Genome-wide association study of drought tolerance and biomass allocation in wheat

Abstract

Genome wide association studies (GWAS) are important in discerning the genetic architecture of complex traits such as biomass allocation for improving drought tolerance and carbon sequestration potential of wheat. The objectives of this study were to deduce the population structure and marker-trait association for biomass traits in wheat under drought-stressed and non-stressed conditions. A 100-wheat (Triticum aestivum L.) genotype panel was phenotyped for days to heading (DTH), days to maturity (DTM), shoot biomass (SB), root biomass (RB), root to shoot ratio (RS) and grain yield (GY). The panel was sequenced using 15,600 single nucleotide polymorphism (SNPs) markers and subjected to genetic analysis using the compressed mixed linear model (CMLM) at false discovery rate (FDR < 0.05). Population structure analysis revealed six sub-clusters with high membership ancestry coefficient of ≤0.65 to their assigned sub-clusters. A total of 75 significant marker-trait associations (MTAs) were identified with a linkage disequilibrium threshold of 0.38 at 5cM. Thirty-seven of the MTAs were detected under drought-stressed condition and 48% were on the B genome, where most quantitative trait loci (QTLs) for RB, SB and GY were previously identified. There were seven pleiotropic markers for RB and SB that may facilitate simultaneous selection. Thirty-seven putative candidate genes were mined by gene annotation on the IWGSC RefSeq 1.1. The significant MTAs observed in this study will be useful in devising strategies for marker-assisted breeding for simultaneous improvement of drought tolerance and to enhance C sequestration capacity of wheat.

Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean

“…The SNP markers used had a reproducibility value of 1, polymorphic information content (PIC) values ranging from 0.020 to 0.50, and a mean call rate of 0.93 ranging from 0.84 to 1.00. A total of 15 565 SNP markers and 93 genotypes were used after data imputation where SNP loci and individuals with <20% missing data and rare SNP, with <5% minor allele frequency (MAF) were pruned from the data before analysis following Mathew et al, [ 44 ].…”

“…Before association mapping, best linear unbiased predictors (BLUPs) were derived for the phenotypic traits using the random mixed model in DeltaGen software [ 50 ]. BLUPs minimise the effects of the environmental and seasonal variations, which eliminates the need to conduct marker-trait association for each environment independently [ 44 ]. The BLUPs were used as input in the GWAS analysis.…”

Genome-Wide Association Mapping of Seedling Drought Tolerance in Winter Wheat

“…Firstly, we declared significant QTL and SNPs based on false discovery rate (FDR < 0.05) as a cut-off point. However, the FDR was too stringent in this study, so we finally used a lower cut-off threshold using an unadjusted p -value of <0.001 to declare significant QTL ( Mwadzingeni et al, 2017 ; Sukumaran et al, 2018 ; Mathew et al, 2019 ). Visualization of significant QTL and SNPs was done using Manhattan plots with the qq man R package ( Turner, 2014 ).…”

“…Similarly, studies detected QTL associated with seedling heat tolerance-related traits ( Li et al, 2012 ; Maulana et al, 2018 ) and drought tolerance-related agronomic traits in wheat ( Mwadzingeni et al, 2017 ; Gahlaut et al, 2019 ). Studies have found marker–trait associations for drought stress tolerance on different chromosomes, including 1A, 2A, 2B, 2D, 3D, 4A, 4D, 5A, and 7B, of wheat ( Mwadzingeni et al, 2017 ; Shi et al, 2017 ; Sukumaran et al, 2018 ; Gahlaut et al, 2019 ; Mathew et al, 2019 ). However, few studies on drought tolerance of wheat have been conducted at the seedling stage.…”

Genetics and genomics of root system variation in adaptation to drought stress in cereal crops

“…A GWAS of 91 phenotypically diverse genotypes across 21 countries displayed two significant drought induced major alleles that cause long root lengths under polyethylene glycol (PEG)-induced water stress. The GWAS approach also identified three drought-responsive pleiotropic single nucleotide polymorphism (SNP) markers associated with root dry biomass in a panel of 100 bread wheat genotypes selected on the basis of their breeding history for drought tolerance ( Mathew et al , 2019 ). Another study identified five significant markers causing extended rooting lengths under drought stress conditions using a mapping population consisting of two introgressed populations ( Bhatta et al , 2018 ).…”