Networking and Bayesian analyses of genetic affinity in cotton germplasm

Cotton is one the most important economic crop plant to mankind. A narrow genetic base and limited genetic diversity exists in cotton due to long time cultivation practice and artificial selection of this crop plant. Hybridization is the main task of cotton breeding and thorough search for identification of novel genetic diversity is of immediate need in cotton breeding. Therefore, present study undertakes bioinformatics analysis of genetic diversity versus genetic relationship of cotton germplasm including diploid and tetraploid cottons genotypes and their hybrids. Simple sequenced repeats (SSR) and Expressed sequence tagged-SSR (EST-SSR) markers were used in this study. Tetraploid cotton genotypes showed higher genetic diversity compared to diploid plants. AMOVA test showed significant genetic difference between these two polyploidy groups. Bayesian STRUCTURE analysis produced 9 distinct population groups, while K-Means clustering suggested 2–3 major genetic subgroups in the present germplasm. Networking and reticulation analysis showed high degree of gene exchange among most of the studied plants. Coalescence analysis showed gene duplication and gene extinction along with allotetraploid nature of cotton as the main mechanisms for bringing about new genetic variation in cotton. Obtained data can help us to plan a better hybridization and selection plan for cotton.