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Genetics. Jan 2004; 166(1): 389–417.
PMCID: PMC1470701

A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium).


We report genetic maps for diploid (D) and tetraploid (AtDt) Gossypium genomes composed of sequence-tagged sites (STS) that foster structural, functional, and evolutionary genomic studies. The maps include, respectively, 2584 loci at 1.72-cM ( approximately 600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM ( approximately 500 kb) intervals detected by 662 probes (D). Both diploid and tetraploid cottons exhibit negative crossover interference; i.e., double recombinants are unexpectedly abundant. We found no major structural changes between Dt and D chromosomes, but confirmed two reciprocal translocations between At chromosomes and several inversions. Concentrations of probes in corresponding regions of the various genomes may represent centromeres, while genome-specific concentrations may represent heterochromatin. Locus duplication patterns reveal all 13 expected homeologous chromosome sets and lend new support to the possibility that a more ancient polyploidization event may have predated the A-D divergence of 6-11 million years ago. Identification of SSRs within 312 RFLP sequences plus direct mapping of 124 SSRs and exploration for CAPS and SNPs illustrate the "portability" of these STS loci across populations and detection systems useful for marker-assisted improvement of the world's leading fiber crop. These data provide new insights into polyploid evolution and represent a foundation for assembly of a finished sequence of the cotton genome.

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Selected References

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  • Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998 Mar;8(3):175–185. [PubMed]
  • Jiang C, Wright RJ, El-Zik KM, Paterson AH. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4419–4424. [PMC free article] [PubMed]
  • Jiang CX, Chee PW, Draye X, Morrell PL, Smith CW, Paterson AH. Multilocus interactions restrict gene introgression in interspecific populations of polyploid Gossypium (cotton). Evolution. 2000 Jun;54(3):798–814. [PubMed]
  • Kim HJ, Triplett BA. Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol. 2001 Dec;127(4):1361–1366. [PMC free article] [PubMed]
  • Konieczny A, Ausubel FM. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 1993 Aug;4(2):403–410. [PubMed]
  • Lander ES, Green P. Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci U S A. 1987 Apr;84(8):2363–2367. [PMC free article] [PubMed]
  • Creating the gene ontology resource: design and implementation. Genome Res. 2001 Aug;11(8):1425–1433. [PMC free article] [PubMed]
  • Reinisch AJ, Dong JM, Brubaker CL, Stelly DM, Wendel JF, Paterson AH. A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics. 1994 Nov;138(3):829–847. [PMC free article] [PubMed]
  • Bowers John E, Abbey Colette, Anderson Sharon, Chang Charlene, Draye Xavier, Hoppe Alison H, Jessup Russell, Lemke Cornelia, Lennington Jennifer, Li Zhikang, et al. A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics. 2003 Sep;165(1):367–386. [PMC free article] [PubMed]
  • Saranga Y, Menz M, Jiang CX, Wright RJ, Yakir D, Paterson AH. Genomic dissection of genotype x environment interactions conferring adaptation of cotton to arid conditions. Genome Res. 2001 Dec;11(12):1988–1995. [PubMed]
  • Senchina David S, Alvarez Ines, Cronn Richard C, Liu Bao, Rong Junkang, Noyes Richard D, Paterson Andrew H, Wing Rod A, Wilkins Thea A, Wendel Jonathan F. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol Biol Evol. 2003 Apr;20(4):633–643. [PubMed]
  • Wright RJ, Thaxton PM, El-Zik KM, Paterson AH. D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel avenues for evolution. Genetics. 1998 Aug;149(4):1987–1996. [PMC free article] [PubMed]
  • Zdobnov EM, Apweiler R. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001 Sep;17(9):847–848. [PubMed]
  • Wendel JF. New World tetraploid cottons contain Old World cytoplasm. Proc Natl Acad Sci U S A. 1989 Jun;86(11):4132–4136. [PMC free article] [PubMed]
  • Zhao XP, Si Y, Hanson RE, Crane CF, Price HJ, Stelly DM, Wendel JF, Paterson AH. Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res. 1998 May;8(5):479–492. [PubMed]
  • Wendel Jonathan F, Cronn Richard C, Johnston J Spencer, Price H James. Feast and famine in plant genomes. Genetica. 2002 May;115(1):37–47. [PubMed]

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