Genome-wide association mapping for component traits of drought and heat tolerance in wheat

The study material in GWAS panel with 282 advanced breeding line of bread wheat genotypes from IARI stress breeding program was selected to map the genomic regions responsible for Drought and heat tolerance component traits.

Phenotypic data:

The GWAS panel was evaluated at multiple locations namely, IARI, New Delhi - DL (28.6550° N, 77.1888° E, MSL 228.61 m), ARI, Pune - PUNE (18.5204° N, 73.8567° E, MSL 560m), IIWBR, Karnal - IIWBR (29.6857° N, 76.9905°E, MSL 243m), IARI, Jharkhand - JR (24.1929° N, 85.3756° E, MSL 580m) and IARI RS, Indore - IND (22.7196° N, 75.8577° E, MSL 553 m) with augmented RCBD design. Three tratments viz, IR (Irrigated), RI (Restricted irrigated) and LS (Late sown) were imposed for control, drought and heat stress, respectively.  Data was collected on traits like Days to heading (DH), Days to maturity (DM), Normalized Difference Vegetation Index (NDVI) at anthesis and grain filling stage, chlorophyll content (SPAD) of flag leaf at post anthesis stage, Plant height (PH), Canopy temperature (CT), Grain weight per spike (GWPS), Thousand Grain weight (TGW), Plot Yield (PLTY) and Biomass.

Genotypic data:

Genomic DNA of the GWAS panel was extracted from the leaves of seedlings by Cetyl Trimethyl Ammonium Bromide (CTAB) method. The panel was genotyped using Axiom Wheat Breeder’s Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >20%, and heterozygote frequency >25% were removed from the analysis. The remaining set of 10546 high-quality SNPs was used in GWAS analysis.

The detailed information of the methods and software used, data analysis and GWAS is provided at doi: 10.3389/fpls.2022.943033

Methods
Description of methods used for collection/generation of data: Standard procedure for data collection was followed as given in manual ‘Wheat Physiological Breeding II: A Field Guide to Wheat Phenotyping’ (Pask et al., 2012). Data was collected on traits like Days to heading (DH), Days to maturity (DM), Normalized Difference Vegetation Index (NDVI) at anthesis and grain filling stage, chlorophyll content (SPAD) of flag leaf at post anthesis stage, Plant height (PH), Canopy temperature (CT), Grain weight per spike (GWPS), Thousand Grain weight (TGW), Plot Yield (PLTY) and Biomass. The genotypes were genotyped using Axiom Wheat Breeder’s Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs.

Methods for processing the data: The GWAS panel of 280 genotypes were genotyped using Axiom Wheat Breeder’s Genotyping Array (Affymetrix, Santa Clara, CA, United States) having 35,143 genome-wide SNPs. The monomorphic, markers with minor allele frequency (MAF) of <5%, missing data of >20%, and heterozygote frequency >25% were removed from the analysis. The remaining set of 10546 high-quality SNPs was used in GWAS analysis.