Development, Characterization and Transferability of Peach Genic SSRs to some Rosaceae species
Rajinder Kaur *
Department of Biotechnology, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
Shilpa .
Department of Biotechnology, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
Era Vaidya
Department of Biotechnology, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
Krishan Kumar
Department of Fruit Science, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India
*Author to whom correspondence should be addressed.
Abstract
Aims: The present study was carried out to extract expressed sequence tags-simple sequence repeats (EST-SSRs) for peach (Prunus persica L.) and to study their transferability across some Rosaceae species such as apricot, apple, rose and strawberry.
Study Design: Cross-transferability check of Prunus EST-SSRs to some Rosaceae species.
Place and Duration of Study: Sample: Department of Biotechnology, Dr Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan-173230, Himachal Pradesh, India, between January 2012 and November 2012.
Methodology: SSRs were identified in EST sequences using SSR Identification Tool (SSRIT) and PRIMER3 software was used to design primers which were used to carry out PCR. Data generated by PCR for all the genotypes was used to calculate transferability of Prunus persica EST-SSRs to other Rosaceae species under study. Data analysis was done through NTSYSpc Version 2.02h by creating dendrograms in all the species under study.
Results: 2000 EST sequences were downloaded from the National Centre for Biotechnology Information (NCBI) web site. Sequences were assembled into contigs and singletons. 124 sequnces were found to contain SSRs using SSRIT. Out of these 43 were used for primer designing using PRIMER3 software which were custom synthesized and used for polymorphism study in six genotypes of peach. Thirty-eight primers showed scorable amplification, 20 being polymorphic. These 20 polymorphic primers of peach were then further used to carry out transferability studies in apricot, apple, rose and strawberry revealing 50%, 95%, 95% and 45% transferability, respectively. Dendrograms were generated using NTSYS ver.2.02h. The coefficient values were found to range from 0.483 to 0.711 in six peach genotypes and 0.451 to 0.975 in all 22 genotypes under study.
Conclusion: Thus it can be concluded from the present study that ESTs of peach produce high polymorphism in different Rosaceous species, indicating their cross-transferability to different members of Rosaceous family.
Keywords: EST-SSR, prunus, Rosaceae, transferability