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Geographical description and molecular characterization of genetic structure and diversity using a 6K SNP array in Turkish oat germplasm

Cömertpay, Gönül, Habyarimana, Ephrem, Baloch, Faheem Shehzad, Güngör, Hüseyin, Dokuyucu, Tevrican, Akkaya, Aydın, Dumlupinar, Ziya
Canadian journal of plant science 2018 v.99 no.1 pp. 12-21
Avena sativa, algorithms, cultivars, gene banks, gene pool, genetic distance, genetic variation, genomics, germplasm, heterozygosity, inbreeding, inbreeding coefficient, kinship, landraces, oats, population structure, provenance, single nucleotide polymorphism, Turkey (country)
Cultivated oat (Avena sativa L. and Avena byzantina Koch) is native to Turkey, a secondary center of oat diversity. Oat breeding has received less attention relative to other cereals. In this work, the diversity of oat landraces collected from different regions of Turkey as well as obtained from different gene banks was investigated using 3293 high quality SNP markers. Expected heterozygosity (Hs), observed heterozygosity (Ho), inbreeding coefficient (Fis), and overall genetic diversity (Ht) of the oat gene pool were 0.22, 0.01, 0.96, and 0.38, respectively. The value of the genetic differentiation (Fst) metric for genetic structure was 0.41 and indicated that kinship was more of a determinant for population structure than the geographical provenance. The populations from different geographical regions shared a great proportion of genetic diversity. Clustering using model-based STRUCTURE, principal coordinates (PCoA), and neighbour-joining (NJ) algorithms were mostly comparable except for five discrepantly clustered accessions in NJ and PCoA relative to STRUCTURE, which can be attributed to the relatively reduced resolution power in the NJ and PCoA approaches. SNP markers partitioned all oat accessions into four main groups (A, B, C, and D) with 10 unclassified accessions. Some landraces were identical based on genetic distance and can represent duplications in gene banks. The data presented in this work represent the initial results on genetic diversity as investigated in Turkish oat, and are an important resource for systematicians, geneticists, and breeders interested in Turkish oat germplasm. These results are expected to open new opportunities for further studies in oat genomics and cultivar development.