Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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Author: search.filters.author.Çelik, İbrahimScopus Q: search.filters.scopusQuartile.Q2

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  • Article
    Citation - WoS: 40
    Citation - Scopus: 46
    Genome-Wide Snp Discovery and Qtl Mapping for Fruit Quality Traits in Inbred Backcross Lines (ibls) of Solanum Pimpinellifolium Using Genotyping by Sequencing
    (BioMed Central Ltd., 2017) Çelik, İbrahim; Gürbüz, Nergiz; Uncu, Ali Tevfik; Frary, Anne; Doğanlar, Sami
    Background: Solanum pimpinellifolium has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of S. pimpinellifolium requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection. Results: In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and S. pimpinellifolium (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified. S. pimpinellifolium contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species. Conclusions: The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from S. pimpinellifolium (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population.
  • Article
    Citation - WoS: 9
    Citation - Scopus: 8
    Morphological and Molecular Diversity in Turkish Sesame Germplasm and Core Set Selection
    (Crop Science Society of America, 2015) Frary, Anne; Tekin, Pelin; Çelik, İbrahim; Furat, Şeymus; Uzun, Bülent; Doğanlar, Sami
    The conservation of plant germplasm is essential to ensure future breeding gains and crop bio-diversity. To be truly useful, such germplasm must be characterized for morphological traits and genetic diversity. In this work, agro-morphological diversity was assessed in 137 Turkish sesame (Sesamum indicum L.) genotypes (129 accessions and eight cultivars) by examination of eight qualitative and nine quantitative traits. As expected, morphological variability in the cultivars was low with broader diversity present in sesame accessions. However, some accessions were identified with interesting features, such as increased number of capsules and seed yield, which could be employed in future cultivar development. The sesame genotypes were analyzed for molecular genetic diversity with 140 amplified fragment length polymorphism (AFLP) loci. The results indicated a relatively low level of variability with an average dissimilarity value of 0.33 for all genotypes. Population structure was also examined and indicated that the material fell into two subpopulations. As most of the accessions (82%) were obtained from the U.S. Department of Agriculture (USDA) and are not yet housed in the Turkish national sesame germplasm collection, the data were used to identify a core set of 22 accessions that should be preserved in Turkey. The importance of using both molecular and morphological data for core selection is highlighted with a focus on germplasm preservation and breeding. © Crop Science Society of America