title: Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data.
abstract: Effective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine inter-primer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon- and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.
authors.affiliation: Eastern Mediterranean Agricultural Research Institute, Doğankent, Adana, Turkey.
authors.forename: G
authors.initials: G
authors.lastname: Cömertpay
authors.affiliation: Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant Izzet Baysal University, Bolu, Turkey.
authors.forename: F S
authors.initials: FS
authors.lastname: Baloch
authors.affiliation: Department of Biotechnology, University of Çukurova, Adana, Turkey.
authors.forename: M
authors.initials: M
authors.lastname: Derya
authors.affiliation: Department of Biotechnology, University of Çukurova, Adana, Turkey.
authors.forename: E E
authors.initials: EE
authors.lastname: Andeden
authors.affiliation: Department of Biotechnology, University of Çukurova, Adana, Turkey.
authors.forename: A
authors.initials: A
authors.lastname: Alsaleh
authors.affiliation: Thrace Agricultural Research Institute, Edirne, Turkey.
authors.forename: H
authors.initials: H
authors.lastname: Sürek
authors.affiliation: Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey.
authors.forename: H
authors.initials: H
authors.lastname: Özkan
mesh_terms: D000483:Alleles; D001665:Binding Sites; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D018895:Microsatellite Repeats; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D000069600:Plant Breeding; D018626:Retroelements; D014421:Turkey
chemical_list: D017931:DNA Primers; D005819:Genetic Markers; D018626:Retroelements