Browsing by Author "Yildiz, Mehtap"

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Analysis of Genetic Diverity Among Different Melon Accessions Using Peroxidase Gene Markers
(Parlar Scientific Publications (p S P), 2020) Kocak, Metin; Turan, Sibel; Erdinc, Ceknas; Yildiz, Mehtap
Plant peroxidases encoded by a broad multi gene family have important roles in many physiological events such as salt tolerance, auxin metabolism, seeding, protection against pathogens and oxidative stress. In this study the genetic diversity and population structure of 45 different melon (Cucumis melo L.) genotypes from a variety of regions in Turkey and different countries were investigated using peroxidase gene polymorphism markers. 12 polymorphic primers were used to obtain 97 scorable bands for the 45 melon genotypes. Of these bands, only 62.9% were determined to be polymorphic. The number of bands per primer ranged from 6 to 11 and the average number of bands was 8.08. The lowest and the highest polymorphism information contents (PIC) were 0.49 (Pox 12 FaRa) and 0.99 (Pox 13), respectively. The mean PIC value was 0.75. The lowest genetic similarity was found between CU-365 (conomon) and CU-247 (0.143), on the other hand, the highest genetic similarity was observed between CU-360 (cantalopensis) and CU-389 (cantalopensis) (0.875). Using the STRUCTURE computer program, all melon accessions were determined to separate into two subpopulations. These results support the usability of the PDX gene marker system in genetic diversity studies. Also, the data obtained are considered to be a guide for other studies to be performed on melons in the future.
Application of Ipbs-Retrotransposons Markers for the Assessment of Genetic Diversity and Population Structure Among Sugar Beet (Beta Vulgaris) Germplasm From Different Regions of the World
(Springer, 2025) Sadik, Gokhan; Yildiz, Mehtap; Taskin, Bilgin; Kocak, Metin; Cavagnaro, Pablo Federico; Baloch, Faheem Shehzad
Sugar beet is an important agricultural crop product that has been produced and consumed worldwide since the eighteenth century and can adapt to various climatic and soil conditions. The two fundamental building blocks of any crop improvement program are germplasm resources, which contain genetic diversity and phenotypic expression of desired traits. In this study, a total of 58 sugar beet genotypes including 12 from Turkey, 4 from India, 12 from the United States of America, 16 from Iran, 12 from England and Beta vulgaris L. subsp. maritima L. Arcang. as wild species were characterized using 15 inter-primer binding site (iPBS) markers that produced intense and polymorphic bands in the germplasm library. Using these 15 iPBS markers, 102 polymorphic bands were produced and the average number of polymorphic bands was determined as 6.8. Polymorphism information content (PIC) values ranged between 0.58 and 0.83, and the average PIC value was found to be 0.70. It was determined that the most genetically different genotypes were PI 590697-US11 and PI 171508-TR8, with a distance of 0.73. Clustering algorithms Unweighted Pair Group Method Algorithm (UPGMA) and Principal Coordinate Algorithm (PCoA) confirmed that genotypes are an important factor in clustering, and STRUCTURE analysis divided sugar beet gene resources into six populations. Also, the analysis of molecular variance (AMOVA) showed that there was 8% variance among populations and 92% variance within populations. This is the first study to investigate the genetic diversity and population structure of sugar beet germplasm using the iPBS-retrotransposon marker system. The results of this research emphasized that iPBS markers are very successful and effective in examining the genetic diversity of sugar beet germplasm. The results obtained in this study provide a theoretical basis for future selection and breeding of superior sugar beet germplasm sources.
Assessment of Genetic Diversity Among 131 Safflower (Carthamus Tinctorius L.) Accessions Using Peroxidase Gene Polymorphism (Pogp) Markers
(Springer, 2022) Yildiz, Mehtap; Altaf, Muhammad Tanveer; Baloch, Faheem Shehzad; Kocak, Metin; Sadik, Gokhan; Kuzgun, Cansu; Tuncturk, Murat
Background Safflower (Carthamus tinctorius L.) is an old oilseed crop with a 1.4 GB genome size and its flowers are used for food coloring, dyes and pharmaceutical industries. It was domesticated from its putative wild ancestor Carthamus palestinus about forty-five hundred years ago in the fertile crescent region.The current study was aimed to determine the genetic diversity, population structure and to check the applicability of iPBS-retrotransposons markers. Methods and results Eleven POGP primers yielded 70 bands of which 61 were highly polymorphic with 87.14% polymorphism. A great level of genetic variation was examined with higher values of overall gene diversity (0.27), genetic distance (0.53), number of effective alleles (1.46), Shannon's information index (0.41) and polymorphism information contents (0.71). Analysis of molecular variance revealed high genetic variation with 79% within the population. The STRUCTURE, PCoA and Neighbor-joining analysis separated the safflower germplasm into 2 major populations and 1 un-classified population. The accessions which were from Asian countries i.e., China, Afghanistan, Turkey, Iran and Pakistan were genetically similar and clustered together in both populations A and B. The maximum genetic distance was measured 0.88 between Pakistan 26 x Pakistan 24. Conclusion Findings of this research such as maximum diversity indices, higher PIC values showed the effectiveness and utility of POGP markers for the evaluation of genetic relationships among safflower accessions. The results of this study also showed that POGP markers are less effective compared to ISSRs, iPBS-retrotransposons and DArTSeq markers. AMOVA showed high genetic variation (79%) within a population and maximum genetic distance was found between the accessions Pakistan 26- Pakistan 24 and may be suggested as candidate parents for future breeding activities of safflower. The accessions from the fertile crescent region were clustered together and proved the origin of safflower domestication. This study highlights genetic variation among safflower germplasm and could be helpfull for parental selection and planning for future breeding programs.
Case Study: Things To Be Considered for High-Throughput Phenotyping in Genomic Studies
(Springer, 2023) Kwon, Soon-Hwa; Ku, Ki Bon; Tomar, Vipin; Yildiz, Mehtap; Kang, Seok-Beom; Park, Yosup; Han, Gyung Deok
High-throughput phenotyping (HTP) enables breeders and researchers to have massive data sets accurately and objectively. It could be applied to plant breeding for screening stress tolerance and biodiversity among wild species in the gene bank, which can be a breakthrough in the phenotyping bottleneck. However, there are many factors to be considered. Thus, this study is designed to show an example of phenotyping traits using yield and image data in citrus using the Normalized Difference Vegetation Index (NDVI) and Red, Green, and Blue (RGB) images. The results using image analysis showed that R2 in linear regression ranged from 0.79 to 0.91, depending on the methods which were used in the current study. However, the results from NDVI were proven to be false, unlike those of RGB images. This means that researchers and breeders must be very cautious when dealing with new technologies to avoid being misled to the wrong conclusion when they try to associate this data with genomic data.
Characterization of a Diverse Okra (Abelmoschus Esculentus L. Moench) Germplasm Collection Based on Fruit Quality Traits
(Mdpi, 2025) Yildiz, Mehtap; Sirke, Sibel Turan; Kocak, Metin; Mancak, Ibrahim; Ozkaya, Aslihan Agar; Abak, Kazim; Cavagnaro, Pablo Federico
Okra is an important dietary component of many Asian countries, providing high levels of dietary fiber, phytonutrients (e.g., antioxidant vitamins and pigments), and essential minerals. Evaluation of okra germplasm collections can improve the curation of genebanks and help identify superior materials for breeding. In this study, 66 okra accessions from diverse geographical origins were characterized based on fruit quality traits, including fruit fresh (FFW) and dry weights (FDW), dry matter (DM), diameter, length, and diameter of the fruit peduncle; concentration of vitamin C, chlorophyll a and b, and total chlorophyll; and color-chroma values. Significant (p < 0.05) and substantial variation was found among the accessions for all traits. Mean FFW and FDW varied nearly three-fold, with ranges of 3.76-9.99 g and 0.43-1.34 g, respectively, with a range in DM content of 10.5-19.4%. Vitamin C and total chlorophyll content varied 6.4- and 8.3-fold, with ranges of 12.8-82.8 and 1.07-8.91 mg/100 g fw, respectively, with substantial variation also observed in chlorophyll composition. Significant positive correlations were found between vitamin C and total and subtypes of chlorophyll levels (r = 0.29-0.32), whereas the strongest correlations were between FFW and FDW (r = 0.88) and between total chlorophyll and chlorophyll subtypes a and b (r = 0.90-0.95). Additionally, a dendrogram constructed based on these phenotypic data grouped the accessions in general agreement with their geographical origins and fruit traits. Overall, our results revealed broad phenotypic diversity in the evaluated germplasm, which is exploitable in okra breeding programs aimed at increasing fruit quality and nutraceutical value.
Correction: Population Structure, Genetic Diversity, and GWAS Analyses with GBS-Derived SNPs and Silicodart Markers Unveil Genetic Potential for Breeding and Candidate Genes for Agronomic and Root Quality Traits in an International Sugar Beet Germplasm Collection
(BMC, 2025) Bahjat, Noor Maiwan; Yildiz, Mehtap; Nadeem, Muhammad Azhar; Morales, Andres; Wohlfeiler, Josefina; Baloch, Faheem Shahzad; Cavagnaro, Pablo Federico
Determination of the Effective Radiation Dose for Mutation Breeding in Purple Carrot (Daucus Carota L.) and Possible Variations Formed
(Springer, 2022) Yarar, Gulistan; Kocak, Metin; Denli, Nihal; Cavagnaro, Pablo F.; Yildiz, Mehtap
Background Plant breeding allows altering the genetic structure of plants to meet human needs. The use of radiation technology for inducing mutations and -thereby- new phenotypic variants has become increasingly common as a tool for developing new crops. The aim of this study was to determine the effective gamma irradiation dose for inducing mutations in purple carrot. Methods and results Increasing gamma radiation doses [0, 50, 100, 200, 300, 400, 500, and 600 Gy] were applied to purple carrot seeds. The irradiated seeds were sown in pots and the emergence and survival rates of the seedlings were analyzed. Considering plant emergence (%) as a response variable, the LD50 dose was 387.5 Gy. Analysis of root length, root width (shoulder diameter) and plant height in control (0 Gy) and irradiated plants (50-600 Gy) revealed an inverse association between these morphological traits and radiation dose. SRAP and ISSR markers were used to identify DNA polymorphisms in irradiated and control plants. The range of amplicons per primer set revealed by ISSR and SRAP markers was 4-10 and 2-13, respectively. In the ISSR analysis of the irradiated carrots (for the 8 doses used), we obtained range values for the average Nei's gene diversity, Shannon's information index, and polymorphism information content (PIC) of 0.13-0.25, 0.20-0.35, and 1.39-1.67, respectively, whereas in the SRAP analysis, the range values for these parameters were 0.15-0.25, 0.23-0.37, and 0.43-0.58, respectively. Cluster analysis revealed three main groups; (a) non-irradiated (control) plants, (b) plants from the 600 Gy dose, and (c) a third group with two subgroups: one with individuals from the lowest irradiation doses (50-200 Gy) and a second group with individuals from the highest irradiation doses (300-500 Gy). Conclusions This is the first report on determining effective mutagen doses and genetic characterization of induced mutagenesis via gamma irradiation in purple carrot. ISSR and SRAP markers were successful in detecting variations among different levels of mutagen doses.
Diversity Study of Common Buckwheat Germplasm in the Republic of Korea Using Gbs
(Springer, 2022) Park, Ji Eun; Kang, Yuna; Han, Gyung Deok; Yildiz, Mehtap; Kim, Seong-Hoon; Kim, Changsoo; Chung, Yong Suk
Common buckwheat is widely cultivated worldwide. Due to its bioactive compounds, there are vigorous studies on protein and metabolism. However, there are not many studies using genetic approaches. Especially researches on genetic diversity in common buckwheat germplasm are rare, although it is crucial for breeding better cultivars. Thus, the current study examined the genetic diversity of the randomly selected common buckwheat germplasm found in the Republic of Korea. The results show that there are not many genetic variances among those wild common buckwheat germplasm that were used in the current study. Although it needs to test more number of germplasm, it seems that more diversity is required to be able to breed cultivars for the future.
Dna Molecular Markers in Plant Breeding: Current Status and Recent Advancements in Genomic Selection and Genome Editing
(Taylor & Francis Ltd, 2018) Nadeem, Muhammad Azhar; Nawaz, Muhammad Amjad; Shahid, Muhammad Qasim; Dogan, Yildiz; Comertpay, Gonul; Yildiz, Mehtap; Baloch, Faheem Shehzad
With the development of molecular marker technology in the 1980s, the fate of plant breeding has changed. Different types of molecular markers have been developed and advancement in sequencing technologies has geared crop improvement. To explore the knowledge about molecular markers, several reviews have been published in the last three decades; however, all these reviews were meant for researchers with advanced knowledge of molecular genetics. This review is intended to be a synopsis of recent developments in molecular markers and their applications in plant breeding and is devoted to early researchers with a little or no knowledge of molecular markers. The progress made in molecular plant breeding, genetics, genomic selection and genome editing has contributed to a more comprehensive understanding of molecular markers and provided deeper insights into the diversity available for crops and greatly complemented breeding stratagems. Genotyping-by-sequencing and association mapping based on next-generation sequencing technologies have facilitated the identification of novel genetic markers for complex and unstructured populations. Altogether, the history, the types of markers, their application in plant sciences and breeding, and some recent advancements in genomic selection and genome editing are discussed.
Exploring Secondary Structures Within the Nuclear Ribosomal Dna Internal Transcribed Spacers (Nr Dna Its) for Enhanced Phylogenetic Insights in Medicago Sativa (Alfalfa)
(Springer, 2024) Furan, M. Alp; Genli, Gulistan; Yildiz, Mehtap; Sun, Hyeon-Jin
ITS sections, which are situated inside the ribosomal DNA operon, are recognized for their high levels of diversity and slow rate of evolution, which makes them important for plant phylogenetic studies. The objective of this work is to use the internal transcribed spacer (ITS) regions of 18 alfalfa (Medicago sativa) genotypes/varieties to determine their genetic relationships and to verify possible genetic markers for variety identification and classification. This has been done by validating the secondary structures of the ITS regions and observing the effects of the relationships among the lowest energy state, the total number of possible secondary structure hairpins, and (GC) content. The results indicated that the length of the ITS sequences varied between 426 and 629 nucleotides and that the G + C content of the ITS region varied between 46.6 and 50%. In this study, the analysis of molecular variance (AMOVA) was used to validate the effectiveness of configuration analysis and revealed that fluctuations in the data accounted for a substantial amount of the observed total variance. Moreover, 94 percent of the genotypes analyzed exhibited a significant degree of variety. This shows that a large fraction of the observed variation is likely attributable to genetic variables. Population four, comprising Bilensoy80, Emily, Quin, Vendor, and Felicia, had the highest degree of heterozygosity at 68.8%, whereas population two, including Gozlu1, Prosementi, Nimet and Local (Van), had the lowest level at 37.5%. The original Shannon's approach as an unbiased estimator employed in population genetics research validated the differences among alfalfa genotypes with the AMOVA analysis results of this study. Individual differences were found to be 59%, whereas population differences were found to be 41%. There have been a few ITS studies on Medicago sativa that have utilized ITS as a phylogenetic marker to estimate connections and define new taxonomic categories (e.g., tribes). However, our research also includes an analysis of the secondary structure of these sequences and the results of this study imply that ITS sequence and secondary structure data can be utilized to understand the intraspecific genetic makeup of different alfalfa varieties.
Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the Ipbs-Retrotransposon Marker System
(Mdpi, 2019) Karik, Unal; Nadeem, Muhammad Azhar; Habyarimana, Ephrem; Ercisli, Sezai; Yildiz, Mehtap; Yilmaz, Abdurrahim; Baloch, Faheem Shehzad
Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon's information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant.
Exploring the Genetic Variations and Population Structure of Turkish Pepper (Capsicum Annuum L.) Genotypes Based on Peroxidase Gene Markers
(Springer Heidelberg, 2018) Akyavuz, Rifat; Taskin, Bilgin; Kocak, Metin; Yildiz, Mehtap
Capsicum is thought as one of the most diverse and significant genera due to its varied uses in different parts of the world. In this study, we worked with a total of 71 pepper genotypes from different locations of Turkey to investigate the level of their diversity using the peroxidase gene polymorphism (POGP) markers to reveal their population structure. For this purpose, 14 peroxidase primer pairs were used. They produced 139 bands (mean = 9.9 bands/primer), of which similar to 85.6% were polymorphic in the all germplasm collection. Polymorphism information content (PIC) ranged between 0.48 and 0.97 with an average of 0.75. Range and mean values for gene diversity (h) were 0.09-0.22 and 0.17, respectively. Shannon's information index (I) per POGP marker ranged from 0.18 to 0.35 with a mean of 0.29. Using three clustering methods (unweighted pair-group method with arithmetic means, principal coordinate analysis, and STRUCTURE) revealed a clear separation of all the C. annuum accessions from C. frutescens and C. chinense accessions in our study. Clusters did not establish an association between the accessions and their geographical origin. This is the first study exploring the population structure through the genetic diversity of Turkish peppers from different regions of the country based on the peroxidase gene markers.
Expression and Mapping of Anthocyanin Biosynthesis Genes in Carrot
(Springer, 2013) Yildiz, Mehtap; Willis, David K.; Cavagnaro, Pablo F.; Iorizzo, Massimo; Abak, Kazim; Simon, Philipp W.
Anthocyanin gene expression has been extensively studied in leaves, fruits and flowers of numerous plants. Little, however, is known about anthocyanin accumulation in roots of carrots or other species. We quantified expression of six anthocyanin biosynthetic genes [phenylalanine ammonia-lyase (PAL3), chalcone synthase (CHS1), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR1), leucoanthocyanidin dioxygenase (LDOX2), and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT)] in three carrot inbreds with contrasting root color: solid purple (phloem and xylem); purple outer phloem/orange xylem; and orange phloem and xylem. Transcripts for five of these genes (CHS1, DFR1, F3H, LDOX2, PAL3) accumulated at high levels in solid purple carrots, less in purple-orange carrot, and low or no transcript in orange carrots. Gene expression coincided with anthocyanin accumulation. In contrast, UFGT expression was comparable in purple and orange carrots and relatively unchanged during root development. In addition, five anthocyanin biosynthesis genes [FLS1 (flavonol synthase), F3H, LDOX2, PAL3, and UFGT] and three anthocyanin transcription factors (DcEFR1, DcMYB3 and DcMYB5) were mapped in a population segregating for the P (1) locus that conditions purple root color. P (1) mapped to chromosome 3 and of the eight anthocyanin biosynthesis genes, only F3H and FLS1 were linked to P (1). The gene expression and mapping data suggest a coordinated regulatory control of anthocyanin expression in carrot root and establish a framework for studying the anthocyanin pathway in carrots, and they also suggest that none of the genes evaluated is a candidate for P (1).
A Gene-Derived Snp-Based High Resolution Linkage Map of Carrot Including the Location of Qtl Conditioning Root and Leaf Anthocyanin Pigmentation
(Bmc, 2014) Cavagnaro, Pablo F.; Iorizzo, Massimo; Yildiz, Mehtap; Senalik, Douglas; Parsons, Joshua; Ellison, Shelby; Simon, Philipp W.
Background: Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F-2, F-3 and F-4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. Results: Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F-3-F-4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color. All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. A total of 15 significant QTL for all anthocyanin pigments and for RTPE mapped to six chromosomes. Eight QTL with the largest phenotypic effects mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped. Comparative mapping with two other carrot populations segregating for purple color indicated that carrot anthocyanin pigmentation is controlled by at least three genes, in contrast to monogenic control reported previously. Conclusions: This study generated the first high resolution gene-derived SNP-based linkage map in the Apiaceae. Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for RTPE, largely condition anthocyanin accumulation in carrot roots and leaves. Loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds.
Genetic and Phenotypic Variation of Turkish Okra (Abelmoschus Esculentus L. Moench) Accessions and Their Possible Relationship With American, Indian and African Germplasms
(Springer india, 2016) Yildiz, Mehtap; Ekbic, Ercan; Duzyaman, Eftal; Serce, Sedat; Abak, Kazim
Okra is an important vegetable crop that provides a significant portion of vitamins and minerals for populations in several countries. Okra has been cultivated in Turkey for centuries, and was likely introduced by the Arabs from Africa in ancient times. In this study, we aimed to clarify the genetic variation within 35 Turkish okra germplasm, by comparing it against 25 different genotypes from India, Africa, and the United States, using 30 morphological characters and 19 sequence-related amplified polymorphism (SRAP) primer combinations. Fruit, leaf, and stem color were the primary characteristics to distinguish the okra accessions. Those features, among 30 individual phenotypic traits, explained 42 % of phenotypic variation in the first three axes of the principal component analysis (PCA) with leaf shape, flower size, cotyledon length, fruit-surface angularity, cotyledon width, and petal color. Phenotypic observation results showed that while 1051 Togo (10.76), Red Wonder (7.99), TR-05-1 (7.2), 1159 Togo (7.17), and Red Balady (7.15) were found to be more divergent accessions, Cajun Queen (5.06), Perkins Spineless (5.09), Jade (5.18), TR-01-1 (5.2), and DLGG (5.32) were the closest okra accessions. According to phenotypic data, Turkish okra accessions were located adjacent to the Indian, American, and African okra accessions in clusters three and four. However, marker data showed that African okra possessed a more distinct form compared to the other okra germplasms. Nineteen SRAP primer combinations produced 92 bands and 29 (31.5 %) of them were found to be polymorphic among okra accessions. 1051 Togo was found to be the most divergent accession in phenotypic observation.
Genetic Diversity Analysis in the Turkish Pepper Germplasm Using Ipbs Retrotransposon-Based Markers
(Tubitak Scientific & Technological Research Council Turkey, 2020) Yildiz, Mehtap; Kocak, Metin; Nadeem, Muhammad Azhar; Cavagnaro, Pablo; Barboza, Karina; Baloch, Faheem Shehzad; Keles, Davut
Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean 8.6 bands/primer), of which similar to 92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPG MA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper gennplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.
Inter-Primer Binding Site (Ipbs) Retrotransposon Markers Provide Insights Into the Genetic Diversity and Population Structure of Carrots (Daucus, Apiaceae)
(Tubitak Scientific & Technological Research Council Turkey, 2022) Yildiz, Mehtap; Arbizu, Carlos, I
Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n = 18 chromosome (subclade A') separated from the other two species D. pusillus and D. muricatus, which were positioned into two individual clusters. The other Glade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic diversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that clusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters of 41.85% and 58.15%, respectively. The highest population divergence (F-st) was observed between clusters 2 and 3 (0.579), on the other hand, clusters 1 and 4 depicted the lowest F-st with 0.160. Our research highlighted that iPBS markers were successful and effective to study Daucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity.
Microsatellite Isolation and Marker Development in Carrot - Genomic Distribution, Linkage Mapping, Genetic Diversity Analysis and Marker Transferability Across Apiaceae
(Bmc, 2011) Cavagnaro, Pablo F.; Chung, Sang-Min; Manin, Sylvie; Yildiz, Mehtap; Ali, Aamir; Alessandro, Maria S.; Simon, Philipp W.
Background: The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with similar to 21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results: Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F-2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F-2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F-2, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions: The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.
Morphological and Molecular Characterization of Turkish Landraces of Cucumis Melo L
(Univ Agr Sci & veterinary Med Cluj-napoca, 2014) Yildiz, Mehtap; Akgul, Nursen; Sensoy, Suat
Twenty-four accessions covering different groups of Cucumis melo L. from Eastern and South-eastern Anatolian regions of Turkey were characterized by using 43 morphological traits and 207 markers obtained from 31 ISSR and 16 SSR primers. The genetic relatedness was studied by examining the Euclidian/UPGMA dendrogram obtained from the combined phenotypic-molecular data. In the combined morphological-molecular dendrogram, there were two main clusters. Sweet and non-sweet melon groups were separated and the flexuous group accessions were discriminated from the sweet ones, but the momordica group accession was clustered with the sweet ones. Unclear South-eastern Anatolian accessions were sub-clustered separately among the sweet ones. Principle component analysis (PCA) of morphological characters was used in detail CO discriminate melon accessions. The cumulative proportion of variation reached 44% by first three PCA axes. The first component was mainly based on sex expression, ovary index, ovary shape, flesh thickness, seed cavity length, seed cavity width, soluble solids content, fruit shape, aroma, netting, and taste. The PCA plot based on all measured traits allowed distinction between flexuous group, subsp. agrestis and reticulatus group. A high variation among groups was observed for the fruits characters. Netting, aroma and abscission of peduncle represent reticulatus group; a small fruit size, strong typical aroma and secondary colour distribution characterize dudatm group. Monoecy, very long fruit shape and mature fruit rind colour discriminate flexuous group; Ovary index, fruit size and flesh width distinguish subsp. agrestu group. These findings indicated wide range of variations for investigated characteristics in Turkish gene pool that provides a good source of diversity to use in melon improvement program for better yield and other traits of interest.
An Overview of Haploid and Double Haploid Production Methods in Wheat
(2022) Yildiz, Mehtap; Bahjat, Noor; Luna, Sara; Salıh, Sana
For about a century, researchers have been working on haploidy approach. Progressively, they discovered the importance and usefulness of haploids in various research fields. On the other hand, it is suggested that climate change impacts on crop production, especially wheat, requires rapid and efficient methods of plant breeding to produce new cultivars with a sufficient level of biotic and abiotic tolerance to avoid significant production loss. Haploid plants are the source for producing homozygous of pure lines and genetic variability for breeding programs. It reduces the time for producing pure and stable forms of new recombination by half in plant breeding. Furthermore, haploids are source for exclusive male plants generation, induction of mutations, stress resistance and tolerance cultivars, cytogenetic studies, and doubled haploid crops. This review presents a brief overview of the haploid wheat production methods and previous successful experiments on producing haploid wheat.