title: Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information.
abstract: BACKGROUND
  Cotton is the world's most important natural textile fiber and a significant oilseed crop. Decoding cotton genomes will provide the ultimate reference and resource for research and utilization of the species. Integration of high-density genetic maps with genomic sequence information will largely accelerate the process of whole-genome assembly in cotton.
  
  
  RESULTS
  In this paper, we update a high-density interspecific genetic linkage map of allotetraploid cultivated cotton. An additional 1,167 marker loci have been added to our previously published map of 2,247 loci. Three new marker types, InDel (insertion-deletion) and SNP (single nucleotide polymorphism) developed from gene information, and REMAP (retrotransposon-microsatellite amplified polymorphism), were used to increase map density. The updated map consists of 3,414 loci in 26 linkage groups covering 3,667.62 cM with an average inter-locus distance of 1.08 cM. Furthermore, genome-wide sequence analysis was finished using 3,324 informative sequence-based markers and publicly-available Gossypium DNA sequence information. A total of 413,113 EST and 195 BAC sequences were physically anchored and clustered by 3,324 sequence-based markers. Of these, 14,243 ESTs and 188 BACs from different species of Gossypium were clustered and specifically anchored to the high-density genetic map. A total of 2,748 candidate unigenes from 2,111 ESTs clusters and 63 BACs were mined for functional annotation and classification. The 337 ESTs/genes related to fiber quality traits were integrated with 132 previously reported cotton fiber quality quantitative trait loci, which demonstrated the important roles in fiber quality of these genes. Higher-level sequence conservation between different cotton species and between the A- and D-subgenomes in tetraploid cotton was found, indicating a common evolutionary origin for orthologous and paralogous loci in Gossypium.
  
  
  CONCLUSIONS
  This study will serve as a valuable genomic resource for tetraploid cotton genome assembly, for cloning genes related to superior agronomic traits, and for further comparative genomic analyses in Gossypium.
authors.affiliation: State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Zhao
authors.forename: Lv
authors.initials: L
authors.lastname: Yuanda
authors.forename: Cai
authors.initials: C
authors.lastname: Caiping
authors.forename: Tong
authors.initials: T
authors.lastname: Xiangchao
authors.forename: Chen
authors.initials: C
authors.lastname: Xiangdong
authors.forename: Zhang
authors.initials: Z
authors.lastname: Wei
authors.forename: Du
authors.initials: D
authors.lastname: Hao
authors.forename: Guo
authors.initials: G
authors.lastname: Xiuhua
authors.forename: Guo
authors.initials: G
authors.lastname: Wangzhen
mesh_terms: D002874:Chromosome Mapping; D032561:Cotton Fiber; D018744:DNA, Plant / Q000235:genetics*; D020224:Expressed Sequence Tags / Q000378:metabolism; D020440:Gene Duplication / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development; D058977:Molecular Sequence Annotation; D040641:Quantitative Trait Loci / Q000235:genetics; D017422:Sequence Analysis, DNA; D057891:Tetraploidy
chemical_list: D018744:DNA, Plant