title: In silico search, characterization and validation of new EST-SSR markers in the genus Prunus.
abstract: BACKGROUND
  Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight Prunus species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions.
  
  
  RESULTS
  A total of 316 SSRs were identified using MISA software. Dinucleotide SSR motifs (26.31 %) were found to be the most abundant type of repeats, followed by tri- (14.58 %), tetra- (0.53 %), and penta- (0.27 %) nucleotide motifs. An attempt was made to design primer pairs for 316 identified SSRs but these were successful for only 175 SSR sequences. The positions of SSRs with respect to ORFs were detected, and annotation of sequences containing SSRs was performed to assign function to each sequence. SSRs were also characterized (in terms of position in the reference genome and associated gene) using the two available Prunus reference genomes (mei and peach). Finally, 38 SSR markers were validated across peach, almond, plum, and apricot genotypes. This validation showed a higher transferability level of EST-SSR developed in P. mume (mei) in comparison with the rest of species analyzed.
  
  
  CONCLUSIONS
  Findings will aid analysis of functionally important molecular markers and facilitate the analysis of genetic diversity.
authors.affiliation: Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran.
authors.forename: Karim
authors.initials: K
authors.lastname: Sorkheh
authors.affiliation: Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100, Espinardo-Murcia, Spain.
authors.forename: Angela S
authors.initials: AS
authors.lastname: Prudencio
authors.affiliation: Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran.
authors.forename: Azim
authors.initials: A
authors.lastname: Ghebinejad
authors.affiliation: Department of Agronomy, Faculty of Agriculture, Payame Noor University, P.O. Box. 19395-3697, Tehran, Iran.
authors.forename: Mehrana Kohei
authors.initials: MK
authors.lastname: Dehkordi
authors.affiliation: Department of Horticulture, Faculty of Agriculture, University of Ege, Bornova, 35100, Izmir, Turkey.
authors.forename: Deniz
authors.initials: D
authors.lastname: Erogul
authors.affiliation: Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100, Espinardo-Murcia, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Rubio
authors.affiliation: Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100, Espinardo-Murcia, Spain. pmartinez@cebas.csic.es.
authors.forename: Pedro
authors.initials: P
authors.lastname: Martínez-Gómez
mesh_terms: D003198:Computer Simulation; D018744:DNA, Plant / Q000235:genetics*; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant; D005838:Genotype; D018895:Microsatellite Repeats; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D016366:Open Reading Frames; D011110:Polymorphism, Genetic; D027861:Prunus / Q000145:classification / Q000235:genetics*; D012984:Software
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers
keywords: Breeding; EST-SSR; Functional domain marker; In silico analysis; Prunus; SSR mining