A high-density SSR genetic map constructed from a F2 population of Gossypium hirsutum and Gossypium darwinii

• The high density genetic map from an interspecific cross of G. hirsutum × G. darwinii was constructed.
• A total of 2763 markers were mapped covering a genome length of 4176.7 cM.
• Higher distortion and stable distorted loci have been found in this map.
• Two post-polyploidization reciprocal translocations were suggested by duplicate loci.

The cultivated allotetraploid species Gossypium hirsutum, accounts for 90% of the world cotton production, has narrow genetic basis that's why its yield, quality or stress resistance breeding is stagnant. It is therefore, essential to explore desirable genes from Gossypium darwinii which has enviable traits such as high fiber fineness, drought tolerance, fusarium and verticillium resistance. We used G. darwinii as primary plant materials in this study not only to enrich the genetic diversity of exiting germplasm but also to better understand its genome structure. An interspecific high density linkage map of allotetraploid cotton was constructed using F2 population (G. hirsutum × G. darwinii). The map was based entirely on genome-wide simple sequence repeat (SSR) markers. A total of 2763 markers were mapped in 26 linkage groups (chromosomes) covering a genome length of 4176.7 cM with an average inter-locus distance of 1.5 cM. The length of the chromosomes ranged from 84.7 to 238.5 cM with an average length of 160.6 cM. At subgenome length was 2160.7 cM with an average distance of 1.6 cM, where as Dt genome length was 2016 cM with an average distance of 1.4 cM. There were 601 distorted SSR loci. Less number of segregation distortion loci were located in At subgenome than in Dt subgenome. Two post-polyploidization reciprocal translocations of “A2/A3 and A4/A5” were suggested by 44 pairs of duplicate loci.