title: Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts.
abstract: BACKGROUND
  Cotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection.
  
  
  RESULTS
  Using transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3-79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays.
  
  
  CONCLUSIONS
  This large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.
authors.forename: Amanda M
authors.initials: AM
authors.lastname: Hulse-Kemp
authors.forename: Hamid
authors.initials: H
authors.lastname: Ashrafi
authors.forename: Xiuting
authors.initials: X
authors.lastname: Zheng
authors.forename: Fei
authors.initials: F
authors.lastname: Wang
authors.forename: Kevin A
authors.initials: KA
authors.lastname: Hoegenauer
authors.forename: Andrea B V
authors.initials: AB
authors.lastname: Maeda
authors.forename: S Samuel
authors.initials: SS
authors.lastname: Yang
authors.forename: Kevin
authors.initials: K
authors.lastname: Stoffel
authors.forename: Marta
authors.initials: M
authors.lastname: Matvienko
authors.forename: Kimberly
authors.initials: K
authors.lastname: Clemons
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Udall
authors.forename: Allen
authors.initials: A
authors.lastname: Van Deynze
authors.forename: Don C
authors.initials: DC
authors.lastname: Jones
authors.affiliation: Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, USA. stelly@tamu.edu.
authors.forename: David M
authors.initials: DM
authors.lastname: Stelly
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D019295:Computational Biology; D003433:Crosses, Genetic; D017343:Genes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D060005:Genotyping Techniques; D003368:Gossypium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017384:Sequence Deletion; D059467:Transcriptome
chemical_list: D005819:Genetic Markers