Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize

Abstract

Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays 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 F7 recombinant inbred lines (F7RILs). 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 Zm00001d030559 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 Zm00001d030559 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.

Identification of a novel marker and its associated laccase gene for regulating ear length in tropical and subtropical maize lines

“…In the demonstration of a 100 mu (1 mu = 666.67 m 2 ) areas in Kunming, the average yield reached 1134.4 kg per mu, which set a record of the highest yield in 100 mu area in tropical and subtropical regions. Consequently, Yunrui88 was cultivated across an extensive area of 350,000 hectares from 2012 to 2014, and was recognized as a leading variety by the Ministry of Agriculture of China in both 2014 and 2015 (Jiang et al 2023 ). Another notable hybrid, Xingdan106 (Fig.…”

“…In the present study, some parental lines were selected from the hybrids (Yin et al 2022 ; Jiang et al 2023 ). For instance, Ye107 and TRL02 were derived from the US hybrid, and TML418, with the longest ear, was derived from the Monsanto hybrid in Thailand (Table 1 ).…”

“…The MPP was used for conducting GWAS to identify candidate functional genes regulating EL. The mixed linear model of the EMMAX (v intel64-20,120,205) software package was employed for GWAS analysis, and the significant threshold was determined using Plink (v 1.9) to identify SNPs associated with EL of maize (Jiang et al 2023 ). Linkage disequilibrium (LD) analysis was performed using PopLD to determine the distance at which LD decayed by half in the population.…”

“…Linkage disequilibrium (LD) analysis was performed using PopLD to determine the distance at which LD decayed by half in the population. Genes associated with EL were subsequently identified within the 50 kb upstream and downstream of the significantly associated SNPs (Jiang et al 2023 ; Xu et al 2024 ). Haplotype analysis of functional genes was carried out using the Haplotype Caller-based method (Li et al 2022 ).…”

“…In this study, five tropical and subtropical maize lines and a temperate maize line that displayed notable differences in EL were used to establish a multi-parent population. Each of these six inbred lines holds significant breeding value and has served as parental lines in developing elite hybrids (Yin et al 2022 ; Jiang et al 2023 ; Wang et al 2023 ). The objective of this study was to identify molecular markers and candidate genes closely associated with EL of maize, and investigate the regulatory mechanisms of the identified gene.…”