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Expressed SSRs (G. hirsutum)


25 DPA transcriptome of the genotypes, JKC777 (superior fiber quality) and JKC703 (inferior fiber quality) were explored for the identification of expressed SSRs. A total of 920 SSRs in 836 unigenes and 1090 SSRs in 1010 unigenes were resulted in JKC777 and JKC703 respectively. When two genotypes were compared each other for common SSRs with respect to flanking sequences and repeat motif unit, a total of 570 SSRs were found. Besides these common SSRs, JKC777 was revealed to be contained of 350 unique additional SSRs and JKC703, in similar way resulted a total of 520 unique additional SSRs. Thus, the 25DPA transcriptome analysis of both the genotype resulted into a total of 1440 SSRs. The following details of the expressed SSRs analysis are given below:


Summary statistics of screening of cotton (G. hirsutum) transcriptome for putative expressed SSRs

Analysis characteristics JKC777 JKC703
Number of reads 488128 547939
Number of contigs after assembly  16457 17900
Number of SSR containing sequences  836 1010
Number of total SSRs 920 1090
Number of sequences containing more than 1 SSR  77 79
Number of unique SSRs
(after removing redundancy among JKC 777 and JKC 703)
350 520
Total number of SSRs 1440

           Frequency details of expressed SSRs repeat motifs in JKC777 and JKC703