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The objective of present investigation was to utilize and validate tetraploid species derived EST SSR
markers linked to fiber quality traits to generate markers for mapping in diploid cotton species. Six lines
of allotetraploid species viz, G. hirsutum (AD1) and seven and eleven lines of its putative diploid
ancestors viz, G. arboreum (A2) and G. herbaceum (A1) respectively were used for comparative analysis.
Of the total of 41 tetraploid-derived SSR primers, 85.36% gave amplification in both diploid species,
indicating that flanking sequences around repeats are conserved in the diploid and tetraploid species of
cotton. Average number of bands amplified by each primer was 15.57. The average observed mean
heterozygosity was 0.60. DNA sequence information of 10 randomly selected SSR amplicons were used
for phylogenetic analysis of Gossypium sps.which revealed that two diploid species of Gossypium (i.e.;
G.herbaceum & G.arboreum), shares a close genetic similarity with each other. Tetraploid-derived
microsatellites may be useful in comparative genetic mapping of both diploid Gossypium species, for
evolutionary studies and marker assisted selection (MAS) for introgression of agriculturally important
traits from exotic diploid and tetraploid germplasm sources. BLASTn analysis of randomly selected SSR
sequence data showed significant similarity (70-97%) between diploid G. arboreum and G.herbaceum
species and (10-27%) between diploid and tetraploids G. hirsutum species. BLASTx analysis of most of
SSR markers revealed identity with hypothetical and uncharacterized plant protein.
Keywords- Cottons, Tetraploid, Diploid, Gossypium hirsutum, Gossypium herbaceum, Gossypium
arboreum, SSR markers, BLASTn, BLASTx.