Genome-wide marker development for the wheat D genome based on single nucleotide polymorphisms identified from transcripts in the wild wheat progenitor Aegilops tauschii

Abstract

13,347 high-confidence SNPs were discovered through transcriptome sequencing of Aegilops tauschii, which are useful for genomic analysis and molecular breeding of hexaploid wheat. In organisms with large and complex genomes, such as wheat, RNA-seq analysis is cost-effective for discovery of genome-wide single nucleotide polymorphisms (SNPs). In this study, deep sequencing of the spike transcriptome from two Aegilops tauschii accessions representing two major lineages led to the discovery of 13,347 high-confidence (HC) SNPs in 4,872 contigs. After removing redundant SNPs detected in the leaf transcriptome from the same accessions in an earlier study, 10,589 new SNPs were discovered. In total, 5,642 out of 5,808 contigs with HC SNPs were assigned to the Ae. tauschii draft genome sequence. On average, 732 HC polymorphic contigs were mapped in silico to each Ae. tauschii chromosome. Based on the polymorphic data, we developed markers to target the short arm of chromosome 2D and validated the polymorphisms using 20 Ae. tauschii accessions. Of the 29 polymorphic markers, 28 were successfully mapped to 2DS in the diploid F2 population of Ae. tauschii. Among ten hexaploid wheat lines, which included wheat synthetics and common wheat cultivars, 25 of the 43 markers were polymorphic. In the hexaploid F2 population between a common wheat cultivar and a synthetic wheat line, 23 of the 25 polymorphic markers between the parents were available for genotyping of the F2 plants and 22 markers mapped to chromosome 2DS. These results indicate that molecular markers that developed from polymorphisms between two distinct lineages of Ae. tauschii might be useful for analysis not only of the diploid, but also of the hexaploid wheat genome.

The cuticular wax inhibitor locus Iw2 in wild diploid wheat Aegilops tauschii: phenotypic survey, genetic analysis, and implications for the evolution of common wheat

“…tauschii accessions that represented two major lineages, and discovered more than 16,000 high-confidence single nucleotide polymorphisms (SNPs) in 5,808 contigs [31,32]. Contigs with the SNPs were searched with blastn against Ae.…”

Fine mapping of <i>Hch1</i>, the causal D-genome gene for hybrid chlorosis in interspecific crosses between tetraploid wheat and <i>Aegilops tauschii</i>

“…The four Xctg loci of CAPS markers represented high-confidence SNPs derived from the Ae. tauschii RNA-seq-derived SNP information (Iehisa et al, 2012(Iehisa et al, , 2014a. The map length of 7DS was 50.0 cM with an average spacing of 2.78 cM between loci.…”

“…tauschii accessions that represent two major lineages, and more than 16,000 high-confidence single nucleotide polymorphisms (SNPs) were found in 5,808 contigs (Iehisa et al, 2012(Iehisa et al, , 2014a. Contig sequences with the SNPs were used with the BlastN algorithm to search the Ae.…”

“…Scaffolds without genes were anchored based on respective results from BlastN searches against the barley genome. First, high-confidence SNPs (Iehisa et al, 2012(Iehisa et al, , 2014a) plotted on barley 7HS were used for marker development to refine the Hch1 region. Next, SciRoKo software was used with the search mode setting Fine mapping of wheat hybrid chlorosis gene "mismatched; fixed penalty" to identify additional SSR markers in sequence data of candidate scaffolds.…”

“…tauschii genome that covers 4 Gb is also available (Luo et al, 2013). In addition, barley genome information efficiently helps to assign wheat genomic and transcript sequences in silico to the barley physical map (Iehisa et al, 2012(Iehisa et al, , 2014a. Thus, the scaffold sequence data of the Ae.…”