Development and validation of new SSR markers from expressed regions in the garlic genome

Ahmet Ipek,Nihan Sahin,Meryem Ipek,Philipp W. Simon,Asuman Cansev

doi:10.1590/0103-9016-2014-0138

Ahmet Ipek, Nihan Sahin + Show 3 more

Open Access

https://doi.org/10.1590/0103-9016-2014-0138

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Journal: Scientia Agricola	Publication Date: Feb 1, 2015
Citations: 26	License type: cc-by

Affiliation: Uludağ University, Namık Kemal University

Abstract

Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC) of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.

Highlights

Garlic (Allium sativum L.) is one of the important cultivated species of the genus Allium and it is classified as belonging to the Alliaceae family
This study aimed to develop new simple sequence repeat (SSR) markers from the garlic expressed sequence tags (ESTs) sequences and to validate the utility of these markers by evaluating genetic relationships between diverse garlic clones
Twenty one of these garlic clones had been previously characterized with amplified fragment length polymorphism (AFLP) markers (Ipek et al, 2003) and they were selected to represent ten phylogenetic groups identified in this AFLP genetic diversity assessment study

Summary

Introduction

Garlic (Allium sativum L.) is one of the important cultivated species of the genus Allium and it is classified as belonging to the Alliaceae family. The genetic diversity between garlic clones has generally been assessed using amplified fragment length polymorphism (AFLP), randomly amplified polymorphic DNA (RAPD) and isozyme markers (Ipek et al, 2003; Buso et al, 2008; Ipek et al, 2008a, Paredes et al, 2008; Morales et al, 2013). Molecular markers have been utilized for the development of a low density genetic map for garlic (Ipek et al, 2005; Zewdie et al, 2005). In order to increase the density of the genetic maps and anchor dominant markers such as AFLPs and RAPDs, it is essential to develop co-dominant DNA markers like simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) for the garlic genome

Objectives

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