A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

• Published in: bioRxiv
• Main Authors: Grewal, Surbhi, Coombes, Benedict, Ryan Joynson, Hall, Anthony, Fellers, John, Cai-Yun, Yang, Scholefield, Duncan, Ashling, Stephen, Isaac, Peter, King, Ian, King, Julie
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 01.10.2021
• Subjects: Amblyopyrum muticum; Chromosomes; Diploids; Gene polymorphism; Genetic diversity; Genomes; Genotyping; Polyploidy; Recombination; Single-nucleotide polymorphism; Species; Whole genome sequencing
• DOI: 10.1101/2021.09.29.462370

Many wild relative species are being used in pre-breeding programmes to increase the genetic diversity of wheat. Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterise wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based KASP markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and PCR-amplicon-based sequencing of the wild species. But chromosome-specific KASPs assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum and development of a SNP discovery pipeline that generated ~38,000 SNPs in single-copy wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as functional. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines. Competing Interest Statement P.I. was employed by the company iDna Genetics Ltd. R.J. was employed by Earlham Institute while this work was carried out. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Footnotes * https://opendata.earlham.ac.uk/wheat/under_license/toronto/Grewal_et_al_2021-09-13_Amybylopyrum_muticum/