Characterization of dinucleotide and trinucleotide EST-derived microsatellites in the wheat genome |
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Authors: | Agata Gadaleta Giacomo Mangini Giuseppina Mulè Antonio Blanco |
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Institution: | (1) Department of Agro-Forestry and Environmental Biology and Chemistry, University of Bari, Via Amendola 165/A, 70126 Bari, Italy;(2) Institute of Sciences of Food Production, National Research Council (CNR), 70126 Bari, Italy |
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Abstract: | Over the past decade microsatellites or simple sequence repeats (SSRs) have attracted a considerable amount of attention from
researchers. The aim of the present paper was to analyse expressed sequence tag-derived SSR (EST-SSR) marker variability in
wheat and to investigate the relationships between the number and type of repeat units and the level of microsatellite polymorphism.
Two hundred and forty-one new EST-SSR markers available in a public database () were characterized in eight durum wheat cultivars (Svevo, Ciccio, Primadur, Duilio, Meridiano, Claudio, Latino, Messapia),
two accessions of Triticum turgidum var. dicoccoides (MG4343, MG29896), one accession of T. turgidum var. dicoccum (MG5323) and in the common wheat cv. Chinese Spring. Of these, 201 primer pairs (83.4%) amplified PCR products successfully,
while the remaining 40 (16.6%) failed to amplify any product. Of the EST-SSRs analysed, 45.2% of the primer pairs amplified
one or two PCR products. Multiple discrete PCR products were observed among both di- and trinucleotide EST-SSR markers (31.2
and 40.5%, respectively). Markers based on dinucleotide microsatellites were more polymorphic than those based on trinucleotide
SSRs in the 12 wheat genotypes tested (68.9 and 52.7%, respectively). An average of 2.5 alleles for dinucleotide and 2.0 alleles
for trinucleotide SSRs was observed. The data reported in the present work indicate the presence of a significant relationship
between motif sequence types and polymorphism. The primer set based on the AG repeat motif showed the lowest percentage of
polymorphism (55.0%), while the primer set based on the AC repeat motif showed t he highest percentage (85.0%). Among trinucleotide
SSRs, the AGG microsatellite markers showed the highest percentage of polymorphism (70.0%), and the ACG motif the lowest value
(25.0%). The characterization of these new EST-SSR markers and the results of our studyon the effect of repeat number and
type of motifs could have important applications in the genetic analysis of agronomically important traits, quantitative trait
locus discovery and marker-assisted selection. |
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Keywords: | EST-SSR Microsatellites Molecular markers Wheat |
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