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Identification and cross-species amplification of microsatellite markers derived from expressed sequence data of rose species

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Abstract

Genic SSR markers derived from public expressed sequence tags (ESTs) data are valuable and cost effective marker resources for genome mapping and diversity studies. Owing to their derivation from the transcribed regions which often have putative functions, these markers can be easily associated with desired trait. In the present study, 19 novel SSR markers were identified from 450 non redundant unigenes derived from 3,726 public ESTs of two rose species. Among SSRs, tri-repeats (61.3 %) were most abundant followed by di-repeat (29 %). Newly identified EST-SSR markers recorded significant homology with the known/putative proteins of Arabidopsis thaliana. The cross transferability to 12 rose species ranged from 63.2 to 100 %. Novel SSR loci found to be moderately to highly polymorphic with locus wise average number of alleles and polymorphism information content (PIC) were 4.1 and 0.33, respectively. Cloning and sequencing of EST-SSR size variant amplicons of marker locus Rches12 revealed that the variation in the number of SSR repeat-units was the main source of fragment polymorphism. The high polymorphic potential coupled with high cross-transferability rate demonstrates wider applicability of novel SSR markers in genetic diversity, genome mapping and evolutionary studies in various rose species.

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Fig. 1
Fig. 2

Abbreviations

SSRs :

Simple sequence repeats

ESTs :

Expressed sequence tags

PIC :

Polymorphism information content

PCR :

Polymerase chain reaction

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Acknowledgements

We gratefully acknowledge Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi for financial support. This is IHBT communication 0960.

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Author notes

  1. Pankaj Bhardwaj

    Present address: Central University of Punjab, Bathinda, 151001, India

  2. Rahul Kumar

    Present address: DAV University, Jalandhar, 144012, India

Authors and Affiliations

  1. Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 6, Palampur, H.P., 176061, India

    Ram Kumar Sharma, Anil Chaudhary, Himanshu Sharma, Pankaj Bhardwaj, Vikas Sharma, Rahul Kumar & Paramvir Singh Ahuja

Authors
  1. Ram Kumar Sharma
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  2. Anil Chaudhary
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  3. Himanshu Sharma
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  4. Pankaj Bhardwaj
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  5. Vikas Sharma
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  7. Paramvir Singh Ahuja
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Correspondence to Ram Kumar Sharma.

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Sharma, R.K., Chaudhary, A., Sharma, H. et al. Identification and cross-species amplification of microsatellite markers derived from expressed sequence data of rose species. J. Plant Biochem. Biotechnol. 24, 359–364 (2015). https://doi.org/10.1007/s13562-014-0287-1

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  • DOI: https://doi.org/10.1007/s13562-014-0287-1

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