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Data from: Genome-wide association study for grain yield and component traits in wheat (Triticum aestivum L.)

Cite this dataset

Khan, Hanif; Krishnappa, Gopalareddy (2022). Data from: Genome-wide association study for grain yield and component traits in wheat (Triticum aestivum L.) [Dataset]. Dryad.


The study material in GWAS panel with 280 common bread wheat genotypes was selected from All India Coordinated Research Project on Wheat and Barley to map the genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY).

Phenotypic data:

The GWAS panel was evaluated at five different environments during the 2020-21 Rabi (winter) season: E1-University of Agricultural Sciences, research farm, Dharwad (15°29'20.71"N, 74°59'3.35"E, 750m AMSL), E2-ICAR-Indian Agricultural Research Institute, New Delhi (28°38′30.5″N, 77°09′58.2″E, 228 m AMSL), E3-Indian Agricultural Research Institute, Jharkhand (24°16'58.4"N, 85°21'16.1"E, 651m AMSL), E4-ICAR-Indian Institute of Wheat and Barley, Karnal (29°41'8.2644''N, 76°59'25.9692''E,  250m AMSL), and E5-Punjab Agricultural University, Ludhiana (30o54' N, 75o48'E, 247m AMSL). The genotypes were planted in an augmented block design along with repeated checks (DBW187, MACS6222, WH1124, and WH1142). All the genotypes of a GWAS panel were phenotyped for six quantitative traits i.e. GWPS (gm), GY (gm), PH (cm) at five locations, GFD (days), DH (days) at four locations and GNPS (number) at two locations. Phenotypic data were analyzed using the R package ‘augmentedRCBD’

Genotypic data:

Genomic DNA of the GWAS panel was extracted from the leaves of 21 days-old 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 14,790 high-quality SNPs was used in GWAS analysis. 


Indian Council of Agricultural Research (ICAR) and Bill & Melinda Gate foundation (BMGF) under the project ICAR-BMGF (Project Code:1011099)*, Award: 1011099