Browsing by Author "Kaya, HB"

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    The use of CRISPR-Cas-based systems in bacterial cell factories
    Kolasinliler, G; Aagre, MM; Akkale, C; Kaya, HB
    Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas system has been the focus since its first introduction to genome editing research. It acts as an adaptive immune system in many prokaryotes by detecting and degrading viral/invasive DNA/RNA repurposed for targeted genome editing in various organisms, including bacterial species relevant to industrial biotechnology. Targeted genome editing in bacteria has been implemented for multiple purposes, such as method development, understanding knowledge of metabolic processes and improving the productivity of industrial products. With the increasing share of biotechnological products, bac-teria have been the subject in the field of genome editing.This review summarizes the immunological mechanisms of CRISPR-Cas systems, the variation in classification of CRISPR-Cas systems by highlighting their features and the current applications of CRISPR-based genome editing in industrially relevant bacteria. In addition, an extensive literature review focused on recent advances has been presented in bacterial species according to industrial significance.
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    Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Turkiye
    Kaya, HB; Dilli, Y; Oncu-Oner, T; Ünal, A
    Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Turkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Turkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r(2) was between 0.45 and 0.2 and became flat when r(2) was 0.05. The average LD decay for the entire genome was 30 kb when r(2 =) 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.
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    Spelling Changes and Fluorescent Tagging With Prime Editing Vectors for Plants
    Wang, L; Kaya, HB; Zhang, N; Rai, R; Willmann, MR; Carpenter, SCD; Read, AC; Martin, F; Fei, ZJ; Leach, JE; Martin, GB; Bogdanove, AJ
    Prime editing is an adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase fusion and a guide RNA amended with template and primer binding site sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of prime editing in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for prime editing in dicots as well as monocots, their validation in Nicotiana benthamiana, rice, and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.
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    Genetic diversity of Crocus antalyensis B. Mathew (Iridaceae) and a new subspecies from southern Anatolia
    Erol, O; Sik, L; Kaya, HB; Tanyolaç, B; Küçüker, O
    Crocus antalyensis B. Mathew is a bulbous plant endemic to Turkey. It is morphologically variable within the western part of Anatolia. Amplified fragment length polymorphism (AFLP) marker system was used to detect genetic variation among the Crocus taxa. Twenty-two primer combinations were used to screen for polymorphism among the samples. Genetic variation ranged from 0.44 to 0.69. We demonstrated the efficiency of the AFLP marker system for discriminating between individual C. antalyensis specimens. A high level of genetic variation was present among C. antalyensis specimens collected from different locations in Turkey. We also observed that C. antalyensis subspp. are genetically distinct from their relative Crocus flavus Haw. subsp. dissectus Baytop & B. Mathew. A new subspecies of C. antalyensis B. Mathew from southern Turkey is described. It is characterized by striped outer perianth segments, waist-shaped flowers, and glabrous throat of the perianth. A composite image of the new subspecies is presented.
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    Genetic diversity of Lilium candidum natural populations in Türkiye evaluated with ISSR and M13-tailed SSR markers
    Tokgöz, HB; Çetin, Ö; Kaya, HB; Akkale, C; Yildirim, H; Pirhan, AF; Kaya, E; Altan, F
    The Liliaceae family includes the perennial, herbaceous, monocotyledonous plant Lilium candidum (L. candidum). The cosmetics, fragrance, and pharmaceutical industries regularly use L. candidum. It has been widely used in traditional medicine for wound healing, and its anti-inflammatory, antidiabetic, antimicrobial, and anticancer effects have been demonstrated in various studies. Natural populations of L. candidum are significantly affected by biotic and abiotic factors such as anthropological pressure, diseases, pathogen attacks, fossil fuel pollution, and climate change. Overcollection and destruction of its habitat put L. candidum into the endangered category. Therefore, it is of great importance to preserve this plant's genetic diversity, which plays a crucial role in adapting to different conditions, preserving evolutionary potential, and breeding studies. Molecular markers are essential in breeding and evolution studies to conserve genetic resources. Because of its economic and medical importance, various DNA markers have been used to evaluate the genetic diversity of L. candidum accessions. In this study, the genetic diversity of L. candidum, which is native to Turkiye, was determined with ISSR and SSR molecular markers among accessions collected from seven different cities and 76 accessions (Mugla, Izmir, Aydin, Antalya, Balikesir, Denizli, and Manisa). Genetic distances and phylogenetic analysis were carried out using the software TASSEL 5.2.63. The assessment of genetic diversity was visualized through a UPGMA dendrogram. The resulting phylogenetic tree revealed two distinct groups. The closest and farthest accessions were determined according to the genetic distance matrix. It was determined that the highest genetic distance value was between 19 (Balikesir, Kepsut) and 76 (Mugla, Ula) accessions (0.5390946) and the lowest genetic distance value was between 53 (Mugla, Marmaris) and 54 (Mugla, Marmaris) accessions (0.1069968).
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    Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)
    Kaya, HB; Akdemir, D; Lozano, R; Cetin, O; Kaya, HS; Sahin, M; Smith, JL; Tanyolac, B; Jannink, JL
    Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.
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    The genus Crocus, series Crocus (Iridaceae) in Turkey and 2 East Aegean islands: a genetic approach
    Erol, O; Kaya, HB; Sik, L; Tuna, M; Can, L; Tanyolaç, MB
    In this study, a total of 26 Crocus specimens from different locations across Turkey and 2 East Aegean islands (Chios and Samos) were analyzed using 12 amplified fragment length polymorphism (AFLP) primer combinations to obtain information on genetic diversity, population structure, and genetic relationships. A total of 369 polymorphic AFLP bands were generated and scored as binary data. Genetic similarities were determined. Cluster analysis revealed 4 major groups among the 26 genotypes examined in this study. The nuclear DNA contents (2C) of the 26 Crocus specimens were found to range from 5.08 pg in C. asumaniae to 9.75 pg in C. sativus. Polymorphic information content (PIC) values were used to examine the capacity of the various primer pairs to amplify polymorphisms in the Crocus specimens. The PIC values ranged from 0.218 (M-CAA/E-AGC) to 0.512 (M-CAT/E-AAG) and showed an average of 0.34. In sum, we herein used AFLP analysis to identify a high level of polymorphism among Crocus specimens collected from various locations in Turkey and Greece, and our structural analysis yielded 2 reconstructed populations. These findings provide new insight into the relationships among different Crocus genotypes and show that AFLP analysis can be useful for Crocus diversity studies.