Genetic Diversity and Linkage Disequilibrium Analysis of Photoperiod Response in Exotic Cottons, Gossypium hirsutum L

Upland cotton (Gossypium hirsutum L.) has a narrow genetic basis that limits the improvement of cultivars. Exotic accessions offer the possibility to broaden resources for cotton breeding and a sampling are presently being used in development of nested association mapping (NAM) populations. We studied the diversity of these exotic accessions, ‘converted’ to day-neutral flowering, and DNA marker associations with day-neutral genes/QTLs by screening 45 G. hirsutum accessions which include 19 short-day exotic lines, 20 of their counterpart backcross day-neutral lines, the day-neutral donor line and 5 historically-important cultivars with 830 SSR markers evenly distributed on the chromosomes. A total of 1427 dominant loci were used for the analysis, constructing a phylogenetic tree using these data. The rates of the converted polymorphic loci from progenitors to backcross accessions range from 6.80-28.94%, noting that some of this variation is due to different numbers of backcrosses. These loci are not randomly distributed on chromosomes and some appear to stay together as blocks, showing linkage disequilibrium and low recombination rates in some genomic regions. Six closely-related pairs of backcross accessions and their recurrent parents were used for association studies. Three markers were closely associated with photoperiod sensitivity. This study provides an initial picture of the diversity of exotic accessions being used in a crossing program toward NAM development, also identifying DNA markers for day-neutral flowering and providing a potential foundation for day-neutral gene/QTL cloning.