Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

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Author: search.filters.author.Frary, AnneWoS Q: search.filters.wosQuartile.Q2

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Now showing 1 - 10 of 24
  • Article
    Citation - WoS: 5
    Citation - Scopus: 5
    De-Sealing Reverses Habitat Decay More Than Increasing Groundcover Vegetation
    (MDPI, 2023) Couch, Virginia; Salata, Stefano; Saygın, Nicel; Frary, Anne; Arslan, Bertan
    Modeling ecosystem services is a growing trend in scientific research, and Nature-based Solutions (NbSs) are increasingly used by land-use planners and environmental designers to achieve improved adaptation to climate change and mitigation of the negative effects of climate change. Predictions of ecological benefits of NbSs are needed early in design to support decision making. In this study, we used ecological analysis to predict the benefits of two NbSs applied to a university masterplan and adjusted our preliminary design strategy according to the first modeling results. Our Area of Interest was the IZTECH campus, which is located in a rural area of the eastern Mediterranean region (Izmir/Turkey). A primary design goal was to improve habitat quality by revitalizing soil. Customized analysis of the Baseline Condition and two NbSs scenarios was achieved by using local values obtained from a high-resolution photogrammetric scan of the catchment to produce flow accumulation and habitat quality indexes. Results indicate that anthropogenic features are the primary cause of habitat decay and that decreasing imperviousness reduces habitat decay significantly more than adding vegetation. This study creates a method of supporting sustainability goals by quickly testing alternative NbSs. The main innovation is demonstrating that early approximation of the ecological benefits of NbSs can inform preliminary design strategy. The proposed model may be calibrated to address specific environmental challenges of a given location and test other forms of NbSs.
  • Article
    Citation - WoS: 4
    Citation - Scopus: 4
    Mapping of Quantitative Trait Loci for the Nutritional Value of Fresh Market Tomato
    (Springer, 2023) Gürbüz Çolak, Nergiz; Tek Eken, Neslihan; Ülger, Mehmet; Frary, Anne; Doğanlar, Sami
    The incidence of many diseases, such as cancer, cardiovascular diseases, and diabetes, is associated with malnutrition and an unbalanced daily diet. Vegetables are an important source of vitamins and essential compounds for human health. As a result, such metabolites have increasingly become the focus of breeding programs. Tomato is one of the most popular components of our daily diet. Therefore, the improvement of tomato's nutritional quality is an important goal. In the present study, we performed targeted metabolic profiling of an interspecific Solanum pimpinellifolium x S. lycopersicum inbred backcross line (IBL) population and identified quantitative trait loci responsible for the nutritional value of tomato. Transgressive segregation was apparent for many of the nutritional compounds such that some IBLs had extremely high levels of various amino acids and vitamins compared to their parents. A total of 117 QTLs for nutritional traits including 62 QTLs for amino acids, 18 QTLs for fatty acids, 12 QTLs for water-soluble vitamins, and 25 QTLs for fat-soluble vitamins were identified. Moreover, almost 24% of identified QTLs were confirmed in previous studies, and 40 possible gene candidates were found for 18 identified QTLs. These findings can help breeders to improve the nutritional value of tomato.
  • Article
    Citation - WoS: 8
    Citation - Scopus: 8
    Association Analysis of Germination Level Cold Stress Tolerance and Candidate Gene Identification in Upland Cotton (gossypium Hirsutum L.)
    (Springer, 2022) Akköse Baytar, Asena; Peynircioğlu, Ceng; Sezener, Volkan; Frary, Anne; Doğanlar, Sami
    Cotton originated from ancestors in the Gossypium genus that grew in semi-desert habitats. As a result, it is adversely affected by low temperatures especially during germination and the first weeks of growth. Despite this, there are relatively few molecular studies on cold stress in cotton. This limitation may present a future breeding handicap, as recent years have witnessed increased low temperature damage to cotton production. Cold tolerance is a sustainable approach to obtain good production in case of extreme cold. In the present study, 110 Upland cotton (Gossypium hirsutum) genotypes were evaluated for cold tolerance at the germination stage. We identified vigorous genotypes with cold-related parameters that outperformed the panel’s average performance (x¯ = 76.9% CG, 83.9% CSI, 167.5 CWVI). Molecular genetic diversity analysis with 101 simple sequence repeat (SSR) markers yielding 416 loci was used to select tolerant genotypes that could be important materials for breeding this trait. A total of 16 marker-cold tolerance trait associations (p < 0.005) were identified with 10 of them having major effects (PVE > 10%). Based on the positions of these markers, candidate genes for cold tolerance in the G. hirsutum genome were identified. Three of these markers (BNL0569, CIR081 and CIR202) are important candidates for use in marker-assisted breeding for cold tolerance because they mapped to genes previously associated with cold tolerance in other plant species such as Arabidopsis thaliana, rice and tomato.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Molecular Mapping of Qtls for Fiber Quality Traits in Gossypium Hirsutum Multi-Parent Recombinant Inbred Lines
    (Springer, 2021) Akköse Baytar, Asena; Peynircioğlu, Ceng; Sezener, Volkan; Frary, Anne; Doğanlar, Sami
    Cotton is a valuable fiber crop which supplies raw material to more than 50 industries and is produced in more than 70 countries worldwide. The superiority of cotton fiber over other crops is primarily dependent on its quality. However, further improvements in fiber length and strength are required for modern processing technology and for cotton to maintain its position in the global market. Association mapping enables identification of QTLs controlling fiber quality-related traits which can be useful in cotton breeding. In the present study, we performed genetic diversity, linkage disequilibrium and association mapping analyses in 157 G. hirsutum multi-parent recombinant inbred lines using a total of 102 SSR markers. The population had depressed genetic variability (14%), a result of inbreeding of modern cotton genotypes. Despite this, we identified 11 significant and stable marker-trait associations for seed cotton yield, lint percentage, fiber length and fiber strength (p < 0.005). We also detected QTL co-localizations with positive and negative marker additive effects. Our results indicate that selection against negative alleles may be as important as selection for positive alleles. Analysis of the effects of allelic combinations at different QTLs revealed significant and stable marker clusters that can be selected for or against to provide maximum quality gains in cotton fiber quality.
  • Article
    Citation - WoS: 7
    Citation - Scopus: 10
    Association Mapping of Agro-Morphological Traits in European Hazelnut (corylus Avellana)
    (Springer, 2019) Frary, Amy; Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Balık, Selda Kayalak; Kızılcı, Gökhan; Doğanlar, Sami; Frary, Anne
    More than half of European hazelnut (Corylus avellana) production occurs in Turkey. Despite this dominance, the yield of Turkish cultivars has remained stagnant over the past 10years with Italian yield nearly double that in Turkey. This difference is due to Turkey's unique cultivation system; hazelnuts are grown in bushy clusters (ocak system), not as single trees. Current hazelnut breeding efforts are shifting toward the development of materials for single plant orchards which are much higher yielding; thus, there is a need to explore germplasm for relevant agro-morphological traits and to determine their genetic control. The objectives of this study were to examine data for 44 such traits in 390 hazelnut accessions: 16 cultivars, 232 landraces and 142 wild individuals from nine provinces in Turkey and to map the loci associated with these characteristics using simple sequence repeat markers. Comparison of cultivars, landraces and wild hazelnut accessions revealed the effects of domestication and selection on the crop and indicated that useful alleles for traits such as cropping and reduced alternate bearing may exist in the wild germplasm. A total of 145 quantitative trait loci (QTL) were detected with the largest proportions identified for involucre (26%) and inflorescence (14%) morphology. Several markers co-localized with more than one trait including markers for male catkin abundance which were shared with plant vigor and height. Similarly, markers for female flower abundance co-localized with suckering and alternate bearing. Such markers and their linked QTL should be studied in more detail as they might help breeders select for plant vigor, decreased suckering and increased flower production: traits which will be extremely useful for Turkey's transition to single plant orchards.
  • Article
    Citation - WoS: 18
    Citation - Scopus: 29
    Cry1ac-Mediated Resistance To Tomato Leaf Miner (tuta Absoluta) in Tomato
    (Springer Verlag, 2017) Şelale, Hatice; Dağlı, Fatih; Mutlu, Nedim; Doğanlar, Sami; Frary, Anne
    Tomato leaf miner (Tuta absoluta) is a major pest of tomato in regions with hot climates such as South America and the Mediterranean. This insect feeds on almost every part of the plant and forms galleries while feeding on the plant’s inner tissues. Thus, it can cause plant death and is costly and difficult to control with chemical sprays. In this study, we transferred a modified Bacillus thuringiensis cry1Ac gene to tomato plants via Agrobacterium tumefaciens mediated transformation. Introduction of the cry1Ac gene to the tomato genome was confirmed with PCR and Southern blot analysis in 12 independent events. Insertion sites of the transgene in the tomato genome were determined with TAIL-PCR (thermal asymmetric interlaced polymerase chain reaction) for four selected transgenic lines. Cry1Ac gene expression was verified at both the transcriptional and translational levels, with RT-qPCR and Western blot analyses, respectively. Expression of the Cry1Ac protein in tomato resulted in T. absoluta mortality rates of 38–100% depending on transgenic line. In addition, gallery formation was reduced in 57–100% of the transgenic plants. Moreover, it was found that a single copy of the gene in the hemizygous condition is sufficient to confer tolerance to leaf miner. This is the first reported development of tomato plants resistant to T. absoluta. These transgenic plants are promising for development of commercial tomato cultivars resistant to leaf miner, which will limit the use of environmentally harmful chemicals for control of this pest.
  • Article
    Citation - WoS: 17
    Citation - Scopus: 20
    Molecular Genetic Diversity of the Turkish National Hazelnut Collection and Selection of a Core Set
    (Springer Verlag, 2017) Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Kayalak Balık, Selda; Kızılcı, Gökhan; Duyar, Ömür; Doğanlar, Sami; Frary, Anne
    European hazelnut (Corylus avellana L.) is an economically and nutritionally important nut crop with wild and cultivated populations found throughout Europe and in parts of Asia. This study examined the molecular genetic diversity and population structure of 402 genotypes including 143 wild individuals, 239 landraces, and 20 cultivars from the Turkish national hazelnut collection using simple sequence repeat (SSR) markers. A total of 30 SSR markers yielded 407 polymorphic fragments. Diversity analysis of the Turkish hazelnut genotypes indicated that they fell into three subpopulations according to ad hoc statistics and neighbor-joining algorithm. Although all cultivars clustered together, they overlapped with the wild accessions and landraces. Thus, the dendrogram, principal coordinate, and population structure analyses suggest that they share the same gene pool. A total of 78 accessions were selected as a core set to encompass the molecular genetic and morphological diversity present in the national collection. This core set should have priority in preservation efforts and in trait characterization.
  • Article
    Citation - WoS: 30
    Citation - Scopus: 36
    Molecular Genetic Diversity and Association Mapping of Nut and Kernel Traits in Slovenian Hazelnut (corylus Avellana) Germplasm
    (Springer Verlag, 2017) Öztürk, Süleyman Can; Öztürk, Saniye Elvan; Çelik, İbrahim; Stampar, Franci; Veberic, Robert; Doğanlar, Sami; Solar, Anita; Frary, Anne
    European hazelnut (Corylus avellana L.), cultivated in several areas of the world including Europe, Anatolia, and the USA, is an economically important nut crop due to its high mineral, oleic acid, amino acid, and phenolic compound content and pleasant flavor. This study examined molecular genetic diversity and population structure of 54 wild accessions and 48 cultivars from the Slovenian national hazelnut collection using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Eleven AFLP primer combinations and 49 SSR markers yielded 532 and 504 polymorphic fragments, respectively. As expected for a wind-pollinated, self-incompatible species, levels of genetic diversity were high with cultivars and wild accessions having mean dissimilarity values of 0.50 and 0.60, respectively. In general, cultivars and wild accessions clustered separately in dendrogram, principal coordinate, and population structure analyses with regional clustering of the wild material. The accessions were also characterized for ten nut and seven kernel traits and some wild accessions were shown to have breeding potential. Morphological principal component analysis showed distinct clustering of cultivars and wild accessions. An association mapping panel composed of 64 hazelnut cultivars and wild accessions had considerable variation for the nut and kernel quality traits. Morphological and molecular data were associated to identify markers controlling the traits. In all, 49 SSR markers were significantly associated with nut and kernel traits [P < 0.0001 and LD value (r2) = 0.15–0.50]. This work is the first use of association mapping in hazelnut and has identified molecular markers associated with important quality parameters in this important nut crop.
  • Article
    Citation - WoS: 15
    Citation - Scopus: 18
    Molecular 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, Sami
    Cotton 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: 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.