Addition of 455 Microsatellite Marker Loci to the High-DensityGossypium hirsutum TM-1 x G. barbadense 3-79 Genetic Map

Four hundred fifty-five new microsatellite, also known as simple sequence repeat (SSR) marker loci, were added to the previously published 2072-locus genetic map that was constructed using 186 recombinant inbred lines (RILs) from an interspecific cross between Gossypium hirsutum TM-1 and G. barbadense 3-79. The augmented high-density map contained 2527 loci (2280 SSRs and 247 single nucleotide polymorphisms) and covered 3430 centiMorgans (cM) with an average marker locus interval of 1.36 cM. An addition of 455 new marker loci (a net increase 21.96%) resulted in only 50 cM or 1.48% net increase of total genetic distance, but reduced the number of large gaps (> 10 cM) from 21 to 14. Approximately 400 pairs of duplicate SSR loci were present in this augmented map. Most duplicate loci were mapped between homeologous chromosomes. Duplicate loci within a chromosome were observed in at least nine chromosomes. The telomeric regions are hot spots for intrachromosomal locus duplication. This augmented map is a saturated genetic map of tetraploid cotton genome whose total genetic distance is estimated at approximately 3500 cM.