Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea

Abstract

A sample of 15 cultivars and 56 Pisum accessions from the JIC germplasm core collection has been studied using a modi®cation of the SSAP (sequencespeci®c ampli®cation polymorphisms) technique; the speci®c primer was designed to correspond to the polypurine tract (PPT) of PDR1, a Ty1-copia group retrotransposon of pea. Most of these SSAP products were shown to be PDR1 derived. The PDR1 SSAP markers are more informative than previously studied AFLP or RFLP markers and are distributed throughout the genome. Their pattern of variation makes them ideal for integrating genetic maps derived from related crosses. Data sets obtained with AFLP and PDR1 SSAP markers were used to construct neighbour-joining trees and for principal component analysis. These data sets give greater resolution than hitherto available for the characterisation of variation within Pisum, showing that the genus has three main groups: P. fulvum, P. abyssinicum and all other Pisum spp. P. abyssinicum is not a subgroup of cultivated P. sativum, as was previously thought, but has probably been domesticated independently. Modern cultivars are shown to form a single group within Pisum as a whole.

Comparison of Genetic Structure Assessed by Amplified Fragment Length Polymorphism and Retrotransposon-based Sequence-specific Amplification Polymorphism for Portuguese Populations of Pinus pinea L.

“…The number of polymorphic SSAP fragments was about one and a half times that at AFLP ( Table 2). This result is in agreement with previous studies, for example, SSAP revealed two to threefold higher polymorphism per primer combination than AFLPs in Hordeum vulgare , Pisum (ELLIS et al, 1998), Triticum aestivum (QUEEN et al, 2004), and Anacardium occidentale (SYED et al, 2005). Moreover, SSAP was found to be the most informative system for estimating genetic diversity in tomato and pepper, in a study comparing SSAP with AFLP and SSR, producing about fourto nine-fold more polymorphic fragments than AFLP, and achieving the highest number of polymorphic bands per assay (MAY TAM et al, 2005).…”

“…Moreover, SSAP was found to be the most informative system for estimating genetic diversity in tomato and pepper, in a study comparing SSAP with AFLP and SSR, producing about fourto nine-fold more polymorphic fragments than AFLP, and achieving the highest number of polymorphic bands per assay (MAY TAM et al, 2005). In fact, one advantage of SSAP over AFLP is that higher levels of polymorphism are achieved (ELLIS et al, 1998), and fewer experiments are needed to generate the desired numbers of markers. SSAP generates more polymorphic markers than AFLP, probably due to the higher retrotransposition mutation rate relative to base mutation.…”

“…Moreover, retrotransposon markers generate taxonomic data that are more consistent with morphological criteria than AFLP-based markers (ELLIS et al, 1998). The reason for this is, yet, unclear, but according to QUEEN et al, (2004) it may reflect two facts.…”

“…Some studies have directly compared retrotransposon marker methods with AFLP, and they revealed that retrotransposon markers are more polymorphic than AFLP (e.g. ELLIS et al, 1998;MAY TAM et al, 2005;SYED et al, 2005;QUEEN et al, 2004;e.g. WAUGH et al, 1997;YU and WISE, 2000).…”

Survey of transposable elements in sugarcane expressed sequence tags (ESTs)

“…Recently, reports were published evaluating the utility of TEs as source to develop molecular markers showing that TEs are highly polymorphic in terms of insertion sites and their internal structure (Ellis et al, 1998). Furthermore, TE-derived markers efficiently distinguished rice cultivars (Fukuchi et al, 1993).…”