Detection of T. urartu Introgressions in Wheat and Development of a Panel of Interspecific Introgression Lines

Abstract

Tritcum urartu (2n = 2x = 14, AuAu), the A genome donor of wheat, is an important source for new genetic variation for wheat improvement due to its high photosynthetic rate and disease resistance. By facilitating the generation of genome-wide introgressions leading to a variety of different wheat–T. urartu translocation lines, T. urartu can be practically utilized in wheat improvement. Previous studies that have generated such introgression lines have been unable to successfully use cytological methods to detect the presence of T. urartu in these lines. Many have, thus, used a variety of molecular markers with limited success due to the low-density coverage of these markers and time-consuming nature of the techniques rendering them unsuitable for large-scale breeding programs. In this study, we report the generation of a resource of single nucleotide polymorphic (SNP) markers, present on a high-throughput SNP genotyping array, that can detect the presence of T. urartu in a hexaploid wheat background making it a potentially valuable tool in wheat pre-breeding programs. A whole genome introgression approach has resulted in the transfer of different chromosome segments from T. urartu into wheat which have then been detected and characterized using these SNP markers. The molecular analysis of these wheat-T. urartu recombinant lines has resulted in the generation of a genetic map of T. urartu containing 368 SNP markers, spread across all seven chromosomes of T. urartu. Comparative analysis of the genetic map of T. urartu and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of the 4/5 translocation in T. urartu also present in the A genome of wheat. A panel of 17 wheat-T. urartu recombinant lines, which consisted of introgressed segments that covered the whole genome of T. urartu, were also selected for self-fertilization to provide a germplasm resource for future trait analysis. This valuable resource of high-density molecular markers specifically designed for detecting wild relative chromosomes and a panel of stable interspecific introgression lines will greatly enhance the efficiency of wheat improvement through wild relative introgressions.

Exploiting the genome of Thinopyrum elongatum to expand the gene pool of hexaploid wheat

“…speltoides (King et al 2018), Th. bessarabicum (Grewal et al 2018a), T. urartu (Grewal et al 2018b) and T. timopheevii (Devi et al 2019) all show complete male sterility. Some of the GISH results obtained here, however, are not fully supportive of the D genome similarity (see below).…”

Scale development and utilization of universal PCR-based and high-throughput KASP markers specific for chromosome arms of rye (Secale cereale L.)

“…Winfield et al [49] developed high-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool based on exome capture and NGS, which can achieve the tracking of the introgression and subsequent fate of chromosomal segments from wheat relatives in wheat breeding. A Wheat-Relative SNP Genotyping Array has also been developed and used to identify the wild relative introgressions in a wheat background [50][51][52][53]. However, these SNP genotyping platforms are limited in practical breeding due to their inflexibility in assay design, identification and costly equipment for application, although they are high-throughput and highefficient [54].…”

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

“…It has been suggested that interspecific crossing of wheat with its wild relatives can enrich wheat's gene pool with novel diversity (Reynolds et al ., ). One strategy, recently called ‘introgressiomics’ (Prohens et al ., ), consists of a whole‐genome introgression approach involving transfer of chromosome segments from the entire genome of a wild relative species into the wheat background, irrespective of any traits that the wild relative might carry and a number of such studies have already been undertaken (Grewal et al ., ,b; King et al ., , ; Valkoun, ). In this prebreeding strategy, the interspecific hybrids are repeatedly backcrossed to the elite wheat parent to reduce the number and size of the introgressed segments and self‐fertilized to obtain stable homozygous introgressions that can be utilized for trait analysis (King et al ., ).…”

“…Many of these have been developed into high‐density SNP arrays (Allen et al ., ; Rimbert et al ., ; Wang et al ., ; Winfield et al ., ) for high‐throughput genotyping in wheat. An Axiom ® Wheat‐Relative SNP Genotyping Array has also been developed and used in studies for the identification and characterization of wild relative introgressions in a wheat background (Grewal et al ., ,b; King et al ., , ). Although these SNP genotyping platforms can be ultra‐high‐throughput and efficient, their use in crop breeding has been limited because they are inflexible in their design and use (Rasheed et al ., ).…”

“…A recent study successfully converted a panel of PCR markers to KASP™ markers for functional genes in wheat (Rasheed et al ., ). A number of array‐based, putative co‐dominant SNPs have been reported for various wild relatives (Grewal et al ., ,b; King et al ., , ), which could potentially be converted into KASP™ assays. However, it is difficult to design PCR primers for array‐based probes due to the high level of sequence polymorphism between wheat and its wild relatives.…”