Genome-wide association analysis of agronomic traits in wheat under drought-stressed and non-stressed conditions

Abstract

This study determined the population structure and genome-wide marker-trait association of agronomic traits of wheat for drought-tolerance breeding. Ninety-three diverse bread wheat genotypes were genotyped using the Diversity Arrays Technology sequencing (DArTseq) protocol. The number of days-to-heading (DTH), number of days-to-maturity (DTM), plant height (PHT), spike length (SPL), number of kernels per spike (KPS), thousand kernel weight (TKW) and grain yield (GYLD), assessed under drought-stressed and non-stressed conditions, were considered for the study. Population structure analysis and genome-wide association mapping were undertaken based on 16,383 silico DArTs loci with < 10% missing data. The population evaluated was grouped into nine distinct genetic structures. Inter-chromosomal linkage disequilibrium showed the existence of linkage decay as physical distance increased. A total of 62 significant (P < 0.001) marker-trait associations (MTAs) were detected explaining more than 20% of the phenotypic variation observed under both drought-stressed and non-stressed conditions. Significant (P < 0.001) MTA event(s) were observed for DTH, PHT, SPL, SPS, and KPS; under both stressed and non-stressed conditions, while additional significant (P < 0.05) associations were observed for TKW, DTM and GYLD under non-stressed condition. The MTAs reported in this population could be useful to initiate marker-assisted selection (MAS) and targeted trait introgression of wheat under drought-stressed and non-stressed conditions, and for fine mapping and cloning of the underlying genes and QTL.

Genome-Wide Detection of SNP Markers Associated with Four Physiological Traits in Groundnut (Arachis hypogaea L.) Mini Core Collection

“…This is not surprising given the low polymorphism rate and PIC values in groundnut which means that detectable recombination is likely to be very low. Several studies have reported LD decay with distance [10,38,39] which agrees with the findings of the present study.…”

Validation of Grain Yield QTLs from Soft Winter Wheat Using a CIMMYT Spring Wheat Panel

“…Phenotypic datasets for association mapping included BLUP trait values across geographic regions (Asia, Africa, North America, and by individual countries) and by growing season (2010 and 2011) and BLUE calculated for each individual environment (see Supplemental Table S2 for the complete description of the datasets used for GWAS). A P value of < 0.001 was used as the threshold for defining significant SNP as the measured traits have generally low to moderate heritability (Arguello et al, 2016; Mwadzingeni et al, 2017) and due to the observed deviations on the quantile‐quantile plots. Polymorphic SNPs for the winter wheat loci were separated according to allele calls, and the mean GY for these were compared using t test at P < 0.05.…”

The Interrelationship of Agronomic and Physiological Traits as Affected by Irrigation Regimes in Wheat: Application of Multivariate Statistical Analyses

“…The development of drought-tolerant genotypes as well as genotypes with higher water-use efficiency (WUE) is of global interest due to a rapid decrease in water resources destined to agriculture (Araus et al 2008). A large number of morphological and physiological traits have been found to be linked to drought tolerance in cereals (Condon et al 2004;Reynolds et al 2005;Araus et al 2008;Mora et al 2015;Mwadzingeni et al 2017).…”