Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato

Abstract

Characterization of nearly 1,000 cultivated potato accessions with simple sequence repeats (SSRs; also referred to as microsatellites) has allowed the identification of a reference set of SSR markers for accurate and efficient genotyping. In addition, 31 SSRs are reported here for a potato genetic map, including new map locations for 24 of them. A first criterion for this proposed reference set was ubiquity of the SSRs in the eight landrace cultivar groups of the potato, Solanum tuberosum. All SSRs tested in the present study displayed the same allele phenotypes and allele size range in the diverse germplasm set as in the advanced potato cultivar germplasm in which they were originally discovered. Thirteen of 13 SSR products from all cultivar groups are shown to cross-hybridize with the corresponding SSR product of the source cultivar to ascertain sequence homology. Other important SSR selection criteria are quality of amplification products, locus complexity, polymorphic index content, and well-dispersed location on a potato genetic map. Screening of 156 SSRs allowed the identification of a highly informative and userfriendly set comprising 18 SSR markers for use in characterization of potato genetic resources. In addition, we have identified true-and pseudo-multiplexing SSRs for even greater efficiency.

The single Andigenum origin of Neo-Tuberosum potato materials is not supported by microsatellite and plastid marker analyses

“…The three Andigenum-based breeding controls falling in the Andigenum cluster and the fact that the SSR alleles are widely dispersed neutral markers not chosen for linkage to Chilotanum traits (Ghislain et al 2004) validate this conclusion based on the analysis of the SSRs and the plastid marker.…”

“…DNA dilutions were performed to achieve a Wnal concentration of 3 ng/ l using 96-well plates. We used 24 SSR markers from a new Potato Genetic Identity kit (Table 1; paper under review; Herrera et al 2006) that updates one by Ghislain et al (2004). PCR reactions were performed and carried out as described in Spooner et al (2007).…”

“…We assessed this base broadening with a representative sample from the CIP potato collection that is currently grown world wide including Neo-Tuberosum original clones, and their derivatives. We assessed overall diversity with simple sequence repeats (SSRs or microsatellites) that represent a reWnement (paper in review; Herrera et al 2006) of a set of SSR markers chosen to represent all 12 potato linkage groups, highly polymorphic and with no selected function (Ghislain et al 2004). To assess maternal contributions of Andean and Chilean germplasm we also screened these materials with a 241-bp plastid deletion marker in the trn V-UAC/ndhC intergenic region of the plastid DNA molecule, which is absent in 94% (or 95%) of the Andean tetraploid landraces and present in 86% (or 81%) of the tetraploid Chilean landraces, depending on the studies of Hosaka (2004) or Spooner et al (2007).…”

Genetic analysis of the cultivated potato Solanum tuberosum L. Phureja Group using RAPDs and nuclear SSRs

“…DNA extraction, microsatellite primers, and PCR conditions Genomic DNA was obtained using standard protocols used at CIP (Ghislain et al 1997). Its concentration was estimated by visually comparing the intensity of undigested genomic DNA with of the upper band (11,490 bp) of 1 g of DNA (Gibco-BRL, Gaithersburg, MD, USA) digested with PstI (equivalent to 280 ng) and subjected to electrophoresis on a 1% agarose gel stained with ethidium bromide.…”

“…Its concentration was estimated by visually comparing the intensity of undigested genomic DNA with of the upper band (11,490 bp) of 1 g of DNA (Gibco-BRL, Gaithersburg, MD, USA) digested with PstI (equivalent to 280 ng) and subjected to electrophoresis on a 1% agarose gel stained with ethidium bromide. We have used the potato genetic identiWcation (PGI) kit described in Ghislain et al 2004. The primers and ampliWcation conditions used in the present study are listed in Table 2.…”