Target Region Amplification Polymorphism (TRAP) as a Tool for Detecting Genetic Variation in the Genus Pelargonium

Abstract

<jats:p> <jats:italic>Pelargonium</jats:italic> was a priority genera collected by the Ornamental Plant Germplasm Center (OPGC) until a recent reorganization. To preserve genetic diversity for future breeders, OPGC collects heirloom cultivars, breeding lines, and wild species. The current <jats:italic>Pelargonium</jats:italic> collection at OPGC consists primarily of cultivars originating from <jats:italic>P. ×hortorum</jats:italic> and <jats:italic>P. ×domesticum</jats:italic>. Target region amplification polymorphism (TRAP) has the advantage of producing a large number of markers through use of sequence information that is already available. Our first goal was to determine the feasibility of TRAP for the analysis of this large collection, so that in the future the most diverse genotypes may be retained. To achieve this goal, we first modified existing DNA extraction techniques to account for the high levels of phenolic compounds present in some <jats:italic>Pelargonium</jats:italic> species by combining several washes to remove the phenolics with the addition of high levels of antiphenolic compounds. Second, we evaluated the TRAP procedure using the DNA isolated from 46 accessions. For 44 accessions, one or two primer combinations generated enough fragments to discriminate each of the accessions, and similar clades were produced by cluster analysis of the polymorphic fragments amplified by different primer combinations. All the scorable fragments were polymorphic, for one primer combination there were 148 markers from one image and the other produced 160 markers on two images. These results demonstrate that TRAP is an effective method for molecular characterization of ornamental collections.</jats:p>

Construction of Soybean Mutant Diversity Pool (MDP) Lines and an Analysis of Their Genetic Relationships and Associations Using TRAP Markers

“…In the rapid, efficient PCR-based TRAP marker system, expressed sequence tag database information and bioinformatics tools are used to generate polymorphic markers around targeted candidate gene sequences. Previous studies of lettuce (Lactuca sativa) [34], sugarcane (Saccharum officinarum) [35], spinach (Spinacia oleracea) [29], geranium (Pelargonium inquinans) [36], sunflower (Helianthus annuus) [37], and faba beans (Vicia faba) [16] have demonstrated that TRAP markers are useful for assessing genetic diversity. Using this system in the present study, we PCR-amplified 551 fragments with 16 primer combinations and observed considerable variation in the percentage of polymorphic amplicons among primer pairs-from 32.35% to 84.00% (Table 4).…”

Comparative analysis on the diversity of Auricularia auricula-judae by physiological characteristics, somatic incompatibility and TRAP fingerprinting

“…It uses a fixed primer of about 18 nucleotides, which is designed from the target-expressed sequence tag (EST) or gene sequence, as well as an arbitrary primer of about the same length, with either an AT or GC-rich core to anneal with an intron or exon, respectively (Hu and Vick 2003). As a simple yet powerful technique for estimating genetic diversity, TRAP has been successfully used for sugarcane, sunflower, Porphyra, Pelargonium, lettuce, and Spinacia oleracea germplasm diversity (Alwala et al 2006;Yue et al 2009;Qiao et al 2007;Palumbo et al 2007;Hu et al 2005;Hu et al 2007). Although TRAP has been introduced into fungi and proved to be reliable for analyzing genetic diversity of Lentinula edodes in China (Xiao et al 2010b), it was for the first time adopted in the present study for analyzing the diversity of A. auricula-judae.…”

Genetic diversity and relationship among faba bean (Vicia faba L.) germplasm entries as revealed by TRAP markers

“…TRAP uses a fixed primer designed against the known DNA gene sequence and pairs it with arbitrary primers that target the intron or exon regions with an AT-rich or GC-rich core (Li and Quiros, 2001) to amplify the DNA fragments. Published studies applying TRAP to lettuce (Hu et al , 2005), sugarcane (Alwala et al , 2006), Geranium (Palumbo et al , 2007), spinach (Hu et al , 2007) and sunflower (Yue et al , 2009) have suggested that TRAP is a useful marker system for germplasm diversity assessments. The objective of this study was to evaluate the usefulness of TRAP in revealing genetic diversity at both population and individual levels.…”