Genome‐wide association studies and QTL mapping uncover the genetic architecture of ear tip‐barrenness in maize

Abstract

Ear tip-barrenness (ETB) phenotype threatens crop yield, because it reduces the kernel number per ear. The genetic basis of ETB in maize remains largely unknown. Herein, a genome-wide association study (GWAS) and quantitative trait loci (QTL) mapping were jointly applied to identify the significant genetic loci interrelated with ETB. Six significant SNPs were detected at a stringent P-value threshold (1.95 × 10 −6). Additionally, four environment-stable SNPs were co-detected across a single environment and best linear unbiased prediction (BLUP) model at a less stringent P-value threshold (1 × 10 −4). The above 10 SNPs were closely linked to 6 candidate genes, which mainly involved seed development, photosynthesis and ethylene response. Moreover, the ratio of superior allele at each significant SNP ranged from 0 to 83.33% in 30 investigated maize elite lines. QTL mapping identified 14 QTL with phenotypic variation explained (PVE) ranging from 3.64 to 7.09%, of which one QTL (qETB2-1) was repeatedly identified in two environments. Combined analysis of GWAS and QTL mapping showed that one SNP (PZE-102175229, chromosome 2: 217 66 Mb) was located in the QTL (qETB2-2, chromosome 2: 215 90-217 82 Mb). Eighteen gene models situated in the linkage disequilibrium (LD) region of the co-localized SNP were further used to evaluate their correlation with ETB by candidate gene association analysis. Two superior haplotypes and two superior alleles were detected among 74 lines for Zm00001d007195, Zm00001d007197 and Zm00001d007201. These results provide more information for clarifying the molecular mechanism of ETB and for speeding up the genetic improvement of maize varieties.

Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

“…Moreover, the association panel was demonstrated to have remarkable phenotypic variations in germination traits under low temperature with the higher coefficients of variations (CVs) (0.77, 0.65, 0.45, 0.37, and 0.42 for FG, TG, RL, SL and RRS, respectively) ( Table 1 ). The observed CVs in this study were generally higher than those of the other traits among this panel in the previous studies ( Li et al, 2020 ; Liu et al, 2020 ; Ma et al, 2018 ). Estimations of broad heritability using SAS v 9.3 indicated that the H B 2 of these investigated traits ranged from 86.96%-96.56% ( Table 1 ), suggesting that these chilling-germination traits were mainly genetically controlled.…”

Quantitative trait loci mapping of maize (Zea mays) ear traits under low‐phosphorus stress

“…We identified QTL that regulate both EW and EKW on chromosomes 1 and 5, and Ma et al (2019) detected similar QTL in a BC 3 F 2 population constructed from Chang 7–2 and Zheng Duqing. Zhao et al (2021) and Li et al (2020) also detected a QTL controlling BTL on chromosome 1. Liu et al (2015) used three F 2:3 populations for QTL mapping and detected loci on the same segment of chromosome 4 as qERN4‐1 in the present study, suggesting that this region contains highly reliable loci that control ear‐related traits.…”

GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber

“…Of the 21 SNPs identified, SNP_29277326, within a MYB recognition site in the CsPPR promoter, might be the most significant. The expression levels could be affected by the genetic loci variation in promoter ( Yu et al., 2019 ; Li et al., 2020 ; Zhang et al., 2020 ). qRT-PCR and contrasting haplotypes further identified its expression level by the effect of the promoter.…”