Diverse reference genomes detect variants in the US winter wheat

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^vS), 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.