Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i> L.) — Oak Academic Publishing
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Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i> L.)
Department of Biochemistry, University of Lucknow, Lucknow, India
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Department of Biochemistry, University of Lucknow, Lucknow, India
,
College of Basic Sciences & Humanities, Sardarkrushinagar Agricultural University Dantiwada, Banaskantha, India
,
Department of Biochemistry, University of Lucknow, Lucknow, India
,
Department of Biochemistry, University of Lucknow, Lucknow, India
1 Department of Biochemistry, University of Lucknow, Lucknow, India
2 Department of Biochemistry, University of Lucknow, Lucknow, India
3 College of Basic Sciences & Humanities, Sardarkrushinagar Agricultural University Dantiwada, Banaskantha, India
4 Department of Biochemistry, University of Lucknow, Lucknow, India
5 Department of Biochemistry, University of Lucknow, Lucknow, India
Papaya ( Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crop s . Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as they are derived from conserved genic portion. Development of EST-SSRs markers through in silico approach is cheaper, less time consuming and labour-intensive. In this study, we aimed to mine SSRs and developed EST-SSR primers from papaya floral ESTs. A total of 75,846 papaya floral ESTs were downloaded from public database National Centre for Biotechnology Information (NCBI). A total of 26,039 floral unigenes (7961 contigs and 18,078 singletons) were generated after assembly of these ESTs. From these floral unigenes, 433 , 782 perfect SSRs, 204,968 compound SSRs and 6061 imperfect SSRs were mined, respectively. In perfect SSRs, mononucleotide repeats were most abundant (94.7%) followed by tri- (3.1%) and di-nucleotide repeats (1.7%). The frequencies of tetra-, hexa- and penta-nucleotide repeats accounted for only (0.17%), (0.04%) and (0.03%), respectively. In mononucleotide repeats, the most abundant motif was A/T (69.3%) and in di- and tri-nucleotide repeats were AG/CT (61%) and AAG/CTT (31%), respectively. In imperfect SSRs, mononucleotide repeats (56.5%) were most abundant. 176 different types of motifs were identified. A total of 3807 primer pairs for floral papaya ESTs were successfully designed. These developed EST-SSR primers are being used for the genetic improvement of papaya such as study of cross-transferability across genera/species, evaluation of genetic diversity, and identification of sex-specific markers. These EST derived SSRs can also be used in filling gaps in existing linkage maps in papaya.
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SSR Mining
EST-SSR
SSR Motifs
Primer Pairs
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