Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuumL.)

Abstract

A novel set of informative microsatellite markers for pepper (Capsicum annuum L.) is provided. Screening of approximately 168 000 genomic clones and 23 174 public database entries resulted in a total of 411 microsatellite-containing sequences that could be used for primer design and functional testing. A set of 154 microsatellite markers originated from short-insert genomic libraries and 257 markers originated from database sequences. Of those markers, 147 (61 from genomic libraries and 86 from database sequences) showed specific and scoreable amplification products and detected polymorphisms between at least 2 of the 33 lines of a test panel consisting of cultivated and wild Capsicum genotypes. These informative markers were subsequently surveyed for allelic variation and information content. The usefulness of the new markers for diversity and taxonomic studies was demonstrated by the construction of consistent phylogenetic trees based on the microsatellite polymorphisms. Conservation of a subset of microsatellite loci in pepper, tomato, and potato was proven by cross-species amplification and sequence comparisons. For several informative pepper microsatellite markers, homologous expressed sequence tag (EST) counterparts could be identified in these related species that also carry microsatellite motifs. Such orthologs can potentially be used as reference markers and common anchoring points on the genetic maps of different solanaceous species.

Mapping for Axillary Shooting, Flowering Date, Primary Axis Length, and Number of Leaves in Pepper (Capsicum annuum)

“…Amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) polymorphisms were scored according to Minamiyama et al (2006a). The SSR primer pairs used in this study were developed from genomic libraries and/ or databases by Huang et al (2001), Lee et al (2004), Minamiyama et al (2006a), Nagy et al (2007) and Yi et al (2006). We also developed new SSR markers from an expressed sequence tag (EST) database search.…”

“…Previously published SSR markers were used for the present mapping (Huang et al, 2001;Lee et al, 2004;Minamiyama et al, 2006aMinamiyama et al, , 2007Nagy et al, 2007;Yi et al, 2006). In addition, AFLP and some of the newly developed SSR markers were used.…”

Transferability and characterization of microsatellite markers in five Bromeliaceae species belonging to the subfamilies Pitcairnioideae and Bromelioideae

“…SSR markers can be transferred between related species and genera, which considerably reduces their costs (Ferreira & Grattaplaglia 1998). SSR transferability has been reported to many families of plants, including Fabaceaea (Peakall et al 1998, Kölliker et al 2001) Cucurbitaceae (Katzir et al 1996), Poaceae (Saghai Maroof et al 1994, Röder et al 1995, Thiel et al 2003, Solanaceae , Smulders et al 1997, Nagy et al 2007, Moon et al 2008; Euphorbiaceae (Yu et al 2011) and Bromeliaceae (Sarthou et al 2003, Paggi et al 2008. Thus, in this paper eight microsatellite markers previously developed for Pitcairnia albiflos and five markers developed for Pitcairnia geysksii were used in cross-amplification tests of five other neotropical Bromeliaceae species (Pitcairnia flammea, Aechmea nudicaulis, Aechmea ramosa, Billbergia horrida and Billbergia euphemiae).…”

Novel and highly informative Capsicum SSR markers and their cross-species transferability

“…Several reports describe the development of microsatellite markers for use in genetic studies of Capsicum (Sanwen et al, 2000;Lee et al, 2004;Minamiyama et al, 2006;Yi et al, 2006;Nagy et al, 2007;Portis et al, 2007;Kong et al, 2012;Sugita et al, 2013). However, it can be noted that the number of publicly available molecular markers based on polymerase chain reaction (PCR) for peppers, including SSR markers, is still limited.…”