September 2023: VMAP 1.1 Track is added to wheat Chinese Spring IWGSC RefSeq v1 genome browser

Added Genetic Variation Map (VMAP 1.1) Track

Publication: Nature, Zhao et al (2023)

Here we performed a genus-level sampling of Triticum–Aegilops species and conducted whole-genome sequence analyses to disentangle the deep past of wheat since the rise of agriculture ~10,000 yr ago. By applying novel and sophisticated population genomics approaches, we could precisely trace demographic events of wheat and predict its future population dynamics across space and time. The parallel reconstruction of demographic histories of both bread wheat and its relatives provides an inspiring example of the Holocene evolution of the entire gene pool pertaining to a crop species, insights from which will benefit biodiversity conservation, and breeding of bread wheat and many other crops.

By applying the cross-ploidy variation discovery pipeline, we identified ~78 million high-quality single nucleotide polymorphisms (SNPs) and constructed version 1.1 of the whole-genome genetic variation map of wheat (VMap 1.1). The false-positive error rate of variant calling, that is, the proportion of segregating sites in the reference accession, Chinese Spring, was only 0.011%, which is similar to the error rates of high-quality SNPs in previous studies.

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