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Novel in silico EST-SSR markers and bioinformatic approaches to detect genetic variation among peach (Prunus persica L.) germplasm

  • Mehrana Koohi Dehkordi
  • Tayebeh Beigzadeh
  • Karim SorkhehEmail author
Original Paper
  • 18 Downloads

Abstract

Because there are thousands of peach cultivars, cultivar classification is a critical step before starting a breeding project. Various molecular markers such as simple sequence repeats (SSRs) can be used. In this study, 67 polymorphic primers produced 302 bands. Higher values for SI index (1.903) suggested higher genetic variability in the genotype under investigation. Mean values for observed alleles (Na), expected heterozygosity (He), effective alleles (Ne), Nei’s information index (h), and polymorphic information content (PIC) were 4.5, 0.83, 5.45, 0.83, and 0.81, respectively. The dendrogram constructed based on Jaccard’s similarity coefficients outlined four distinct clusters in the entire germplasm. In addition, an analysis of molecular variance (AMOVA) showed that 70.68% of the total variation was due to within-population variation, while 29.32% was due to variation among populations. According to this research, all primers were successfully used for the peach accessions. The EST-SSR markers should be useful in peach breeding programs and other research.

Keywords

Expressed sequenced tags (EST) Simple sequence repeats (SSR) Prunus persica L. Genetic diversityl 

Abbreviations

PIC

Polymorphic information content

UPGMA

Unweighted pair group method with arithmetic average

AMOVA

Analysis of molecular variance

EST

Expressed sequenced tags

SSR

Simple sequence repeats

PCR

Polymerase chain reaction

SI

Shannon’s information index

h

Nei’s information index

He

Expected heterozygosity

Ho

Observed hetrozygosity

Ne

Effective alleles

Na

Observed number of alleles

MCMC

Markov chain Monte Carlo,

MAS

Marker-assisted selection

Notes

Supplementary material

11676_2019_922_MOESM1_ESM.docx (67 kb)
Supplementary material 1 (DOCX 66 kb)

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Copyright information

© Northeast Forestry University 2019

Authors and Affiliations

  • Mehrana Koohi Dehkordi
    • 1
  • Tayebeh Beigzadeh
    • 1
  • Karim Sorkheh
    • 2
    Email author
  1. 1.Department of Agronomy, Faculty of AgriculturePayame-Noor UniversityTehranIran
  2. 2.Department of Agronomy and Plant Breeding, Faculty of AgricultureShahid Chamran University of AhvazAhvazIran

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