Simple Sequence Repeat ?SSR? Linkage Map Of D Genome Diploid Cotton Derived From An Interspecific Cross Between D_3-d And D_3-k

The challenge in tetraploid cotton cultivars is the narrow genetic base occasioned by long periods of inbreeding and intensive selection among the cultivated cotton genotypes and therefore,the bottleneck is how to obtain interspecific hybrids and introduce the germplasm directly from wild cotton to elite cultivars.Construction of genetic maps has provided insight into understanding the genome structure,interrelationships between organisms in relation to evolution,and discovery of genes that carry important agronomic traits in plants.In this study,we generated an interspecific hybrid lines between two wild diploid cotton,Gossypium davidsonii and Gossypium klotzschianum,and genotyped 188 F₂ populations in order to develop a genetic map.We screened 12,560 Simple Sequence Repeat?SSR?primers developed by South West University,China thus the acronym SWU and obtained 1000 polymorphic markers which accounted for only 8%.A total of 928 polymorphic primers were successfully scored and only 728 were effectively linked across the 13 chromosomes,but with an asymmetrical distribution.The map length was 1,480.23 cM,with an average length of 2.182 cM between adjacent markers.High segregation distortions were observed in chromosomes 2,5,7 and 8;most of the distorted markers were skewed towards G.klotzschianum.A high percentage of the markers on the map developed,and for the physical map of G.raimondii,exhibited highly significant Collinearity,with two types of markers duplication;intra and inter-chromosomal duplications.A total 94 markers were found to be duplicated,with the highest number showing inter-chromosomal duplication as opposed to intra chromosomal duplication.The genetic and physical maps of the Dt sub-genome showed good syntenic block formation.Along the SSR regions of the map developed,a total of 2,063 genes were obtained,and were distributed in all the 13 chromosomes;the highest number of genes was found in chr09 with 269genes while the least number of genes was detected in chr13 with 58 genes.The genes were analysed for their physiochemical properties,gene structure and their functional annotations.From the RNA expression analysis top 100 highly up regulated genes were selected in the various tissues,out of these 27 genes were highly expressed and identified as the key genes with diverse roles in plant hormone signaling,development and defense mechanisms against varied abiotic and biotic stress factors.The achievement of developing the F₂ population and its genetic map construction may be a landmark in establishing a new tool for the genetic improvement of cultivars by use of the novel alleles from the wild cotton.Our map had an increased recombination length compared to other maps developed from other D genome cotton species.