ABSTRACT

SSR marker has proved valuable in plant genomic studies due to its polymorphic nature and high transferability rate across taxa. SSRmarkers derived from conserved coding genomic regions in papaya using EST sequences are extremely useful as functional markers because they have a higher likelihood of association with regions coding for protein. In the present study, we have made utilized publicly available EST sequence data of papaya to mine and identify and develop markers from annotated EST-SSR sequences. The papaya EST sequence (77528) retrieved from NCBI was processed and assembled using EGassembler. Using the MISA and KRAIT programmes, 144 non-redundant perfect SSRs were selected from assembled contig and singleton sequences. Mono/dinucleotide repeats (80.5%) were the most common among SSR motifs found in the papaya EST sequence, followed by a trinucleotide (12.5%), tetranucleotide (4.86%), and hexanucleotide repeat (2.08%). AG/AT, AAT, and AAG repetitions were discovered to be prevalent among the SSR repeat sequence types. Furthermore, the amino acids coded by each trinucleotide SSRs motif had the greatest distribution of Lysine, followed by Arginine, Asparagine, Isoleucine, Threonine, and Serine. Interpro study utilizing Blast2GO to annotate non-redundant EST-SSR sequences identified numerous significant functional domains such as AP2/ERF, 14-3-3 protein, calmodulin binding, WRKY transcription factor, and metal ion binding. The bulk of SSRs (67%) were found in the UTR region, with just 33% found in the coding region. Primer pairs for 128 SSR sequences in and around the ORF region were created using Primer3 and virtually tested for desired amplification with the FastPCR programme. The EST-SSR markers and characterized functional domains in our study will facilitate genetic diversity and marker-assisted breeding studies in papaya.