gene-based association analyses revealed that the variant located in Cyclin11 promoter affected the ESL among different lines. Cyclin11 showed the highest expression in the ear shank 15 days after silking among diverse tissues of maize, suggesting its role in modulating ESL. Our study contributes to the understanding of the genetic mechanism underlying maize ESL and genetic modification of maize dehydration rate and kernel yield.

Power Up Plant Genetic Research with Genomic Data

“…Using the single-nucleotide polymorphism (SNP) and insertion/deletion (INDEL) information from F2 resequencing, the same genomic region was also rediscovered. Similarly, Liang et al made use of 267 maize double-haploid (DH) lines and 336 inbred lines to map the genomic loci associated with the ear shank length, a trait determining the grain yield and kernel dehydration rate [ 9 ]. Using previously available bin maps and SNP data, they successfully identified 16 QTLs and 23 SNPs associated with the ear shank length via QTL mapping and genome-wide association studies (GWAS), respectively.…”