A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum x Gossypium barbadense backcross population

An interspecific Gossypium hirsutum x Gossypium barbadense backcross population of 75 BC1 plants was evaluated for 1014 markers. The map consists of 888 loci, including 465 AFLPs, 229 SSRs, 192 RFLPs, and 2 morphological markers, ordered in 37 linkage groups that represent most if not all of the 26 chromosomes, altogether spanning 4400 cM Loci were not evenly distributed over linkage groups, and 18 of the 26 long groups had a single dense region. This paper proposes a partially revised list of the 13 pairs of homoeologous A/D chromosomes of the 2n = 4x = 52 tetraploid cotton genome. The major revisions, which involve the c3-c17, c4-c22, c5-D08, and c10-c20 homocologous pairs, are based on the mapping of 68 SSR and RFLP loci with a known chromosome assignment, as well as on comparative alignments with previously published G. hirsutum x G. barbadense maps. The overall congruency in the locus orders and distances of common SSR and RFLP loci in these maps allows for an estimation of the consensus length that reaches a minimum of 5500 cM, and is encouraging for future efforts aimed at developing an integrated map of cultivated cotton. The present map also provides a firm framework for precision mapping of Mendelian components of quantitative traits in cotton.