title: Genotyping by Sequencing (GBS) in Apricots and Genetic Diversity Assessment with GBS-Derived Single-Nucleotide Polymorphisms (SNPs).
abstract: Genotyping by sequencing (GBS), which is a highly promising technique for molecular breeding, has been implemented in apricots, including Turkish, European, and Plum Pox Virus-resistant accessions. DNA samples were digested with the ApeKI restriction enzyme to construct a genome-complexity-reduced 90-plex GBS library. After filtering the raw sequences, approximately 28 G of clean data were generated, and 17,842 high-quality single-nucleotide polymorphism (SNP) loci were discovered. A total of 561 SNP loci with 0 or 1 missing reads for the 90 accessions produced 1162 markers that were used for the cluster and population structure analysis of the same collection. The results of the SNP analysis indicated that the relation of the European accessions with the western Turkish apricots was accurately positioned. The resistant accessions from different sources were clustered together, confirming the previous finding that SEO/Harlayne-type resistance probably originated from the same source. The Malatya accessions produce most of the world's dried apricots and are likely to be a genetically distinct group. Simple sequence repeat (SSR) and self-incompatibly (SI) locus characterization of the accessions was also included. SI genotyping supported the SNP findings, demonstrating both the reliability of SNP genotyping and the usefulness of SI genotyping for understanding the history of apricot breeding. The SSR genotyping revealed a characterization similar to that of SNP genotyping with a slightly lower resolution in the dendrogram. In conclusion, the GBS approach was validated in apricots, with the discovery of a large number of SNPs, and was demonstrated to be reliable by fingerprinting the accessions in a more informative manner.
authors.affiliation: Genome and Stem Cell Research Center, Erciyes University, Kayseri, Turkey. kgurcan@erciyes.edu.tr.|Department of Agricultural Biotechnology, Erciyes University, Kayseri, Turkey. kgurcan@erciyes.edu.tr.
authors.forename: Kahraman
authors.initials: K
authors.lastname: Gürcan
authors.affiliation: Genome and Stem Cell Research Center, Erciyes University, Kayseri, Turkey.|Department of Agricultural Biotechnology, Erciyes University, Kayseri, Turkey.
authors.forename: Saffet
authors.initials: S
authors.lastname: Teber
authors.affiliation: Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey.
authors.forename: Sezai
authors.initials: S
authors.lastname: Ercisli
authors.affiliation: Department of Horticulture, Erciyes University, Kayseri, Turkey.
authors.forename: Kadir Uğurtan
authors.initials: KU
authors.lastname: Yilmaz
mesh_terms: D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D060467:Disease Resistance; D060005:Genotyping Techniques / Q000379:methods*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D000068219:Prunus armeniaca / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant
keywords: Genetic diversity; Self-incompatibility; Simple sequence repeats; Stone fruits