1. Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data
- Author
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Ahmad Alsaleh, Enver Ersoy Andeden, Muazzez Derya, Sürek H, Gönül Cömertpay, Faheem Shehzad Baloch, Hakan Özkan, Çukurova Üniversitesi, BAİBÜ, Ziraat Fakültesi, Tarla Bitkileri Bölümü, and Baloch, Faheem Shehzad
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetic Markers ,Genotype ,Retroelements ,Turkey ,Population structure ,Retrotransposon ,Locus (genetics) ,iPBS-Retrotransposon ,Biology ,Bioinformatics ,01 natural sciences ,03 medical and health sciences ,Genetics ,Cluster Analysis ,Rice variety ,Allele ,Molecular Biology ,Alleles ,Phylogeny ,DNA Primers ,Genetic diversity ,Rice Variety ,Oryza sativa ,Binding Sites ,Rice Diversity ,food and beverages ,Genetic Variation ,Oryza ,General Medicine ,Sequence repeat ,SSR ,Plant Breeding ,030104 developmental biology ,Genetics, Population ,iPBS-retrotransposon ,Rice diversity ,Primer binding site ,010606 plant biology & botany ,Microsatellite Repeats - Abstract
WOS:000373880200020 PubMed: 26909982 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 interprimer 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.
- Published
- 2016