Development and validation of an exome-based SNP marker set for identification of the St, Jr and Jvs genomes of Thinopyrym intermedium in a wheat background

Abstract

Key message Cytogenetic analysis and array-based SNP genotyping of wheat– Th. intermedium introgression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes of Th. intermedium (StJ r J vs , 2 n = 6 x = 42). Abstract Thinopyrum intermedium (2 n = 6 x = 42, StJ r J vs ) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat– Th. intermedium introgression lines and the Axiom ® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1J vs , 2J vs , 3J vs and 7J vs . The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat. Electronic supplementary material The online version of this article (10.1007/s00122-019-03300-9) contains supplementary material, which is available to authorized users.

Rapid identification of homozygosity and site of wild relative introgressions in wheat through chromosome‐specific KASP genotyping assays

“…The Axiom ® Wheat‐Relative Genotyping Array has been used to genotype various wheat–wild relative introgression populations (Cseh et al ., ; Grewal et al ., ,b; King et al ., , ). To cost‐effectively genotype the self‐fertilized progenies of these introgression lines, while maintaining high‐throughput scale and flexibility, it was necessary to change the format of genotyping from the Axiom ® array to KASP assays.…”

“…Due to a lack of availability of high‐quality reference genomes with ordered pseudomolecules for the wild species used in this study (except for T. urartu ; Ling et al ., ), it was not possible to easily ascertain the distribution of the KASP markers in the wild relative species. Thus, we selected various wheat–wild relative introgressions lines from previous studies, where the Axiom ® Wheat‐Relative Genotyping Array had been used for genotyping and genetic mapping (Cseh et al ., ; Grewal et al ., ,b; King et al ., , ). Inclusion of these lines from backcross generations, for each wild relative species, ensured that all linkage groups were being detected by the KASP markers.…”

Development of Specific Thinopyrum Cytogenetic Markers for Wheat-Wheatgrass Hybrids Using Sequencing and qPCR Data

“…The development of cytogenetic markers is a tedious process that requires long and laborious FISH testing of various probes before a suitable probe is found. In many cytogenetic studies aimed at molecular-cytogenetic characterization of wheat–wheatgrass hybrids, the classical FISH probes such as 45S rDNA, pAs1, pSc119.2, and pTa71 are applied [ 32 , 37 , 38 , 39 , 40 , 41 , 42 ]. However, the development of new Thinopyrum -specific probes is necessary as it would enable the precise identification of chromosome rearrangements in amphidiploids and introgression lines and can be used in evolutionary studies of Triticeae [ 40 , 43 , 48 , 49 ].…”

“…One of the basic approaches in the study of WWGHs and introgression lines, along with molecular markers, remains cytogenetic studies with common and specific probes [ 21 , 37 , 38 , 39 , 40 , 41 , 42 ]. This approach enables the discrimination of related subgenomes in amphidiploids, visualization of chromosomal composition, and identification of rearrangements.…”

Molecular cytogenetic characterization of wheat–Elymus repens chromosomal translocation lines with resistance to Fusarium head blight and stripe rust

“…Most translocational genotypes between wheat and wild related species from genera Aegilops , Secale , Hordeum , Thinopyrum , Agropyron , Dasypyrum , Leymus , and Psathyrostachys have been successfully produced in current wheat breeding programme [23–25]. Elymus L. sensu lato species possess resistance or tolerance to various biotic and abiotic stresses, and it serves as an important wild gene pool that can increase the genetic diversity of common wheat [26, 27].…”