GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives

Abstract

Abstract Thinopyrum species are an important source for new genetic variation for wheat improvement because they carry many agronomically important traits, such as abiotic/biotic resistances. Accurate identification of exogenous chromosome(s) or chromosome segments or genes is very important after alien genetic material has been successfully introduced into wheat, but remains challenging. Here, we report the development of a high-resolution wheat-Thinopyrum elongatum array, named GenoBaits®WheatplusEE, to trace alien genetic information through genotyping with a target sequencing system and a liquid chip. A total of 90000 capture probes derived from two species were integrated into one chip, including 10000 and 80000 within wheat and Th. elongatum, respectively. The capture probes were designed to be preferentially located in genes and evenly distributed across the genome, supporting the development of a roadmap guiding each alien genes. The array was applied to high-throughput identification of the alien chromosomes or segments in Thinopyrum and distantly related species, as well as derivatives. Our results validated that the GenoBaits®WheatplusEE array could direct identification of the breakpoint for the alien segment, the alien chromosome copy number, and the wheat chromosome variation by target sequencing the sample only once. Additionally, we can efficiently and cost-effectively genotype, supporting the exploration of subgenome composition, phylogenetic relationships, and important gene (e.g., Fhb7 gene) polymorphisms among Thinopyrum species and derivates. We expect GenoBaits®WheatplusEE to become a popular tool or model that empowers future exploration of the wild germplasm for wheat improvement.