Primary synthetic is one of the major resources that has been utilized in spring wheat breeding worldwide to improve drought tolerance and pest resistance but little research has been conducted in winter wheat backgrounds. Texas A&M Wheat breeding and genetic programs have utilized synthetic hexaploid wheat to introduce novel alleles from various tetraploid durum wheat (Triticum turgidum L.) and diploid tauschii (Aegilops tauschii L.) into the hard red winter wheat for more than 20 years.

In this study, two adapted popular wheat cultivars TAM 111 and TAM 112 were designated as recurrent parents and backcrossed with 21 synthetic hexaploid wheat lines, then those derived lines were advanced for five generations to generate a set of 298 BC1F5:7 synthetic derived wheat lines (SDLs) as a multi-reference advanced-backcross nested association mapping population (MR-AB-NAM).

Took advantages on the pedigrees and population structure, genotyping-by-sequencing (GBS) and skim-seq were used to impute a large set of 28 million single nucleotide polymorphisms (SNPs) and insertion deletions (Indels) from parental whole genome sequencing (WGS) data. Yield and quality traits of the population was evaluated in 13 environments across Texas for genome-wide association analyses to identify significant marker-trait associations and performing genomic selections.

These developed SDLs provided novel genetic resources and broadened the winter bread wheat gene pool. Significant SNPs linked to target beneficial alleles were used to explore the efficient utilization of synthetic wheat in breeding programs. In addition, genomic prediction with multiple traits/environments/models provided in-depth knowledge for the breeding application of SHW.