Skip to content
Research Article Open access CC BY 4.0

Development, Characterization and Transferability of Peach Genic SSRs to some Rosaceae species

Rajinder Kaur, Shilpa ., Era Vaidya, Krishan Kumar

Advances in Research · pp. 165–180 · Published 4 Oct 2014

10.9734/AIR/2015/8804

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.  

EST-SSR prunus Rosaceae transferability

References (61)

  1. 1 Primer3 on the WWW for General Users and for Biologist Programmers [DOI]
  2. 2 Mathematical model for studying genetic variation in terms of restriction endonucleases. [DOI]
  3. 3 The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis [DOI]
  4. 4 Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) [DOI]
  5. 5 A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene.
  6. 6 Strategies for microsatellite isolation: a review [DOI]
  7. 7 Genic microsatellite markers in plants: features and applications [DOI]
  8. 8 Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat [DOI]
  9. 9 Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.) [DOI]
  10. 10 Comparative mapping and marker-assisted selection in Rosaceae fruit crops [DOI]
  11. 11 Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.) [DOI]
  12. 12 AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterisation and cross-species amplification in Prunus [DOI]
  13. 13 Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum [DOI]
  14. 14 Cross-species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants [DOI]
  15. 15 How much effort is required to isolate nuclear microsatellites from plants? [DOI]
  16. 16 Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome [DOI]
  17. 17 Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats [DOI]
  18. 18 Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping [DOI]
  19. 19 Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population [DOI]
  20. 20 Cross-species transferability and mapping of genomic and cDNA SSRs in pines [DOI]
  21. 21 High transferability of bread wheat EST-derived SSRs to other cereals [DOI]
  22. 22 Genetic linkage maps of rose constructed with new microsatellite markers and locating QTL controlling flowering traits [DOI]
  23. 23 Simple‐sequence repeat (SSR) markers of Japanese plum (Prunus salicina Lindl.) are highly polymorphic and transferable to peach and almond [DOI]
  24. 24 New set of microsatellite loci isolated in apricot [DOI]
  25. 25 SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility [DOI]
  26. 26 Development and characterization of polymorphic microsatellites from Prunus avium‘Napoleon’ [DOI]
  27. 27 Prunus microsatellite marker transferability across rosaceous crops [DOI]
  28. 28 Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs [DOI]
  29. 29 Development and transportability across Prunus species of 42 polymorphic almond microsatellites [DOI]
  30. 30 Identification of microsatellite polymorphisms in an expressed portion of the rye genome [DOI]
  31. 31 Simple sequence repeat (SSR) analysis for assessment of genetic variability in apricot germplasm [DOI]
  32. 32 Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs [DOI]
  33. 33 Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species [DOI]
  34. 34 The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping [DOI]
  35. 35 Cross-transferable polymorphic SSR loci in Prunus species [DOI]
  36. 36 The development and mapping of functional markers in Fragaria and their transferability and potential for mapping in other genera [DOI]
  37. 37 A set of EST‐SSRs isolated from peach fruit transcriptome and their transportability across Prunus species [DOI]
  38. 38 Development of new genomic microsatellite markers from robusta coffee (Coffea canephoraPierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies [DOI]
  39. 39 Development and bin mapping of strawberry genic-SSRs in diploid Fragaria and their transferability across the Rosoideae subfamily [DOI]
  40. 40 The application of SSRs characterized for grape (Vitis vinifera) to conservation studies in Vitaceae [DOI]
  41. 41 Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa) [DOI]
  42. 42 Phylogenetic relationships among Cucumis species based on the ribosomal internal transcribed spacer sequence and microsatellite markers [DOI]
  43. 43 EST‐derived microsatellites as a rich source of molecular markers for oats [DOI]
  44. 44 Development of Juglans Regia SSR Markers by Data Mining of the EST Database [DOI]
  45. 45 Cross-species Transferability of Rice Microsatellites in its Wild Relatives and the Potential for Conservation Genetic Studies [DOI]
  46. 46 Rose (Rosa hybrida L.) EST-derived microsatellite markers and their transferability to strawberry (Fragaria spp.) [DOI]
  47. 47 Development of SSR markers from ESTs of gramineous species and their chromosome location on wheat [DOI]
  48. 48 ANALYSIS OF EXPRESSED SEQUENCE TAGS FROM JAPANESE PEAR 'HOUSUI' [DOI]
  49. 49 Development and across-species transferability of microsatellite markers in the genus Limonium (Plumbaginaceae) [DOI]
  50. 50 Development of new SSR markers from EST of SSH cDNA libraries on rose fragrance [DOI]
  51. 51 Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate [DOI]
  52. 52 Analysis of SSRs derived from grape ESTs [DOI]
  53. 53 Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species [DOI]
  54. 54 EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments [DOI]
  55. 55 Comparative Genetic Mapping Between Octoploid and Diploid Fragaria Species Reveals a High Level of Colinearity Between Their Genomes and the Essentially Disomic Behavior of the Cultivated Octoploid Strawberry [DOI]
  56. 56 Genetic diversity of different apricot geographical groups determined by SSR markers [DOI]
  57. 57 Strawberry GenBank-derived and Genomic Simple Sequence Repeat (SSR) Markers and Their Utility with Strawberry, Blackberry, and Red and Black Raspberry [DOI]
  58. 58 Data Mining for SSRs in ESTs and Development of EST-SSR Marker in Tea Plant (Camellia sinensis)
  59. 59 Data mining of ESTs to develop dbEST-SSRs for use in a polymorphism study of cauliflower (Brassica oleraceavar.botrytis) [DOI]
  60. 60 CAP3: A DNA Sequence Assembly Program [DOI]
  61. 61 Computational and Experimental Analysis of Microsatellites in Rice ( Oryza sativa L.): Frequency, Length Variation, Transposon Associations, and Genetic Marker Potential [DOI]

Cited by 6

Exploitation of Walnut (Juglans regia L.) Expressed Sequence Tags for Development of SSR Markers After In Silico Analysis

Sankhyan Shailja, R. Kaur, Chaudhary Shilpa · Proceedings of the National Academy of Sciences, India Section B: Biological Sciences · 2019

Showing 4 of 6 known citations — external sources report more than can currently be individually listed.

Article metrics

Real usage data collected on this platform.

13

Page views

0

PDF downloads

0

Outbound clicks

6

Citations

Views over time

Views by country

Approximate, from request IP at view time — not citizenship or institution. Countries with fewer than 5 views are grouped as "Other".

Traffic sources

Referring site, by host.

Views and downloads exclude known bots/crawlers. Citations combines this platform's own DOI-resolved index with each external source's own reported total — see Cited by above for individually listed citing works. Last refreshed 0 seconds ago.