ArticleFunctional & integrative genomics2017
A large-scale chromosome-specific SNP discovery guideline.
Article in Functional & integrative genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat.Molecular biology reports · 2020Article
- Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides.Plant biotechnology journal · 2018Article
- Omics Approaches for Engineering Wheat Production under Abiotic Stresses.International journal of molecular sciences · 2018Review
- Exploiting the Genomic Diversity of Rice (Frontiers in plant science · 2018Article
- Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat.Scientific reports · 2017Article
- Genetic dissection of plant growth habit in chickpea.Functional & integrative genomics · 2017Article
- High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis.Functional & integrative genomics · 2017Article
- Exploring the heat-responsive chaperones and microsatellite markers associated with terminal heat stress tolerance in developing wheat.Functional & integrative genomics · 2017Article
- Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive.Functional & integrative genomics · 2017Article
- Transcriptome profile of the human placenta.Functional & integrative genomics · 2017Article
- Gene structure of the pregnancy-associated glycoprotein-like (PAG-L) in the Eurasian beaver (Castor fiber L.).Functional & integrative genomics · 2017Article
- Assessment of Genetic Diversity and Structure of Large Garlic (Frontiers in genetics · 2017Article
- DNApod: DNA polymorphism annotation database from next-generation sequence read archives.PloS one · 2017Article
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3 authors.
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Abstract
Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.
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