Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - WoS: 20Citation - Scopus: 24Newly Developed Ssr Markers Reveal Genetic Diversity and Geographical Clustering in Spinach (spinacia Oleracea)(Springer Verlag, 2017) Göl, Şurhan; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnneSpinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.Article Citation - WoS: 6Citation - Scopus: 5Development of Genomic Simple Sequence Repeat Markers in Faba Bean by Next-Generation Sequencing(Springer Verlag, 2017) Abuzayed, Mazen A.; Göktay, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnneFaba bean (Vicia faba L.) is an important food legume crop with a huge genome. Development of genetic markers for faba bean is important to study diversity and for molecular breeding. In this study, we used Next Generation Sequencing (NGS) technology for the development of genomic simple sequence repeat (SSR) markers. A total of 14,027,500 sequence reads were obtained comprising 4,208 Mb. From these reads, 56,063 contigs were assembled (16,367 Mb) and 2138 SSRs were identified. Mono and dinucleotides were the most abundant, accounting for 57.5 % and 20.9 % of all SSR repeats, respectively. A total of 430 primer pairs were designed from contigs larger than 350 nucleotides and 50 primers pairs were tested for validation of SSR locus amplification. Nearly all (96 %) of the markers were found to produce clear amplicons and to be reproducible. Thirty-nine SSR markers were then applied to 46 faba bean accessions from worldwide origins, resulting in 161 alleles with 87.5 % polymorphism, and an average of 4.1 alleles per marker. Gene diversity (GD) of the markers ranged from 0 to 0.48 with an average of 0.27. Testing of the markers showed that they were useful in determining genetic relationships and population structure in faba bean accessions.Article Citation - WoS: 15Citation - Scopus: 18Molecular Diversity and Identification of Alleles for Verticillium Wilt Resistance in Elite Cotton (gossypium Hirsutum L.) Germplasm(Springer Verlag, 2017) Akköse Baytar, Asena; Erdoğan, Oktay; Frary, Anne; Frary, Amy; Doğanlar, SamiCotton is an important crop in the textile, food and pharmaceutical industries. In the present study, a panel of 108 elite cotton (Gossypium hirsutum L.) lines was genotyped with 177 genome-wide SSR markers to assess genetic diversity, linkage disequilibrium, population structure and association analyses. A total of 967 loci were assayed and the lines fell into four main groups with a mean genetic distance of 39%. The linkage disequilibrium (LD) decay rate was estimated to be 20–30 cm (r2 ≤ 0.5). Association analyses were performed with both general linear model and mixed linear model methods to identify SSR marker loci linked to Verticillium wilt resistance. Verticillium wilt is a fungal disease that causes huge yield losses in cotton production throughout the world. A total of 26 marker loci distributed on 14 chromosomes were associated with resistance at p ≤ 0.05. Eight of the 26 associated marker loci were highly significant (p < 0.01). The phenotypic variation explained (r2) by individual markers ranged from 3.2% to 8.2%. Three of the 26 marker loci (JESPR153, JESPR274 and CIR218) were consistent with previous studies. Our results should be useful in improving Verticillium wilt resistance in cotton breeding lines.Article Citation - WoS: 1Citation - Scopus: 1Genetic Diversity and Population Structure of Faba Bean (vicia Faba) From Turkey(American Society for Horticultural Science, 2016) Göl, Şurhan; Doğanlar, Sami; Frary, AnneFaba bean (Vicia faba L.) is an important food and feed legume because of the nutritional value of its seed protein and starch content, good biomass, and high efficiency nitrogen fixation.This study analyzed the molecular genetic diversity and population structure of 101 Turkish faba bean accessions using simple sequence repeat (SSR) markers.A total of 32 SSR markers yielded 281 loci of which 277 (98.6%) were polymorphic.Mean dissimilarity between genotypes was 0.355, a relatively high value which was expected given faba bean’s large genome and limited breeding history.According to the results, faba bean individuals grouped into three main clusters based on both distance matrix (neighbor-joining algorithm) and model-based (population structure) clustering analyses.Clustering was not correlated with seed size or origin within Turkey.Six cultivars were included in the analysis and showed high genetic diversity compared with the landraces, as expected, given the fact that at least some of the cultivars were bred by hybridization.A total of 47 individuals were selected for the core collection to represent the diversity of Turkish faba bean germplasm.This core set encompasses material adapted to all growing regions and should be a priority for morphological characterization. © 2016, American Society for Horticultural Science.All rights reserved.Article Citation - WoS: 9Citation - Scopus: 8Morphological 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, SamiThe 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 AmericaArticle Citation - WoS: 27Citation - Scopus: 31Development of Genomic Simple Sequence Repeat Markers in Opium Poppy by Next-Generation Sequencing(Springer Verlag, 2014) Çelik, İbrahim; Gültekin, Visam; Allmer, Jens; Doğanlar, Sami; Frary, AnneOpium poppy (Papaver somniferum L.) is an important pharmaceutical crop with very few genetic marker resources. To expand these resources, we sequenced genomic DNA using pyrosequencing technology and examined the DNA sequences for simple sequence repeats (SSRs). A total of 1,244,412 sequence reads were obtained covering 474 Mb. Approximately half of the reads (52 %) were assembled into 166,724 contigs representing 105 Mb of the opium poppy genome. A total of 23,283 non-redundant SSRs were identified in 18,944 contigs (11.3 % of total contigs). Trinucleotide and tetranucleotide repeats were the most abundant SSR repeats, accounting for 49.0 and 27.9 % of all SSRs, respectively. The AAG/TTC repeat was the most abundant trinucleotide repeat, representing 19.7 % of trinucleotide repeats. Other SSR repeat types were AT-rich. A total of 23,126 primer pairs (98.7 % of total SSRs) were designed to amplify SSRs. Fifty-three genomic SSR markers were tested in 37 opium poppy accessions and seven Papaver species for determination of polymorphism and transferability. Intraspecific polymorphism information content (PIC) values of the genomic SSR markers were intermediate, with an average 0.17, while the interspecific average PIC value was slightly higher, 0.19. All markers showed at least 88 % transferability among related species. This study increases sequence coverage of the opium poppy genome by sevenfold and the number of opium poppy-specific SSR markers by sixfold. This is the first report of the development of genomic SSR markers in opium poppy, and the genomic SSR markers developed in this study will be useful in diversity, identification, mapping and breeding studies in opium poppy.Article Citation - WoS: 24Citation - Scopus: 26Development of Est-Ssr Markers for Diversity and Breeding Studies in Opium Poppy(John Wiley and Sons Inc., 2013) Şelale, Hatice; Çelik, İbrahim; Gültekin, Visam; Allmer, Jens; Doğanlar, Sami; Frary, AnneAll publicly available opium poppy expressed sequence tag (EST) sequences, totalling 20 885, were assembled into unigenes and examined for simple sequence repeats (SSRs). Nearly 19% of the 14 957 unigenes contained SSRs with 4% harbouring more than one SSR. Average density of the SSRs was 1 SSR per 3.6 kb of non-redundant EST sequence. Trinucleotide SSRs were most frequently identified (39%), and many of the most prevalent motifs were AT-rich. Flanking primers were designed for 86% of the SSRs and 67 primer pairs were tested on 37 opium poppy accessions and seven related species. All markers were transferable to the related species. Polymorphism information content (PIC) values for the markers were intermediate for comparisons within opium poppy (average of 0.27) and slightly higher for comparisons across species (average of 0.29). The markers were found to be useful for diversity analysis as they successfully distinguished among Turkish opium poppy accessions and land races.