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

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) su...

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Bibliographic Details
Published in:Journal of forestry research 2020-08, Vol.31 (4), p.1359-1370
Main Authors: Koohi Dehkordi, Mehrana, Beigzadeh, Tayebeh, Sorkheh, Karim
Format: Article
Language:English
Subjects:
Alleles
Biomedical and Life Sciences
Cultivars
Expressed sequence tags
Forestry
Genetic diversity
Genetic variability
Genotypes
Germplasm
Heterozygosity
Life Sciences
Markers
Original Paper
Plant breeding
Simple sequence repeats
Variance analysis
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Summary: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.
ISSN:1007-662X
1993-0607
DOI:10.1007/s11676-019-00922-z