title: Characterization of wheat DArT markers: genetic and functional features.
abstract: Diversity array technology (DArT) markers are largely used for mapping, genetic diversity, and association mapping studies. For years, they have been used as anonymous genomic markers, as their sequences were not known. As the sequences of 2,000 wheat DArT clones are now available, this study was designed to analyze these sequences with bioinformatic approaches, and to study the genetic features of a subset of 291 markers positioned on the A and B genomes in three durum wheat genetic maps. A set of 1,757 non-redundant sequences was identified, and used as queries for similarity searches. Analysis of the genetic positions of markers corresponding to nearly identical sequences indicates that redundancy of sequences is one of the factors that explains the clustering of these markers in specific genomic regions. Of a total of 1,124 DArT clones (64 %) that represent putatively expressed sequences, putative functions are proposed for more than 700 of them. Of note, many clones correspond to genes that are related to disease resistance, as characterized by leucine-rich repeat domains, and 40 of these clones are positioned in the three genetic maps presented in this study. Finally, DArT markers have been used to find syntenic regions in the Brachypodium and rice genomes. In conclusion, the analyses herein presented contribute to explain the main features of DArT markers observed in genetic maps, as clustering in short chromosome regions. Moreover, the attribution of putative gene functions for more than 700 sequences makes these markers an optimal tool for collinearity studies or for the identification of candidate genes.
authors.affiliation: CRA, Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Marone
authors.forename: Giosuè
authors.initials: G
authors.lastname: Panio
authors.forename: Donatella B M
authors.initials: DB
authors.lastname: Ficco
authors.forename: Maria A
authors.initials: MA
authors.lastname: Russo
authors.forename: Pasquale
authors.initials: P
authors.lastname: De Vita
authors.forename: Roberto
authors.initials: R
authors.lastname: Papa
authors.forename: Diego
authors.initials: D
authors.lastname: Rubiales
authors.forename: Luigi
authors.initials: L
authors.lastname: Cattivelli
authors.forename: Anna M
authors.initials: AM
authors.lastname: Mastrangelo
mesh_terms: D001483:Base Sequence; D058431:Brachypodium / Q000235:genetics; D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers