Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Oct 20;9:125.
doi: 10.1186/1471-2229-9-125.

Sampling Nucleotide Diversity in Cotton

Free PMC article

Sampling Nucleotide Diversity in Cotton

Allen Van Deynze et al. BMC Plant Biol. .
Free PMC article


Background: Cultivated cotton is an annual fiber crop derived mainly from two perennial species, Gossypium hirsutum L. or upland cotton, and G. barbadense L., extra long-staple fiber Pima or Egyptian cotton. These two cultivated species are among five allotetraploid species presumably derived monophyletically between G. arboreum and G. raimondii. Genomic-based approaches have been hindered by the limited variation within species. Yet, population-based methods are being used for genome-wide introgression of novel alleles from G. mustelinum and G. tomentosum into G. hirsutum using combinations of backcrossing, selfing, and inter-mating. Recombinant inbred line populations between genetics standards TM-1, (G. hirsutum) x 3-79 (G. barbadense) have been developed to allow high-density genetic mapping of traits.

Results: This paper describes a strategy to efficiently characterize genomic variation (SNPs and indels) within and among cotton species. Over 1000 SNPs from 270 loci and 279 indels from 92 loci segregating in G. hirsutum and G. barbadense were genotyped across a standard panel of 24 lines, 16 of which are elite cotton breeding lines and 8 mapping parents of populations from six cotton species. Over 200 loci were genetically mapped in a core mapping population derived from TM-1 and 3-79 and in G. hirsutum breeding germplasm.

Conclusion: In this research, SNP and indel diversity is characterized for 270 single-copy polymorphic loci in cotton. A strategy for SNP discovery is defined to pre-screen loci for copy number and polymorphism. Our data indicate that the A and D genomes in both diploid and tetraploid cotton remain distinct from each such that paralogs can be distinguished. This research provides mapped DNA markers for intra-specific crosses and introgression of exotic germplasm in cotton.


Figure 1
Figure 1
Genetic map of 223 SNP markers in 186 recombinant inbred lines from a cross between TM-1 and 3-79. Genetic distances in cM [46].

Similar articles

See all similar articles

Cited by 29 articles

See all "Cited by" articles


    1. Bowman DT. Attributes of Public and Private Cotton Breeding Programs. J Cotton Science. 2000;4:130–136.
    1. Robinson AF, Bell AA, Dighe ND, Menz MA, Nichols PL, Stelly DM. Introgression of resistance to nematode Rotylenchulus reniformis into upland cotton (Gossypium hirsutum) from Gossypium longicalyx. Crop Science. 2007;47:1865–1877. doi: 10.2135/cropsci2006.12.0776. - DOI
    1. He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, Li W. QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum × Gossypium barbadense. Euphytica. 2007;153:181–197. doi: 10.1007/s10681-006-9254-9. - DOI
    1. Zhang T, Yuan Y, Yu J, Guo W, Kohel RJ. Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor Appl Genet. 2003;106:262–268. - PubMed
    1. Frary A, Fulton TM, Zamir D, Tanksley SD. Advanced backcross QTL analysis of a Lycopersicon esculentum × L. pennellii cross and identification of possible orthologs in the Solanaceae. Theoretical and Applied Genetics. 2004;108:485–496. doi: 10.1007/s00122-003-1422-x. - DOI - PubMed

Publication types

LinkOut - more resources