Abstract
BackgroundAegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding. Intraspecific genetic variation of Ae. umbellulata, however, has not been well studied and the genomic information in this species is limited.ResultsTo develop novel genetic markers distributed over all chromosomes of Ae. umbellulata and to evaluate its genetic diversity, we performed RNA sequencing of 12 representative accessions and reconstructed transcripts by de novo assembly of reads for each accession. A large number of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were obtained and anchored to the pseudomolecules of Ae. tauschii and barley (Hordeum vulgare L.), which were regarded as virtual chromosomes of Ae. umbellulata. Interestingly, genetic diversity in Ae. umbellulata was higher than in Ae. tauschii, despite the narrow habitat of Ae. umbellulata. Comparative analyses of nucleotide polymorphisms between Ae. umbellulata and Ae. tauschii revealed no clear lineage differentiation and existence of alleles with rarer frequencies predominantly in Ae. umbellulata, with patterns clearly distinct from those in Ae. tauschii.ConclusionsThe anchored SNPs, covering all chromosomes, provide sufficient genetic markers between Ae. umbellulata accessions. The alleles with rarer frequencies might be the main source of the high genetic diversity in Ae. umbellulata.
Highlights
Aegilops umbellulata Zhuk. (2n = 14), a wild diploid wheat relative, has been the source of trait improvement in wheat breeding
Leaf rust and stripe rust resistance genes [6, 8, 11] and high-molecular weight glutenin subunits [5, 12] have been introduced into bread wheat cultivars
RNA sequencing of 12 Ae. umbellulata accessions To evaluate genetic diversity based on a large number of DNA polymorphisms in the U-genome species Ae. umbellulata, RNA-seq was performed on the 12 representative accessions, generating 3.5–6.1 million paired-end reads per one accession (Table 2)
Summary
Intraspecific genetic variation of Ae. umbellulata, has not been well studied and the genomic information in this species is limited. Ae. umbellulata have been used for breeding of bread wheat and is a considerable resource of disease resistance genes [4,5,6,7,8,9,10]. [8] established introgression lines of leaf and stripe rust resistance genes derived from synthetic hexaploids (AABBUU). Chinese Spring PhI, which carries an epistatic inhibitor of Ph1 gene, induced homologous pairing and resulted in transfer of the leaf and stripe rust resistance genes of Ae. umbellulata into the bread wheat T. aestivum. Ae. umbellulata provides valuable genetic resources for breeding of bread wheat, it has not been well studied and information on its genome is limited. Evaluation of intraspecific genetic diversity based on genome-wide polymorphisms in Ae. umbellulata would impart practical information for designing genetic markers, facilitating the efficient use of Ae. umbellulata for breeding
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