Genome-Wide SSR High Density Genetic Map Construction From An Interspecific Cross Of G. Hirsutum×G. Mustelinum

Cotton, with large genome, is an important crop throughout the world. Conventional breeding has great potential and will play a central role in sustained genetic improvement by incorporating DNA marker technology and molecular breeding. The application of molecular methods to cotton germplasm which have been classified on the basis of morphology and geography has the potential to accelerate the accumulation of genetic information as compared to traditional methods.Extensive genetic variability and large effective breeding populations are essential bases for the crop improvement. Most of the Gossypium species being sexually incompatible, new interspecific hybrids are difficult to develop, unless sterility barrier is overcome. The conventional methods of plant breeding for the transference of desirable agronomic and quality traits of wild species to the commercial cotton have not been proved much helpful. The genetic basis of the commercial cotton can considerably be broadened by overcoming the incompatibility among various species of Gossypium. To enhance the wide genetic basis of cotton genotypes the most diversed cotton genotypes were crossed to develop genetically diverse cultivars having maximum potential for yield and having desireable traits. Genetically more distinct parents will produce maximum hybrid vigor.Recent advances in molecular technology provide a base to construct a high density genetic map which can facilitate genome sequencing, sequence assembly, gene mapping and the design of targeted genetic markers for better understanding and improvement of the cotton plant.In this study, an entire microsatellite (Simple sequence repeat, SSR) PCR-based high density genetic map was constructed using the interspecific cross of G.hirsutum x G.mustelinum and covering a large region of cotton genome. This high density genetic map constitutes of2029SSR mapped markers covering4026.10cM with an average inter-marker distance of2.20cM. Number of marker anchored on the chromosomes varied from23to127with an average of154.85cM. More markers were anchored on At sub-genome (51.70%) than Dt-subgenome (48.30%).The At-subgenome span more distance (2096.71cM) than the Dt-subgenome (1929.39cM).The maximum length of chromosome was209.96cM and the minimum was99.52cM. The largest homeologous chromosome pair was Chr.19(D05) and05(A05) smallest is Chr.20(D10) as far mapped loci are concerned. In this map566loci showed segregation distortion and accounting for27.89%. A total of55segregating hotspot (SDRs) were found on the26cotton chromosomes with27SDRs on the At subgenome and28on the Dt subgenome. More distorted loci were located on the At subgenome than the Dt sub-genome. All the large SDRs revealed skewness toward the heterozygous allele and all the skewed alleles within the SDR segregate in the same direction. A unique intra-chromosomal duplications observed in chromosome24(D08), where3markers viz MON_CGR5433, MON_CGR0152and MON_CGR5423each revealed duplicate loci and their recombination rates on an average is lOcM respectively. The SSR-based map constructed in this study will be useful for further genetic analysis of important quantitative traits, marker assisted selection and genome organization architecture in cotton as well as for comparative genomics between cotton and other species. Moreover this map will lay the foundation for developing chromosome segment substitution lines (CSSLs) from G. mustelinum in an upland cotton background by marker-assisted high throughput selection and also enrich the cotton germplasm by incorporating superior genes especially insect resistance from wild genetic resources.