2.8M SNPs Chinese Spring RefSeq v2.1 dataset

VCF file of 2,799,166 single nucleotide polymorphism (SNP) markers positioned onto the Chinese Spring reference assembly RefSeq v2.1 developed by the International Wheat Genome Sequence Consortium (IWGSC; Zhu et al., 2021). These SNPs were lifted from the 1,000 wheat exome project, originally positioned onto RefSeq v1.0 (He et al., 2019). The SNP projection from RefSeq v1.0 onto RefSeq v2.1 was accomplished using LiftOff (Shumate and Salzberg, 2021).

References

He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, et al: Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics 2019, 51:896-904.

Shumate A, Salzberg SL: Liftoff: accurate mapping of gene annotations. Bioinformatics 2021, 37:1639-1643.

Zhu T, Wang L, Rimbert H, Rodriguez JC, Deal KR, De Oliveira R, Choulet F, Keeble-Gagnère G, Tibbits J, Rogers J, et al: Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. The Plant Journal 2021, 107:303-314..