A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium)

Junkang Rong, Colette Abbey, John E. Bowers, Curt L. Brubaker, Charlene Chang, Peng W. Chee, Terrye A. Delmonte, Xiaoling Ding, Juan J. Garza, Barry S. Marler, Chan Hwa Park, Gary J. Pierce, Katy M. Rainey, Vipin K. Rastogi, Stefan R. Schulze, Norma L. Trolinder, Jonathan F. Wendel, Thea A. Wilkins, T. Dawn Williams-Coplin, Rod A WingRobert J. Wright, Xinping Zhao, Linghua Zhu, Andrew H. Paterson

Research output: Contribution to journalArticle

287 Citations (Scopus)

Abstract

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 (∼600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (∼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.

Original languageEnglish (US)
Pages (from-to)389-417
Number of pages29
JournalGenetics
Volume166
Issue number1
DOIs
StatePublished - Jan 2004

Fingerprint

Sequence Tagged Sites
Gossypium
Genetic Recombination
Genome
Tetraploidy
Diploidy
Chromosomes, Human, 13-15
Polyploidy
Heterochromatin
Centromere
Restriction Fragment Length Polymorphisms
Single Nucleotide Polymorphism
Chromosomes
Population

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium). / Rong, Junkang; Abbey, Colette; Bowers, John E.; Brubaker, Curt L.; Chang, Charlene; Chee, Peng W.; Delmonte, Terrye A.; Ding, Xiaoling; Garza, Juan J.; Marler, Barry S.; Park, Chan Hwa; Pierce, Gary J.; Rainey, Katy M.; Rastogi, Vipin K.; Schulze, Stefan R.; Trolinder, Norma L.; Wendel, Jonathan F.; Wilkins, Thea A.; Williams-Coplin, T. Dawn; Wing, Rod A; Wright, Robert J.; Zhao, Xinping; Zhu, Linghua; Paterson, Andrew H.

In: Genetics, Vol. 166, No. 1, 01.2004, p. 389-417.

Research output: Contribution to journalArticle

Rong, J, Abbey, C, Bowers, JE, Brubaker, CL, Chang, C, Chee, PW, Delmonte, TA, Ding, X, Garza, JJ, Marler, BS, Park, CH, Pierce, GJ, Rainey, KM, Rastogi, VK, Schulze, SR, Trolinder, NL, Wendel, JF, Wilkins, TA, Williams-Coplin, TD, Wing, RA, Wright, RJ, Zhao, X, Zhu, L & Paterson, AH 2004, 'A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium)', Genetics, vol. 166, no. 1, pp. 389-417. https://doi.org/10.1534/genetics.166.1.389
Rong, Junkang ; Abbey, Colette ; Bowers, John E. ; Brubaker, Curt L. ; Chang, Charlene ; Chee, Peng W. ; Delmonte, Terrye A. ; Ding, Xiaoling ; Garza, Juan J. ; Marler, Barry S. ; Park, Chan Hwa ; Pierce, Gary J. ; Rainey, Katy M. ; Rastogi, Vipin K. ; Schulze, Stefan R. ; Trolinder, Norma L. ; Wendel, Jonathan F. ; Wilkins, Thea A. ; Williams-Coplin, T. Dawn ; Wing, Rod A ; Wright, Robert J. ; Zhao, Xinping ; Zhu, Linghua ; Paterson, Andrew H. / A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium). In: Genetics. 2004 ; Vol. 166, No. 1. pp. 389-417.
@article{fd5313b881174c4596b13f0b0fc8d34a,
title = "A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium)",
abstract = "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 (∼600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (∼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.",
author = "Junkang Rong and Colette Abbey and Bowers, {John E.} and Brubaker, {Curt L.} and Charlene Chang and Chee, {Peng W.} and Delmonte, {Terrye A.} and Xiaoling Ding and Garza, {Juan J.} and Marler, {Barry S.} and Park, {Chan Hwa} and Pierce, {Gary J.} and Rainey, {Katy M.} and Rastogi, {Vipin K.} and Schulze, {Stefan R.} and Trolinder, {Norma L.} and Wendel, {Jonathan F.} and Wilkins, {Thea A.} and Williams-Coplin, {T. Dawn} and Wing, {Rod A} and Wright, {Robert J.} and Xinping Zhao and Linghua Zhu and Paterson, {Andrew H.}",
year = "2004",
month = "1",
doi = "10.1534/genetics.166.1.389",
language = "English (US)",
volume = "166",
pages = "389--417",
journal = "Genetics",
issn = "0016-6731",
publisher = "Genetics Society of America",
number = "1",

}

TY - JOUR

T1 - A 3347-Locus Genetic Recombination Map of Sequence-Tagged Sites Reveals Features of Genome Organization, Transmission and Evolution of Cotton (Gossypium)

AU - Rong, Junkang

AU - Abbey, Colette

AU - Bowers, John E.

AU - Brubaker, Curt L.

AU - Chang, Charlene

AU - Chee, Peng W.

AU - Delmonte, Terrye A.

AU - Ding, Xiaoling

AU - Garza, Juan J.

AU - Marler, Barry S.

AU - Park, Chan Hwa

AU - Pierce, Gary J.

AU - Rainey, Katy M.

AU - Rastogi, Vipin K.

AU - Schulze, Stefan R.

AU - Trolinder, Norma L.

AU - Wendel, Jonathan F.

AU - Wilkins, Thea A.

AU - Williams-Coplin, T. Dawn

AU - Wing, Rod A

AU - Wright, Robert J.

AU - Zhao, Xinping

AU - Zhu, Linghua

AU - Paterson, Andrew H.

PY - 2004/1

Y1 - 2004/1

N2 - 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 (∼600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (∼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.

AB - 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 (∼600 kb) intervals based on 2007 probes (AtDt) and 763 loci at 1.96-cM (∼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.

UR - http://www.scopus.com/inward/record.url?scp=12144290265&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=12144290265&partnerID=8YFLogxK

U2 - 10.1534/genetics.166.1.389

DO - 10.1534/genetics.166.1.389

M3 - Article

C2 - 15020432

AN - SCOPUS:12144290265

VL - 166

SP - 389

EP - 417

JO - Genetics

JF - Genetics

SN - 0016-6731

IS - 1

ER -