ArticleApplications in plant sciences2015
SNP discovery in complex allotetraploid genomes (Gossypium spp., Malvaceae) using genotyping by sequencing.
Article in Applications in plant sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 20 citations in OpenAlex.
- Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection.Frontiers in plant science · 2024Article
- High-density 80 K SNP array is a powerful tool for genotyping G. hirsutum accessions and genome analysis.BMC genomics · 2017Article
- Identification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton.Scientific reports · 2017Article
- Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.BMC plant biology · 2017Article
- Article
- Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers.BMC genetics · 2016Article
- Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing.Genetica · 2016Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studySingle-nucleotide polymorphism (SNP) marker discovery in plants with complex allotetraploid genomes is often confounded by the presence of homeologous loci (along with paralogous and orthologous loci). Here we present a strategy to filter for SNPs representing orthologous loci. METHODS AND
resultsUsing Illumina next-generation sequencing, 54 million reads were collected from restriction enzyme-digested DNA libraries of a diversity of Gossypium taxa. Loci with one to three SNPs were discovered using the Stacks software package, yielding 25,529 new cotton SNP combinations, including those that are polymorphic at both interspecific and intraspecific levels. Frequencies of predicted dual-homozygous (aa/bb) marker polymorphisms ranged from 6.7-11.6% of total shared fragments in intraspecific comparisons and from 15.0-16.4% in interspecific comparisons.
conclusionsThis resource provides dual-homozygous (aa/bb) marker polymorphisms. Both in silico and experimental validation efforts demonstrated that these markers are enriched for single orthologous loci that are homozygous for alternative alleles.
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