Association Mapping for Biomass and Kernel Traits in Doubled Haploid Population Derived from Texas Wheat Cultivars

Genetic improvement in wheat yield is the most focused research area for the breeding community to ensure food security and sustainable production. Wheat kernel traits and biomass are considered key contributors to enhance crop yield. A set of 264 doubled haploid (DH) lines mainly derived from two popular Texas wheat cultivars, TAM 114 and TAM 204, were developed at the AgriLife Research Center in Amarillo. The other parents are widely adopted and improved cultivars from the Southern Great Plains. Lines were evaluated in two field environments (Bushland-irrigated & Bush-land-dryland) planted in alpha lattice design during the 2020 crop season. Kernel traits (seed length, width, area, perimeter, and 1000 kernel weight) were collected using the hp Scanjet G4010 photo scanner for image capturing and GrainScan software for image analysis. This procedure offered a high throughput, precise, robust, and cost-effective seed phenotyping platform. Biomass parameters (plant weight, head count, head weight) were collected and processed manually. For genotyping genomic libraries were prepared and sequenced on Illumina NovaSeq 6000 to generate paired end reads of 150 bp. For single nucleotide polymorphism (SNP) calling, sequences were aligned to the IWGSC RefSeq genome assembly v2.1 using the Burrows Wheeler Aligner. The SNP filtration was performed at 50% missing data and 5% minor allele frequency. Finally, a set of 59842 polymorphic markers were retained for genetic analysis. To investigate the marker-trait association and the genomic regions, four genome-wide-association study (GWAS) models were implemented using the R package ‘Genome Association and Prediction Integrated Tool’ (GAPIT). Based on the Bonferroni correction < 8.41E-07 was used as a threshold to declare maker trait associations (MTA) significant. The BLINK model identified 12 MTA on chromosomes 1A, 2A, 2B, 4A, 4B, and 6B. 45% of the lines carried S2A_251496962 marker for the seed perimeter, while 42% and 39% lines carried S2A_498737202 and S2B_792756832 makers for 1000 KW and seed width, respectively. The identified MTA might be representing some known/major genes which need fur-ther confirmation.