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.

The first hexaploid bread wheat reference genome from Chinese Spring was released in 2018 by the International Wheat Genome Sequencing Consortium and is considered as the industry standard reference. To explore the effects of different reference genomes on variant discovery, 29 hexaploid bread wheat ( Triticum aestivum L.) cultivars from the Southern Great Plains of the United States with varying whole genome sequencing depth were aligned to three reference genomes. The reference genomes varied in evolutionary similarity to the cohort of the germplasm analyzed: (1) Jagger, a Kansas State University cultivar, a reference with high similarity, (2) Chinese Spring, a Chinese landrace, the current industry standard, (3) Durum‐ tauschii , an “in silico” hybridization of the reference genomes of tetraploid durum wheat and wild Aegilops tauschii , for an unrepresentative reference. The Jagger reference genome retained more informative variants after filtering. Synteny regions and large introgressions were identified by read alignment coverage, using diverse reference genomes to identify lines containing Aegilops ventricosa (2N ^v S), 1AL:1RS and 1BL:1RS ( Secale cereale ) rye translocations, and a 2.8 Mb contig from TAM 112 known to contain a haplotype harboring greenbug [ Schizaphis graminum (Rondani)] resistance gene Gb3 . The choice of reference genome is important, but any single reference can induce bias. This study with US Southern Great Plains germplasm demonstrated the importance of multiple reference genomes to capture genetic diversity.

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.