Development of a New A^m–Genome‐Specific Single Nucleotide Polymorphism Marker Set for the Molecular Characterization of Wheat–Triticum monococcumIntrogression Lines

Abstract

Cultivated einkorn wheat (Triticum monococcum L. subsp. monococcum, 2n = 2x = 14, A m A m) and its wild relative T. monococcum subsp. aegilopoides are important sources of economically useful genes that can be exploited for wheat (Triticum aestivum L.) breeding. Einkorn has excellent resistance to fungal diseases and gene transfer is relatively simple via standard breeding methods. To fulfill the growing demand by modern prebreeding programs for a cost-effective high-throughput procedure for accurately detecting introgressed chromosomes or chromosome segments from T. monococcum into wheat, we used the Axiom Wheat-Relative Genotyping Array and developed a set of A m genome-specific exome-based single nucleotide polymorphism (SNP) markers suitable for rapid identification of T. monococcum chromatin in a wheat background. We identified 1247 polymorphic SNPs between T. monococcum and wheat. We identified 191 markers across all seven chromosomes of T. monococcum that are also present on an existing Triticum urartu Thum. ex Gandil. genetic map and potentially ordered them on the basis of the high macrocollinearity and conservation of marker order between T. monococcum and T. urartu. The marker set has been tested on leaf-rust-resistant BC 3 F 4 progenies of wheat-T. monococcum hybrids. Two markers (AX-94492165, AX-95073542) placed on the distal end of the chromosome arm 7AL detected a T. monococcum introgression into wheat. The SNP marker set thus proved highly effective in the identification of T. monococcum chromatin in a wheat background, offering a reliable method for screening and selecting wheat-T. monococcum introgression lines, a procedure that could significantly speed up prebreeding programs.

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

“…Genotyping of introgression lines is more efficient when using wild-relative genomespecific SNPs. The Axiom ® Wheat-Relative Genotyping SNP Array was developed (King et al 2017) and used to detect introgressions from various wild species in a wheat background (Grewal et al 2018a;Grewal et al 2018b;King et al 2018;Cseh et al 2019a;Devi et al 2019;Baker et al 2020). Even though these genotyping arrays can be ultrahigh-throughput and efficient, these SNPs cannot distinguish between homozygous and heterozygous individuals which limits their widespread use in crop breeding.…”

Chromosome‐specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines

“…The Axiom ® Wheat‐Relative Genotyping SNP Array was developed with genome‐specific SNPs from exome sequencing of various wheat wild species (Winfield et al., 2016; King et al., 2017). The array was subsequently used to detect introgressions from various wild species in a wheat background (Grewal et al., 2018a; Grewal et al., 2018b; King et al., 2018; Cseh et al., 2019a; Devi et al., 2019; Baker et al., 2020). Even though these genotyping arrays can be ultra‐high‐throughput and efficient, these SNPs cannot distinguish between homozygous and heterozygous individuals which limits their widespread use in crop breeding.…”

Potential Use of Wild Einkorn Wheat for Wheat Grain Quality Improvement: Evaluation and Characterization of Glu-1, Wx and Ha Loci

“…In these cases, although the linkage drag of deleterious alleles linked to desirable alleles in the exotic parent, as a result of the wild nature of this source material, might be a handicap [29], the notable variation in both technological quality aspects and adaptive traits could compensate for any negative impact of the linkage drag. In this respect, the development of DNA markers that facilitate the selection of alleles of interest in a breeding program by marker-assisted selection will be key [30,31].…”