Robust and highly informative microsatellite-based genetic identity kit for potato

Abstract

The fingerprinting of 742 potato landraces with 51 simple sequence repeat (SSR, or microsatellite) markers resulted in improving a previously constructed potato genetic identity kit. All SSR marker loci were assayed with a collection of highly diverse landraces of all species of cultivated potato with ploidies ranging from diploid to pentaploid. Loci number, amplification reproducibility, and polymorphic information content were recorded. Out of 148 SSR markers of which 30 are new, we identified 58 new SSR marker locations on at least one of three potato genetic linkage maps. These results permitted the selection of a new potato genetic identity kit based on 24 SSR markers with two per chromosome separated by at least 10 cM, single locus, high polymorphic information content, and high quality of amplicons as determined by clarity and reproducibility. The comparison of a similarity matrix of 742 landraces obtained with the 24 SSR markers of the new kit and with the entire dataset of 51 SSR markers showed a high correlation (r = 0.94) by a Mantel test and even higher correlations (r = 0.99) regarding topological comparisons of major branches of a neighbor joining tree. This new potato genetic identity kit is able to discriminate 93.5% of the 742 landraces compared to 98.8% with 51 SSR markers. In addition, we made a marker-specific set of allele size standards that conveniently and unambiguously provide accurate sizing of all alleles of the 24 SSR markers across laboratories and platforms. The new potato genetic identity kit will be of particular utility to standardize the choice and allele sizing of microsatellites in potato and aid in collaborative projects by allowing cumulative analysis of independently generated data.

Analysis of genetic stability of in vitro propagated potato microtubers using DNA markers

“…Similarly, previously McGregor et al (2000) analysed 39 potato cultivars using RAPD, ISSR, AFLP and SSR markers and concluded AFLP is the best followed by a multi-locus SSR, RAPD, ISSRs and single locus SSR. Later, Ghislain et al (2009) developed robust and highly informative SSR markers for potato characterization and they were demonstrated in the present study to assess genetic stability. Moreover, in ours study ISSR and RAPD markers produced similar findings, however, due to high annealing temperature (Ta=55°C) and more specific PCR products of ISSR was given merit over RAPD (Ta=36°C).…”

“…Simple sequence repeat (SSR) analysis was carried out by SSR primers summarized in Supplementary Table 1. The PCR amplification was followed as original procedures of Ghislain et al (2009) described by Tiwari et al (2013) followed by analysis of PCR products as per the manufacturers' instruction in '3500 Genetic Analyzer' (Applied Biosystems, California, USA). Amplified fragment length polymorphism (AFLP) analysis was carried out according to the original protocol of Vos et al (1995) using primer sequences listed in Supplementary Table 2 as described in the AFLP® Plant Mapping Protocol in '3500 Genetic Analyzer' (Applied Biosystems).…”

Using SSR to Evaluate the Genetic Diversity of Potato Cultivars from Yunnan Province (SW China)

“…Other SSR sites have been found in the potato genome since then, including highly informative and user-friendly microsatellites (Ghislain et al, 2004). SSR markers have been used to identify French potato cultivars (Moisan-Thiery et al, 2005), discriminate potato germplasm in the INIA Chile breeding program (Mathias et al, 2007), develop a rapid SSR-based identification method for potato cultivars (Reid and Kerr, 2007), develop an SSR-based genetic identity kit for potato (Ghislain et al, 2009), and discriminate genetic relationships in Spanish potato cultivars (de Galarreta et al, 2011). This work has provided insights useful for germplasm management and discrimination of potato cultivars.…”

Allele dosage of PVY resistance genes in potato clones using molecular markers

“…After the adjustment of the DNA concentration, the microsatellite marker STI0003 was used, which is widely applied in the characterization of potato genotypes to confirm the quality of the DNA and prevent the occurrence of false negative results in PCR reactions, following the protocol described by Ghislain et al (2009).…”