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: 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.