Dataset of SSR markers for ISSR-Suppression-PCR to detect genetic variation in Garcinia mangostana L. in Peninsular Malaysia

In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia.


a b s t r a c t
In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia. & 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Subject area
Biology More specific subject area

Plant sciences
Type of data

Data accessibility
The data is available with this article.

Value of the data
These data suggest that ISSR-Suppression-PCR is a useful method to provide information on the genetic variation of selected G. mangostana genotypes in Peninsular Malaysia.
These SSR markers can assist researchers to differentiate between accessions of G. mangostana. Seven out of 15 SSR markers tested on several accessions of G. mangostana showed differences between 3 and 6 bp in allele size revealing genetic variation in this apomictic plant and suggesting the usefulness of these accessions as potential resources for future breeding programs.

Data
15 SSR markers were developed and tested on selected Garcinia mangostana accessions (Table 1) [1]. The data presented here shows that the ISSR-Suppression-PCR technique was very applicable in designing SSR primers and was able to reveal variation of selected germplasm collections [2,3]. These SSR markers can be used to assess genetic variation of G. mangostana. Table 1 List of IP2 and IP3 primers. Each primer pairs was assigned as one SSR locus.

DNA extraction
Total genomic DNA was extracted from frozen leaf material of G. mangostana using DNeasy Plant Mini Kit (QIAGEN). The purity and concentration of the DNA were estimated using Nanodrop ND-100. The quality of DNA was determined through 1% agarose gel electrophoresis and examined under UV (Fujifilm Intelligent Dark Box Las-3000).

PCR amplification
ISSR-Suppression-PCR was conducted to amplify the ISSR fragment with the SSR motif at each end. Three SSR motifs: (AC)n, (GA)n and (AC)n(AG)n were used in this technique. PCR amplification conditions were the following: initial denaturation for 3 min at 94°C, followed by denaturation for 40 s at 94°C; annealing for 45 s at 55°C; elongation for 1 min at 72°C and then 35 cycles of 30 s at 94°C, 45 s at 55°C and 1 min at 72°C; and final extension at 72°C for 10 min. The PCR product was then checked on a 1.5% agarose gel. Amplified fragments of 300-600 bp were excised using a clean razor blade and gel purified using QIAquick Gel Extraction Kit (QIAGEN). The quality of the gel purification product was analyzed using Nanodrop-100 before being used in cloning procedure.

Cloning
The amplified fragments were ligated into a pGEM-T Easy Vector (Promega, USA), following the kit protocol. The ligation products were then transformed into Escherichia coli (TOP10). The transformants were spread on an LB plate containing ampicillin, IPTG, and Xgal. The positive clones were selected using a pipette tip, and the tip was rinsed in the PCR cocktail containing: 5 μL 1 Â PCR buffer, 1 μL 0.2 mM dNTPs, 0.5 μL 10 pmol forward primer (M13F), 0.5 μL 10 pmol reverse primer (M13R), 0.5 μl 2.5 U Taq Polymerase, and distilled water was added up to 20 μL. The PCR conditions were the same as described above. The products of the colony PCR were checked on 1.0% agarose gel. Plasmids were isolated from selected positive clones and sent to First Base Sdn. Bhd. (Malaysia) for sequencing. The obtained sequences were edited using BioEdit software (http://www.softpedia.com/get/Science-CAD/BioEdit.shtml). Primer Premier 5 software (http://primer-premier.softpedia.com/) was used to design IP1, IP2, and IP3 primers.

Urea-denaturing PAGE
The successfully designed SSR primers (designated as IP2 and IP3) were tested on a few accessions of G. mangostana collected from different locations in Peninsular Malaysia (Fig. 1) [1]. The PCR products amplified from these SSR primers were assayed on 8% PAGE gels run for 3 h at 60 V.