Abstract
Compared to tetraploid, diploid cotton especially Gossypium herbaceum are poor in genomic resources including molecular markers. Expressed sequence tags (ESTs) in public databases are valuable resources and offer opportunity for identification of simple sequence repeat (SSR) markers. ESTs data base of cotton were employed for the development of novel EST–SSR markers. Sequence assembly and clustering of 1,31,464 dbESTs (G. hirsutum, 92,570 and G. arboreum, 38,894) resulted in 28,718 unigenes (17,019 singletons and 11,699 contigs) having 1,760 SSRs. On an average, the unigenes contained 1 SSR/16.3kb of unigene. The AG class was the most common among the dinucleotide motifs (45%), whereas the AAG class (25%) was predominant among the trinucleotide motif. A total of 378 novel primers pairs were developed from the ESTs of cotton fiber cells and ovules. A set of 60 primers associated with fiber development were selected and validated on a panel of 23 G. herbaceum and nine G. arboreum genotypes. Among 60, 44 primers d amplified 71 loci; of which 54 (76%) were polymorphic. The polymorphic information content (PIC) ranged from 0.11–0.74. The class II repeat SSR motifs were more polymorphic than class I repeat SSR markers. Nei’s dissimilarity coefficients based on SSR markers among the all pair-wise combinations of genotypes ranged from 0.02 to 0.49 with a mean of 0.24. The UPGMA clustering grouped 32 genotypes in 2 clusters at cut off value of 0.23. The EST–SSR markers developed in our study would be best assets for characterization of germplasm, population structure analysis and QTL mapping in diploid cotton.
Published Version
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