Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L

• Published in: Bioinformation 2015-01, Vol.11 (3), p.145-150
• Main Authors: Chand, Subodh Kumar, Nanda, Satyabrata, Rout, Ellojita, Joshi, Raj Kumar
• Format: Article
• Language: English
• Subjects: Hypothesis
• ISSN: 0973-2063; 0973-8894; 0973-2063
• DOI: 10.6026/97320630011145

Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.