Abstract
BackgroundThe tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses.ResultsWe generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes.ConclusionThe efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.
Highlights
The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it
Out of 11,570 DArT-seq SNP markers filtered based on high call and reproducibility rates, 8522 (~ 74%) were polymorphic in wheat –8430 SNPs were absent in our wheat cultivar, Chinese Spring (CS), while 92 were present but showed presence of both reference and SNP alleles in L. racemosus (Fig. 1c; Table 1)
We developed a total of 8632 polymorphic markers from L. racemosus genome
Summary
The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. While in vitro culture techniques, example embryo rescue, and induction of homoeologous chromosome recombination have been employed to achieve successful distant hybridization and useful gene recombination, integration of appropriate molecular markers into breeding programs to conduct marker-assisted backcrossing can immensely assist in selecting against deleterious genes, fast-tracking the process Unlike their cultivated counterparts, whose genomes have been extensively analyzed, DNA sequence information and molecular markers of these wild species are limited or completely absent in some cases, culminating in a poor understanding of their genome structures and delay in cultivar development and adequate characterization
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