Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada-ku, Kobe, 657-8501, Japan.
Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.
BMC Plant Biol. 2018 Nov 8;18(1):271. doi: 10.1186/s12870-018-1498-8.
Aegilops 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.
To 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.
The 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.
节节麦（2n=14）是一种野生二倍体普通小麦近缘属，是小麦育种中改良性状的来源。然而，节节麦种内遗传变异尚未得到很好的研究，该物种的基因组信息有限。
为了开发分布在节节麦所有染色体上的新型遗传标记，并评估其遗传多样性，我们对 12 个代表性品系进行了 RNA 测序，并对每个品系的reads 进行从头组装以构建转录本。获得了大量的单核苷酸多态性（SNPs）和插入/缺失（indels），并将其锚定到 Ae. tauschii 和大麦（Hordeum vulgare L.）的拟基因组上，这被认为是节节麦的虚拟染色体。有趣的是，尽管节节麦的栖息地狭窄，但它的遗传多样性高于 Ae. tauschii。对节节麦和 Ae. tauschii 之间核苷酸多态性的比较分析表明，没有明显的谱系分化，并且存在频率较低的等位基因主要存在于节节麦中，其模式明显不同于 Ae. tauschii。
锚定的 SNPs 覆盖了所有染色体，为节节麦品系之间提供了足够的遗传标记。频率较低的等位基因可能是节节麦高遗传多样性的主要来源。
