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Genus cotton has total 50 species, diploid species fall into 8 genomic groups (A-G, and K). To the extent of our knowledge, frequency of single nucleotide polymorphisms (SNPs) has not been calculated in genes of multiple genomes of the genus Gossypium. Here we present the frequency of SNPs in the transcribed regions of the multiple genes, and their utility in resolving phylogenies among 11 diploid species representing five of the eight diploid genomes of the genus Gossypium. We explored the expressed sequence tags (ESTs) data set of G. arboreum showing homology with genes encoding for mitochondrial small heat shock protein (MT-sHSP), histone H2B1, S-adenosyl methionine synthetase, cytochrome p450, actin-depolymerizing factor 2, C-terminal domain of helicases and histone H2B3 for designing primers. The resultant PCR products amplifying partial gene sequences were sequenced. In total, 61 SNPs were detected in cotton genomes which include 53 substitutions and 8 Indels in the total 1920 bp genome length. Phylogenetic analysis using this data revealed grouping of genomes comparable with previous studies. A1 and A2 genomes were most similar (98.0%) while D9 and Oryza genomes were least similar (31.2%). Oryza was most distantly related with other genomes. In conclusion SNPs are potent markers to delineate cotton genomes according to their evolutionary positions. [ABSTRACT FROM AUTHOR]

The present study was designed to evaluate genetic diversity among twenty cotton genotypes by employing thirty one SSR markers that were reported from Brookheaven National Laboratories. Out of thirty-one primers, six SSR primers were found polymorphic at different SSR loci. Maximum number of loci (33), were amplified by MNH-93, while minimum (22) by 238-F. Total percentage of informative loci was 36.8%. Genetic diversity matrix of these genotypes was calculated by NTSYS-pc 2.2 software. Genetic similarity coefficients ranged from 0.474 to 0.974. The highest dissimilarity (0.474) was observed between genotype 298-F and CIM-496. Cluster analysis as performed using un-weighted pair group method of arithmetic average algorithm showed that Nei and Li's coefficients ranged from 0.63 to 0.97. The dendrogram of cotton lines showed two major clusters except 238-F forming an out-group from other genotypes, thus showing maximum dissimilarity. Genotypes MNH-93 and K-68/9 showed maximum similarity coefficient of 0.97. Information obtained from the present study can be used to select divergent parents for future breeding programs. [ABSTRACT FROM AUTHOR]