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Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers
(Springer, 2022) Yeken, Mehmet Zahit; Emiralioğlu, Orkun; Çiftçi, Vahdettin; Bayraktar, Harun; Palacıoğlu, Gülsüm; Özer, Göksel
Background Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems. Materials and methods In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification. Results The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin. Conclusions A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.
Assessing Aluminum Stress Resilience in Common Bean Roots: Phenotypic, Histochemical, and PvGST/PvPOD Gene Expression Analysis
(2024) Yeken, Mehmet Zahit
Common bean (Phaseolus vulgaris L.) is grown in various parts of the world. Aluminum (Al) toxicity poses a significant and widespread challenge in marginal areas with unfavorable soil qualities where common bean is grown. In acidic soils, stable forms of Al dissolve into the soil solution and inhibit root growth and function by injuring the root apex with phytotoxic ions. This leads to the development of a smaller root system, adversely affecting crop yield. In this study, the phenotypic evaluation for relative root elongation of 10 common bean genotypes/cultivars under Al stress (50 µM), the impact of Al toxicity using different histochemical dyes (Evan’s blue and Schiff’s reagent) and the expression levels of PvGST (Glutathione S-transferases) and PvPOD (peroxidase) genes in the root tissues of the most resistant/sensitive common beans under Al stress (50 µM) and control conditions (0 µM) were investigated. The maximum relative root elongation value (71.9%) was found in Önceler-98 cultivar, while the lowest value (14.1%) was obtained from Blksr-19 genotype. Histochemical applications used in the study supported phenotypic results. The cracks at the root tip and high blue color intensity were detected in Schiff’s reagent and Evan’s blue dyes in the Blksr-19, respectively. The expression levels of PvGST and PvPOD genes in the root tissue of the Blksr-19 (Al-sensitive) were highly upregulated at 24 h of Al stress treatment. The results revealed that these genes might be involved in the common bean root tissue's defense mechanism against Al stress for the first time. The findings herein will help plant breeders develop common bean cultivars tolerant to Al toxicity.
Assessment of mineral content variations for biofortification of the bean seed
(2018) Yeken, Mehmet Zahit; Akpolat, Hacer; Karaköy, Tolga; Çiftçi, Vahdettin
Germplasm collections are very important for breeder to develop new cultivars with high mineral nutrients and yield. Eighty-three Phaseolus landraces were collected from different provinces of Western Anatolia Region of Turkey in 2015-2016. Twenty common bean lines were selected according to morphological characterization results and weighted scaling method in 2016. Phosphorus (P), potassium (K), copper (Cu), zinc (Zn), manganese (Mn), iron (Fe), calcium (Ca), and magnesium (Mg) contents of these twenty common bean lines and two commercial cultivars were tested under field conditions. Randomized block design with three replicates was used for analysis in 2017 growing season on the experimental farm of Bolu Abant Izzet Baysal University. The results showed high level of variation among lines and cultivars in terms of P (0.94-1.30%), K (2.38-3.59%), Cu (7.80-14.80 mg kg-1), Zn (19.74-66.68 mg kg-1), Mn (7.46-27.25 mg kg-1), Fe (48.98-182.45 mg kg-1), Ca (0.18-0.48 mg kg-1) and Mg (0.56-0.71 mg kg-1) contents. Positive correlations were found between K and Zn (r=0.447; P<0.05), P and Fe (r=0.485; P<0.05), Ca and Mg (r=0.693; P<0.01). In principal component analysis (PCA), the first 4 principal components accounted for approximately 73% of the total variability. The lines, Ylv-14, Ylv-32, Blck-7, Blksr-3 and Brs-22 had superior mineral contents for Fe and P, Cu and Mn, Ca and Mg, Zn, and K, respectively. Therefore, these lines represent promising candidates for biofortifying the bean seed and can be registered as cultivars in Turkey. Moreover, these lines will be used further for identifying the QTL regions by developing biparental mapping populations for an effective breeding program in Turkey in near future.
Assessment of variation in seed morphological traits in Phaseolus sp. landraces from western Anatolia
(Banats Univ Agricultural Sciences & Veterinary Medicine Timisoara, 2019) Cancı, Hüseyin; Yeken, Mehmet Zahit; Kantar, Faik; Bozkurt, Murat; Çiftçi, Vahdettin; Özer, Göksel
Seed size, seed shape and seed colour are easily discernible phenotypic traits of beans in the market. Consumers often have specific preferences to different combinations of seed size, shape and colour. Local landraces are usually grown for their desired organoleptic and seed properties by consumers. This study investigated the variability in seed size attributes, seed shape, visual seed colour properties and seed luminosity/chromaticity properties of the germplasm of 255 landraces representing major local bean types grown in 20 provinces in Western Anatolia Region of Turkey. Measurements were made on seeds from representative single plants for seed size index, 100 seed weight, seed length, seed width, seed thickness, seed width in cross section, seed shape, seed degree of curvature in kidney types, seed shape in cross section, number of seed colors, main seed color, secondary seed colour, distribution of secondary seed color, seed veining, colour of hilum ring and values of L (Luminosity), chromaticity a*, chromaticity b*, chroma (C) and hue angle. Data were statistically analysed, principle component analysis was carried out, the germplasm was classified by UPGMA dendograms and selections were made on the bases of GGE biplot analysis. Landraces showed a considerable diversity for seed size, seed shape and seed colour trait measured. All seed size variables ranged by 2-10-fold within the germplasm. 100-seed weight ranged ten-fold from very small seeded Meso-American types (18.4 g, e.g. AYD-8, KTH-30, MGL-1, DNZ-1 and BRD-24) to very large seeded Andean types (182.3 g, e.g. MGL-37, PKS-1, ANT-33, MGL-31 and ANT-16). Seed shape also varied as kidney-shaped (96 landraces), circular to elliptic (73), circular (58), elliptic (27) and rectangular (1) shapes. Main and secondary seed colours had considerable variation within the germplasm with 151 landraces had white, 31 grey, 31 beige, 23 brown, 8 violet, 5 red and 4 black main seed colour whereas 24 landraces had violet followed by 17 black and 14 red secondary seed colour. Landraces exhibited a large variation for chromaticity and luminosity variables. L value ranged between 20.3 and 90.1 representing a 4.5-fold variation. The landraces in the germplasm were assessed and characterised on the bases of diversity in seed morphological traits. Selections were made using UPGMA dendogram and GGE-biplot for production and breeding bean cultivars for preferences of changing consumer demands.
Batı Anadolu fasulye genetik kaynaklarının biyolojik çeşitliliğinin araştırılması ve karakterizasyonu
(2019) Çancı, Hüseyin; Bozkurt, Murat; Kanta, Faik; Yeken, Mehmet Zahit; Özer, Göksel; Çiftçi, Vahdettin
Bu çalışmada, Batı Anadolu Bölgesi'nde 10 ilde üretilen 156 önemli yerel fasulye ekotipi 2015 yılında toplanmış ve ekotipler arasındaki biyolojik çeşitliliği araştırmak ve karakterize etmek için 2016 yılında Akdeniz Üniversitesi Ziraat Fakültesi'nde tarla denemesi yürütülmüştür. İncelenen karakterler açısından en belirgin değişim kuru sap ve tane veriminde kaydedilirken bunu bitkide bakla sayısı, baklada tane sayısı, bitki boyu ve yüz tane ağırlığı takip etmiştir. En yüksek bitki başına tane verimi MGL-30 (145.6 g), MGL-38 (101.7 g), ANT-43 (87.8 g) ve MGL-26 (81.9 g) genotiplerinden elde edilmiştir. Temel bileşen analizinde, 17 bileşen yerel fasulye genetik kaynaklarındaki varyasyonun %74.9’unu izah etmiştir. Bakla rengi, bitki tipi ve sarılma özelliği en fazla katkı sağlayan özellikler olmuştur. Bitki boyu ve olgunlaşma gün sayısı, biplot analizinde tane verimi ile aynı yönde ve en dar açıya sahip vektörler olmuştur. Morfolojik özellikler kullanılarak üretilen benzerlik dendogramı genotipleri iki ana gruba (A ve B) ve dört alt gruba (A1, A2, B1 ve B2 ) ayrılmıştır. Morfolojik özellikler açısından en uzak gruplarda yer alan MGL-01, KTH-01, MNS-01 ve ANT-13 ile UŞK-01, ANT-01, MGL-05 ve AYD-02 ekotipleri kullanılarak melezleme ıslahı ile yeni çeşitler geliştirilebilir.
Breeding of dry bean cultivars using phaseolus vulgaris landraces in Turkey
(2018) Yeken, Mehmet Zahit; Kantar, Faik; Çancı, Hüseyin; Özer, Göksel; Çiftçi, Vahdettin
Yield and yield components is one of the key objectives of the legume breeding program worldwide. Information on these traits is required for the selection of desirable types and efficient utilization of the genetic diversity in dry bean improvement program. Local landraces of dry beans grown over long time period are more resistant to low input growing conditions its genetic and morphologic properties and quality is more acceptable by the growers. From this perspective, 83 dry bean landraces were collected from different bean growing areas of Western Anatolia Region of Turkey in 2015-2016. The dry bean landraces were grown on the experimental farm of Abant Izzet Baysal University, Bolu during 2016 growing season. A single plant from each dry bean landrace was selected according to morphological characterization results and weighted scaling method, and twenty (8 climber and 12 bush types) dry bean lines were accepted as promising. In the present study, yield and yield components of 12 dry bean lines and 2 commercial cultivars were compared in Bolu province under western black sea ecological condition of Turkey. The experiment was arranged in a Randomized Block Design with three replicates in 2017 growing season on the experimental farm of Abant Izzet Baysal University. Emergence percentage (69.50-96.00%), days to flowering 50% (48.00-52.00 days), days to maturity (86.00-107.33 days), plant height (37.20-58.30 cm), height to first pod (12.50-19.00 cm), number of branches per plant (6.25-8.25), number of pods per plant (16.96- 41.50 pods), seeds per pod (4.00-6.40 seeds), seed yield per plant (25.41-96.83 g plant-1) and 100 seeds weight (29.82-55.35 g) were determined according to IPGRI and EU-CPVO criteria. As a result, lines ÇNK-2, ÇNK-4, YLV-28, YLV-32 and BLCK-7 had superior with respect to yield and yield components and hence selected advanced promising lines will be transferred to regional yield trials required for the official procedures of cultivar registration.
Common bean as a potential crop for future food security: An overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics
(Taylor & Francis, 2021) Nadeem, Muhammad Azhar; Yeken, Mehmet Zahit; Shahid, Muhammad Qasim; Habyarimana, Ephrem; Yılmaz, Hilal; Alsaleh, Ahmad; Hatipoğlu, Rüştü; Çilesiz, Yeter; Khawar, Khalid Mahmood; Ludidi, Ndiko; Ercişli, Sezai; Aasim, Muhammad; Karaköy, Tolga; Baloch, Faheem Shahzad
Common bean is an important legume crop having high quality protein, micronutrients, vitamins and antioxidants, which makes it a "grain of hope" for poor communities. Hence, a good number of breeding activities have been performed on the improvement of various key traits for years. However, recent advancements in molecular markers, sequencing technologies and the completion of the common bean genome sequence have opened numerous opportunities for fine mapping and gene characterization. The availability of these tools together with investigations of quantitative trait loci (QTL) and candidate genes for key traits such as morpho-agronomic, iron and zinc contents, cooking and quality traits, antioxidant activity, biotic and abiotic stresses pave the way to the development of new strategies for common bean genetic improvement. As a food source, it can contribute to the reduction of food scarcity worldwide in the coming years. Therefore, it is very important to take synergic efforts to integrate common bean genetic and genomic resources in breeding activities to ensure food security and contribute significantly to improved livelihoods in developing countries. Moreover, Kompetitive allele specific PCR (KASP) and CRISPR-Cas9 should be used to develop climate resilience common bean varieties. Here, we provide an overview of the evolution of common bean research by highlighting the past and recent advances in genomics, transgenics, transcriptomics and proteomics and also critically discuss the future prospects for further genetic improvement and better expansion of this crop.
Contribution of landraces in wheat breeding
(Springer International Publishing, 2021) Nadeem, Muhammad Azhar; Yeken, Mehmet Zahit; Tekin, Mehmet; Mustafa, Zemran; Hatipoğlu, Rüştü; Aktaş, Husnu; Alsaleh, Ahmad
Agricultural production system is extremely vulnerable to climate change, and this change will heavily affect the grain yields, thereby threating the food security worldwide. People from developing countries are at greatest risk of experiencing food insecurity, and today, millions of people are going to bed hungry. Wheat is serving as a staple food for millions of people around the world. Development of high-yielding wheat varieties during the Green Revolution is considered an important event in agricultural history. However, these plant breeding activities also resulted in genetic erosion in wheat. Moreover, it is also believed that after domestication process, selection process also resulted in the loss of genetic diversity of wheat. Therefore, commercial wheat cultivars are prone to various biotic and abiotic stresses. To combat with climate changes and to serve enough quantity of food with quality, there is a need to harness wheat landraces. Landraces are considered as repository of gene pool that enhance the biodiversity and maintain and stabilize the ecosystem in a sustainable way to make it functional. Wheat landraces are traditional crop populations developed by the farmers through natural and human selection under their years of cultivations and have adaptation to local environment and management practices. Wheat landraces have more genetic diversity compared to their cultivated ones, and breeding community has utilized their potential in development of climate-resilient wheat cultivars. Here, we are exploring the role of landraces in wheat breeding and hoping that provided information will catch the attention of breeding community to collect, conserve, and perform breeding activities using wheat landraces. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2021. All rights reserved.
Determination of Turkish common bean germplasm for morpho-agronomic and mineral variations for breeding perspectives in Turkey
(Kahramanmaras Sutcu Imam Univ Rektorlugu, 2019) Yeken, Mehmet Zahit; Nadeem, Muhammad Azhar; Karaköy, Tolga; Baloch, Faheem Shehzad; Çiftci, Vahdettin
Turkey is lavished with hundreds of common bean landraces. The present study was aimed to investigate the agronomic and mineral variations in 80 common bean landraces collected from 11 different provinces of Turkey. Genotypic variation expressed as a range for some traits like days to maturity (90-141 days), plant height (25.25-361.50 cm), 1000 seeds weight (140-633 g), Iron (66.48-128.05 mg kg(-1)), and Zinc (20.56-42.01 mg kg(-1)). Positive and highly significant correlation of Magnesium with Iron and Zinc was observed and analytic results derived from the first 3 eigenvectors suggested that days to pod setting, Zinc, and 1000 seeds weight were main variation contributing traits. Among the provinces, landraces from Tunceli performed well for agronomic traits and Malatya provinces landraces were found enrich for mineral traits. Landraces E-26 and S-19 reflected higher Fe and Zn contents, and higher yield, respectively. Cluster analysis divided the studied germplasm on the basis of plant height and geographic. Information provided herein can be helpful for the development of candidate varieties having higher yield with greater mineral contents.
Ekmeklik Buğday (Triticum aestivum L.) Genotiplerinin Dane Verimi ve Bazı Önemli Kalite Özellikleri için Trakya Bölgesinde Bulunan Farklı Çevrelerde Testlenmesi
(2023) Gökdere, Halil Ibrahim; Yilmaz, Ali Baran; Tekin, Mehmet; Yeken, Mehmet Zahit; Çiftçi, Vahdettin
Bu çalışma, toplamda 27 çeşit ve çeşit adaylarının dane verimi ve bazı önemli kalite özellikleri bakımından genotip x çevre etkileşimi temel bileşen, GGE biplot ve AMMI analizleri değerlendirmek amacıyla Trakya bölgesini temsil eden dört farklı çevrede 2020-2021 sezonunda yürütülmüştür. Denemeler tesadüf blokları deneme desenine göre dört tekerrürlü yürütülmüş olup ve tarımsal ve kalite özelliklerinden başaklanma gün sayısı, bitki boyu, dane verimi, bin dane ağırlığı, hektolitre ağırlığı, dane sertliği, protein oranı, Zeleny sedimantasyon, Alveograf enerji değeri, yaş gluten oranı ve gluten indeksi çalışma kapsamında incelenmiştir. Çalışmada, dane veriminde en yüksek varyasyon Tekirdağ çevresinde belirlenmiş olup en yüksek verim ise Edirne çevresinde belirlenmiştir. GGE biplot analizine göre iki farklı mega çevre oluşmuş ve iki temel bileşen toplamda %89.97 genotip x çevre ilişkisini açıklamıştır. AMMI temelli varyans analizi sonucunda ise genotip, çevre, tekerrrür ve genotip x çevre interaksiyonu bakımından istatistiki olarak önemli etkiler tespit edilmiştir. En stabil genotipler ise Ez11 ve Rumeli olarak belirlenirken LG Arnova çeşidi dört çevrede de öne çıkan dört genotipten biri olmuştur. Korelasyon analizine sonucunda kalite özellikleri arasında istatistiki olarak önemli (p<0.05) pozitif ilişkiler tespit edilirken dane verimi ile diğer tarımsal ve kalite özellikleri arasında anlamlı bir ilişki belirlenmemiştir. İlk dört temel bileşen 1’in üzerinde eigen değerine sahip olarak bulunmuş ve varyasyonun %74’ünden fazlasını açıklamıştır. LG Arnova, Artek, Axum, Alpan ve Vassa çeşit/çeşit adayları özellikle dane verimi bakımından ilgili çevrelerde öne çıkan çeşitler olmuşlardır. Bu konuda daha detaylı sonuçlar elde etmek için genotiplerin ilgili çevrelerde daha uzun süreyle denenmesi gerekmektedir.
Exploring differentially expressed genes in Phaseolus vulgaris L. during BCMV infection
(Academic Press Ltd- Elsevier Science Ltd, 2024) Yeken, Mehmet Zahit; Celik, Ali; Emiralioglu, Orkun; Ciftci, Vahdettin; Baloch, Faheem Shehzad; Ozer, Goksel
Bean common mosaic virus (BCMV) is a significant pathogen that affects common bean, leading to substantial yield losses and reduced crop quality. To mitigate BCMV attacks, certain genes, including diacylglycerol kinases genes (PvDGKs), genes associated with defense and stress responses (PvGST, PvPAL, PvLOX, and PvPOD), as well as genes related to plant defense (PvPR1, PvPR2, and PvPR3) play an essential functional role in various stress responses in common bean. In this study, the expression levels of PvDGK1, PvDGK2, PvDGK3, PvDGK5a, PvDGK5b, PvDGK6, PvGST, PvPAL, PvLOX, PvPOD, PvPR1, PvPR2, and PvPR3 genes were investigated in the leaves of different common bean genotypes under BCMV infection conditions. Through quantitative real -time PCR analysis, we observed varying expression patterns for all these genes at different time points during viral infection. The tolerant genotype exhibited higher expression levels of all PvDGKs, PvGST, PvPAL, PvPOD, PvPR1, and PvPR2 genes compared to the susceptible genotype, with the PvPR1 gene showing the highest transcript levels. These findings provide the initial evidence of the potential roles of PvDGKs, PvGST, PvPAL, PvLOX, PvPOD, PvPR1, PvPR2, and PvPR3 in responding to the stress induced by BCMV in common bean. The results presented herein will serve as a valuable resource for guiding future breeding studies aimed at addressing BCMV-induced stress in common bean cultivation.
EXPLORING I, bc-12 AND bc-3 GENE LOCUS IN PROMISING COMMON BEAN LINES
(2023) Emiralioğlu, Orkun; Yeken, Mehmet Zahit; Çelik, Ali; Çiftçi, Vahdettin
Common beans (Phaseolus vulgaris L.), known as the \"poor man's meat\", is an internationally important legume crop that appeals to farmers as well as consumers. Many biotic stressors such as bean common mosaic virus (BCMV), bean common mosaic necrosis virus (BCMNV) cause significant yield and quality losses in common bean. The most efficient and cost-effective way to lessen of these factors is to develop resistant cultivars. Local genotypes have been cultivated in many areas for years and have varied distinguishing characteristics as a result of spontaneous mutations. Identifying bean germplasm harboring gene sources is critical for developing resistant cultivars against BCMV and BCMNV. For this purpose, a total of 43 promising common bean lines selected from local genotypes cultivated across various regions of Türkiye were subjected to screening using diverse molecular markers (ROC11, SBD-5 and SW-13) to investigate gene sources associated with BCMV and BCMNV. The findings revealed that 21 lines had both I and bc-12 gene locus. In addition, the bc-12+bc-3 gene loci were discovered to be present in the 8 common bean lines. The combination of I+bc-3 resistance genes, which guarantees immune reaction to BCMV and BCMNV, was found in only one line; YLV-32. These gene sources can be evaluated in marker-assisted breeding to develop modern cultivars resistant to BCMV and BCMNV by breeders.
Fasulye'de DGK (Diacylglycerol kinaz) genlerinin genom düzeyinde tanımlanması ve gen ifade düzeylerinin abiyotik stres faktörleri ile ilişkisi
(Bolu Abant İzzet Baysal Üniversitesi, 2021) Yeken, Mehmet Zahit; Çiftçi, Vahdettin; Özer, Göksel
Diaçilgliserol kinazlar (DGKs), diaçilgliserolü fosfatidik aside dönüştürerek bitkilerde abiyotik ve biyotik stres tepkilerinde önemli rol oynayan bir enzimdir. Fasulye genom dizisi tanımlanmış olmasına rağmen, DGK genlerinin karakterizasyonu ve abiyotik stres faktörlerindeki ifade düzeyleri ile ilgili bir çalışmanın literatürde bulunmadığı belirlenmiştir. Bu çalışmada, fasulye genomundaki DGK gen ailesinin genom çapında analizi, tuz stresi altındaki ifade profilleri, yerel fasulye genotiplerinin soğuk stresine karşı fenotiplenmesi ve fenotipleme sonucu belirlenen genotiplerde DGK genlerinin soğuk stresindeki ifade düzeylerinin tespiti gerçekleştirilmiştir. Çalışmada, protein uzunlukları ve moleküler ağırlıkları sırasıyla 423 ile 727 amino asit (aa) ve 47,31 ile 81,09 kDa arasında değişen korunmuş katalitik alanlar içeren 6 DGK geni (PvDGK1;2;3;5a;5b;6) tanımlanmıştır. Filogenetik analiz sonucunda küme I'de 2, küme II'de 1 ve küme III'de de 3 PvDGK geni gruplanmıştır. qRT-PCR analizi, normal koşullarda kök, gövde, yaprak, çiçek ve bakla dokusunda, tuz stresi altında (150 mM) kök ve yaprak dokusunda (0, 6, 12 ve 24. saat), soğuk stresinde (4 ºC) de yaprak dokusunda (0, 6, 12 ve 24. saat) gerçekleştirilmiştir. Yerel fasulye genotiplerinin soğuk stresine (0 ºC ve 5 ºC) karşı fenotiplenmesinde, Fv/Fm, PIabs, SPAD, NES, L, a, b, chroma, Hue ve görsel değerlendirme kriterleri kullanılmıştır. Genotipler arasında soğuk stresi bakımından önemli varyasyonların olduğu belirlenmiş, en hassas ve en toleranslı 3 fasulye genotipi gen ekspresyon çalışmasına dahil edilmiştir. Çalışma ile fasulyedeki DGK gen ailesinin ilk kez karakterizasyonunu gerçekleştirilmiş ve abiyotik stres tepkisindeki önemi ortaya konulmuştur. Elde edilen bulguların, soğuk stresi ile ilgili yürütülecek ıslah çalışmalarına, DGK gen ailesinin anlaşılması ve fonksiyonel karakterizasyonu üzerine gelecekte yürütülecek araştırmalara yardımcı olacağı düşünülmektedir.
Genome-wide identification and expression analysis of DGK (Diacylglycerol Kinase) genes in common bean
(Springer, 2023) Yeken, Mehmet Zahit; Özer, Göksel; Çiftçi, Vahdettin
Diacylglycerol kinases (DGKs) are a family of enzymes that play an important functional role in various stress responses in plants by converting diacylglycerol to phosphatidic acid. In this study, genome-wide identification of DGK genes, expression analysis under non-stress in various developmental stages and under salt stress in different tissues of common bean were performed for the first time. The 6 DGK gene family members (PvDGK1, 2, 3, 5a, 5b, and 6) having conserved catalytic domains were identified by an exploration of common bean genome via multiple online databases. The protein lengths and molecular weights of PvDGKs were found between 423 and 727 amino acids (aa) and ranging from 47.31 to 81.09 kDa, respectively. Phylogenetic analysis revealed that PvDGK genes grouped into three clusters as described for known plant DGK families; cluster I (PvDGK1, 2), cluster II (PvDGK3) and cluster III (PvDGK5a, 5b, 6) genes, respectively. Quantitative real-time PCR analysis revealed that all PvDGK genes indicated divergent expression patterns in all tissues at different developmental stages under non-stress condition. Furthermore, PvDGK genes were also significantly upregulated in response to salt stress in root and leaf tissues of common bean cultivars at different time points. These results indicated the possible roles of PvDGK genes in developmental stages and salt stress in common bean. The findings herein will guide further investigations on the comprehension and functional characterization of the PvDGKs and the breeding studies to be carried out related to stress in the common bean near future.
Genomics, phenomics, and next breeding tools for genetic improvement of safflower (Carthamus tinctorius L.)
(Springer International Publishing, 2021) Yilmaz, Abdurrahim; Yeken, Mehmet Zahit; Ali, Fawad; Barut, Muzaffer; Nadeem, Muhammad Azhar; Yilmaz, Hilal; Naeem, Muhammad
Safflower is one of the most important oilseed crops with high-quality seed oil. It can be grown especially in the arid and semiarid regions in the world. The main reason why safflower is not widely cultivated is because of its low yield. Various breeding efforts have made a significant contribution to the improvement of safflower; however, it seems necessary to exploit the potentiality of this underutilized plant. The development of new and improved safflower varieties will improve the sustainability of this crop to different environmental conditions. Classic breeding efforts made great efforts in safflower breeding; however, these techniques have been slow to develop complex traits such as yield, oil yield, some quality traits, and biotic-abiotic stress resistance. Recent advancements in molecular markers and genome sequencing technologies enhanced the breeding activities and aided the scientific community to understand and comprehensively explore the genetic diversity and population structure of safflower. Phenotypic and molecular characterization helped the construction of genetic linkage maps, leading to a better understanding of complex quantitative characters for safflower varieties. The present chapter articulates different aspects of safflower including phenomics, chemical content, origin-diffusion, similarity centers, wild relatives, genetic resources, trades, and comprehensive advancement in safflower breeding in terms of classical breeding, tissue culture, QTL mapping, association mapping, transgenic breeding, genome editing, and speed breeding. This information will lead to more short-term solutions in breeding safflower crop and will provide more practical information for breeders in the near future. © Springer Nature Switzerland AG 2021.
Giberellik Asit Dozlarının Ekmeklik Buğdayda (Triticum aestivum L.) Verim ve Kalite Üzerine Etkisi
(2024) Yeken, Mehmet Zahit
Bu çalışmada, ülkemizin farklı bölgelerinde yaygın olarak yetiştirilen Halis ekmeklik buğday çeşidinin tarımsal ve kalite özellikleri üzerine giberellik asit (GA3) dozlarının (1.0 g/da, 0.8 g/da, 0.6 g/da ve kontrol) etkisi araştırılmıştır. Deneme, Sakarya ekolojik koşullarında dört tekerrürlü olarak tesadüf blokları deneme desenine göre 2022-2023 yetiştirme sezonunda yürütülmüştür. Çalışma kapsamında bitki boyu, tane verimi, başakta tane sayısı, m2’de başak sayısı, başakta tane ağırlığı, bin tane ağırlığı ve hektolitre ağırlığı gibi tarımsal özelikler ile protein oranı, yaş gluten, gluten indeksi, rutubet, zeleny sedimantasyon, alveograf enerji değeri, alveograf P/L oranı, farinograf su absorbsiyonu, farinograf gelişme süresi, farinograf stabilite değeri ve farinograf yumuşama değerleri gibi kalite özellikleri incelenmiştir. Varyans analizi sonucunda GA3 uygulamalarının, tane verimi, başakta tane sayısı, m2’de başak sayısı, başakta tane ağırlığı ve hektolitre ağırlığı üzerine istatistiki olarak önemli etkisinin olduğu belirlenmiştir. Yapılan korelasyon analizleri sonucunda özellikler arasında istatistiki olarak önemli pozitif ilişkiler tespit edilmiştir. Temel bileşenler analizine göre ilk dört temel bileşen varyasyonun %73.81’ini açıklamıştır. Sonuç olarak 1.0 g/da GA3 uygulamasının buğday veriminde önemli oranda artışa neden olduğu ancak kalite üzerinde etkili olmadığı tespit edilmiştir.
Host suitability of different common bean varieties in a growth room to the plant-parasitic nematodes Pratylenchus thornei and P. neglectus
(BRILL, 2021) Saleh, Azzam; İmren, Mustafa; Özer, Göksel; Yeken, Mehmet Zahit; Çiftçi, Vahdettin
Pratylenchus thornei and P. neglectus attack common bean and cause economic yield losses throughout cultivated areas in Turkey. The most effective management strategy for the P. thornei and P. neglectus infections is crop rotation with non-host crops and breeding resistant/tolerant varieties. However, parent bean genotypes immune to P. thornei and P. neglectus are not available for breeding programmes; thus, resistant varieties are commonly incorporated as parents. In the present research, a total of 36 common bean varieties were tested in a growth room for their host response to these two nematode pests. The reproduction factor and the population density of both nematode species were calculated. All tested bean varieties showed varying levels of resistance and susceptibility to P. thornei and P. neglectus. Among the dry bean varieties, nine were found to be resistant to P. thornei and three to P. neglectus, with three varieties ('Kantar-05', 'Onceler-98' and 'Karacasehir-90') resistant to both species. Among fresh bean varieties, ten were found to be resistant to P. thornei and four to P. neglectus, with four varieties ('Helda', 'Gina', 'Gelincik' and 'Bourgondia') resistant to both species. The resistant common bean varieties identified in this study are a valuable untapped genetic pool that will offer improved resistance levels to P. thornei and P. neglectus, especially 'Gina' and 'Onceler-98', which seem to possess a great source of resistance to P. thornei and P. neglectus, respectively, and can be used in breeding programmes in the near future.
Identification of resistance sources in common bean (Phaseolus vulgaris) genotypes from Turkey and the reactions of some promising genotypes to bean anthracnose (Colletotrichum lindemuthianum)
(CSIRO Publishing, 2022) Palacıoğlu, Gülsüm; Yeken, Mehmet Zahit; Kantar, Faik; Çancı, Hüseyin; Çiftçi, Vahdettin; Özer, Göksel
Context Among biotic factors, bean anthracnose caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara is one of the most destructive diseases of common bean (Phaseolus vulgaris L.). Resistance in common bean genotypes is controlled by anthracnose resistance loci (designated Co). Aims The objective of this study was to evaluate the presence of Co resistance genes in common bean genotypes from Turkey and to examine promising genotypes as candidates for parent plants in breeding studies. Methods The presence of Co resistance genes in 693 common bean genotypes from 35 provinces of Turkey was determined by 12 SCAR (sequence characterised amplified region), RAPD (random amplified polymorphic DNA), STS (sequence-tagged site) and CAPS (cleaved amplified polymorphic sequence) markers. The disease reaction of 40 agronomically promising genotypes to different pathogen isolates was evaluated in a pot study. Key results The results indicated the presence of Co-1, Co-1(4), Co-1(5), Co-2, Co-3(3), Co-4, Co-4(2), Co-6, Co-10, Co-11 and Co-13 resistance genes, alone or in combination; Co-5 was not detected in any of the genotypes. Among the genotypes, Co-1(5) was the most frequent resistance source, followed by Co-4, Co-6 and Co-11, respectively. Common bean genotypes carrying Co-1(4), Co-2, Co-3(3), Co-11 and Co-13 have been identified for the first time in Turkish germplasm. Five genotypes carrying the various combinations of Co-1, Co-1(5), Co-4, Co-6, Co-10, Co-11 and Co-13 were resistant to all isolates in pathogenicity tests. Conclusions This study is the most comprehensive to date on Co genes linked to the resistance of common bean genotypes throughout Turkey and provides an important gene pool for breeding studies into bean anthracnose. Resistant genotypes identified will be useful as parent plants in resistance breeding studies. Implications Resistance genotypes carrying different Co genes to bean anthracnose will contribute significantly to the disease management strategy.
The influence of different intensities of chalky spot damage on seed germination, grain yield and economic returns of red lentil
(Springer, 2020) Mutlu, Çetin; Çiftci, Vahdettin; Yeken, Mehmet Zahit; Mamay, Mehmet
Chalky spot damage caused by Dolycoris baccarum (L.) and Piezodorus lituratus (F.) causes significant losses to productivity and marketing lentil (Lens culinaris Medik.) in southeastern Anatolia region, Turkey. The chalky spot-damaged grains attract lower price in the market, which decreases productivity. Limited is known about the influence of varying intensities of chalky spot damage on seed germination, productivity and economic returns of lentil in the region. The current study was conducted to assess the influence of varying intensities of chalky spot damage, on seed germination, yield and economic returns of lentil in laboratory and field. Seeds of different lentil cultivars (5 for laboratory and 2 for field studies) were sorted to get 0, 25, 50, 75 and 100% damaged seeds with chalky spot. The data relating to grain weight, reduction and percent reduction in 1000-grain weight were collected. Seed germination of Altintoprak, cagil, Firat-87, Seyran and Tigris with varying chalky spot damage intensities was inferred in laboratory, whereas seed germination and yield of cagil and Tigris cultivars was observed under field conditions. The 1000-grain weight, seed germination percentage under laboratory and field conditions, grain yield and gross income were linearly decreased with increasing intensity of chalky spot damage. The cultivar cagil observed lower reduction in grain yield and gross income compared to Tigris cultivar. It is recommended that non-damaged, certified seeds should be sown in the region to get higher grain yield and economic returns of lentil.
Investigation of Genetic Diversity in Lentil Genotypes Obtain from Different Countries Using SDS-PAGE Methodology
(2024) Yeken, Mehmet Zahit; Baloch, Faheem Shehzad; Nadeem, Muhammad Azhar; Sameeullah, Muhammad; Gürel, Ekrem
In the current study, the characterization of 44 lentil genotypes was performed using SDS-PAGE (Sodium dodecyl sulfate-polyacrylamide gel electrophoresis) technique. The protein bands were scored according to a binary system as the present (1) or absent (0) that ranged 12-20 bands in lentil genotypes. The Jaccard’s coefficient of genetic dissimilarity (GD) was measured, and the mean GD was 0.216. Maximum genetic distance was found as 0.526 between Syria2 with Iraq3 and these genotypes might be recommended for future lentil breeding. AMOVA explored the presence of higher genetic variety within genotypes (83%) than among genotypes (17% variations). STRUCTURE algorithm separated lentil genotypes into two groups mainly on the basis of their geographic. The UPGMA clustering separated lentil genotypes into two main clusters A and B. The PCoA was also conducted to confirm the results of structure and UPGMA analyses. Findings from the PCoA and structure analyses were in full agreement with those obtained by UPGMA. The results might be useful for researchers worldwide who are interested in lentil breeding.

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