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

Background: Genetic improvement in wheat yield is the most focused research area for the breeding community to ensure sustainable production. Wheat kernel traits and biomass are considered key contributors to enhance crop yield. Methods: This study was designed to explore the genetic diversity of kernel and biomass traits in popular wheat varieties from the US Southern Great Plains using 264 doubled haploid (DH) lines mainly derived from TAM 114 or TAM 204. This population was evaluated in two field environments planted in alpha lattice design during the 2020 crop season. Kernel traits were collected using the hp Scanjet G4010 photo scanner for image capturing and GrainScan v3. software for image analysis. Biomass parameters 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. Sequences were aligned to the IWGSC RefSeq genome assembly v2.1 using the Burrows Wheeler Aligner for SNP calling. Results: A total of 59,482 polymorphic SNP markers were retained for genetic analysis after the filtration at 50% missing data and 5% minor allele frequency. To investigate the marker–trait association and the genomic regions, four genome-wide association study models were implemented using the R package GAPIT version 3.5. Based on the Bonferroni correction <8.41 × 10−7 was used as a threshold to declare marker-trait associations (MTAs) significant. The BLINK model identified 12 MTAs on chromosomes 1A, 2A, 2B, 4A, 4B, and 6B. Conclusions: The identified MTAs can be used to develop diagnostic markers for efficient selection and utilization in recombination breeding and cultivar development process.