ArticleG3 (Bethesda, Md.)2015
BAC-End Sequence-Based SNP Mining in Allotetraploid Cotton (Gossypium) Utilizing Resequencing Data, Phylogenetic Inferences, and Perspectives for Genetic Mapping.
Article in G3 (Bethesda, Md.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Detecting Cotton Leaf Curl Virus Resistance Quantitative Trait Loci inPlants (Basel, Switzerland) · 2023Article
- Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of aFrontiers in plant science · 2022Article
- The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton.Frontiers in genetics · 2021Review
- Genetic dissection of the fuzzless seed trait in Gossypium barbadense.Journal of experimental botany · 2018Article
- Construction and characterization of a bacterial artificial chromosome library for Gossypium mustelinum.PloS one · 2018Article
- Article
- Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.Scientific reports · 2017Article
- 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
- Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq.BMC genomics · 2017Article
- Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.PloS one · 2016Article
- Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.G3 (Bethesda, Md.) · 2015Article
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10 authors.
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Abstract
A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies.
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