Exploitation of <i>Malus</i> ESTs for development of SSR markers after <i>in silico</i> analysis

  • Era Vaidya Dr Y S Parmar University 0f Horticulture and Forestry, Nauni - Solan Himachal Pradesh
  • Rajinder Kaur Dr Y S Parmar University 0f Horticulture and Forestry, Nauni - Solan Himachal Pradesh
  • Krishan Kumar Dr Y S Parmar University 0f Horticulture and Forestry, Nauni - Solan Himachal Pradesh
  • Neha Sharma Dr Y S Parmar University 0f Horticulture and Forestry, Nauni - Solan Himachal Pradesh
Keywords: ESTs, EST-SSRs, apple

Abstract

The domestic apple (Malus X domestica) has been extensively characterized for EST sequences and currently 330181 ESTs are available in NCBI. Although this is a valuable resource for marker development but the redundancy in sequences makes the mining out of unique candidates for marker designing cumbersome. Keeping this in view, the present study was undertaken with the aim to remove the data redundancy in apple ESTs and then to develop SSR markers. The EST sequences were assembled into a non – redundant set of 5619 contigs and 59343 singletons (total sequences 64962), indicating 80% reduction in data redundancy. These 64962 sequences were then used to mine out SSR motifs. 4575 EST-SSRs were detected, with dinucleotide repeats being predominant (72%), followed by trinucleotide repeats (25%). These markers were validated by designing primer pairs. 25 of these designed primers were tested on a group of 48 apple accessions. All the markers gave robust amplification, generating 93% polymorphism. These findings indicate the usefulness of EST-SSRs in genome analysis. This study further emphasizes the importance of assembly of the vast amounts of data submitted in public databases. Our results have generated a set of non redundant apple ESTs which is of prime importance for development of marker systems without any repetition or overlapping.

Published
2015-08-26