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Öğe Biotechnological approaches for genetic improvement of fenugreek (Trigonella foenum-graceum L.)(Springer Singapore, 2018) Aasim, Muhammad; Baloch, Faheem Shahzad; Bakhsh, Allah; Sameeullah, Muhammad; Khawar, Khalid MahmoodAbstract Fenugreek (Trigonella foenum-graecum L.) is one of the important medicinal plants of ancient medicinal systems due to its high nutraceutical and pharmaceutical properties. Seeds and leaves of Fenugreek contain phytochemicals like diosgenin and trigonelline. It is a cultivated plant of the modern world for medicinal uses, an edible vegetable, and a forage plant. Advancement in industrial and biotechnological techniques for the isolation of phytochemicals increase the demand of Fenugreek, and its breeding programs are based on improving the secondary metabolites compared to other uses. Recent advancement in modern biotechnological approaches enables researchers to develop elite cultivars of desired traits in a short time. Application of modern techniques like artificial mutations under in vitro conditions, characterization using molecular markers, and development of successful plant tissue culture techniques, genetic transformation techniques, and functional genomics studies have significant potential to improve Fenugreek traits. The study highlights the application of biotechnological approaches used for the development of elite Fenugreek traits for the researchers for future breeding programs. Furthermore, the research gap and areas to improve research have been highlighted in this present study. © Springer Nature Singapore Pte Ltd. 2018.Öğe 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 ShahzadCommon 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.Öğe Deciphering global DNA variations and embryo sac fertility in autotetraploid rice line(2019) Ghourı, Fozia; Zhu, Jiani; Yu, Hang; Wu, Jinwen; Baloch, Faheem Shahzad; Liu, Xiangdong; Shahid, Muhammad QasimAutotetraploid rice is a new germplasm resource obtained by doubling chromosomes through colchicine treatment. There have been many studies on the reproductive characteristics of autotetraploid rice, but little is known about global DNA variations and reasons for low embryo sac fertility in autotetraploid rice. Therefore, an autotetraploid rice line (T446) was used for resequencing and embryo sac fertility was observed. Whole-genome resequencing data revealed 87,229 SNPs and 11,022 InDels in the genome of T446 versus E246 (diploid rice), which had an average of 23.37 SNPs and 2.95 InDels per 100 kb. A total of 17,375 and 17,171 structural variations and 131 and 128 copy number variations were identified in the autotetraploid and its diploid counterpart, respectively. We detected 140 large-effects SNPs and InDel variants that might be related to the embryo sac fertility of autotetraploid rice, including 10 genes that may be closely associated with the development of the embryo sac. Of these, Os02g0292600 and Os06g0565200 were specifically expressed in the ovary. Mature embryo sac fertility was observed through whole-mount eosin B-staining confocal laser scanning microscopy. Many abnormalities were found in the embryo sac of T446, including embryo sac degeneration, embryo sac without female germ unit, abnormal polar nuclei, and poly-eggs, which, in turn, resulted in low seed set. However, whole-genome polymorphisms and genetic differences were high and exhibited broad prospects for genetic improvement. Genetic mutations in genes associated with embryo sac fertility in polyploid rice require further studies.Öğe Development, characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.)(Blackwell Publishing Ltd, 2015) Andeden, Enver Ersoy; Baloch, Faheem Shahzad; Çakır, Esra; Toklu, Faruk; Özkan, HakanLentil is the sixth most important pulse crop terms of production in the world, but the number of available and mapped SSR markers are limited. To develop SSR markers in lentil, four genomic libraries for (CA)n, (GA)n, (AAC)n and (ATG)n repeats were constructed. A total of 360 SSR primers were designed and validated using 15 Turkish lentil cultivars and genotypes. The most polymorphic repeat motifs were GA and CT, with a mean number of alleles per locus of 7.80 and 6.55, respectively. Seventy-eight SSR primers amplified a total of 400 polymorphic alleles, whereas 71 SSR primers produced markers within the expected size range. For 78 polymorphic SSR primers, the average number of alleles per locus was 5.1 and PIC value ranged from 0.07 to 0.89, with an average of 0.58. A linkage map was constructed using 92 individual F2 plants derived from a cross between Karacadağ × Silvan, with 47 SSR markers. The SSR markers developed in this study could be used for germplasm classification and identification and mapping of QTL in lentil. © 2015 Blackwell Verlag GmbH.Öğe Fasulye (Phaseolus Vulgaris) Tohumlarında ve Baklalarında Çinko (Zn) Birikimini İncelemek İçin Metal Tolerans Proteinlerinin (MTP) Belirlenmesi, Moleküler Ifadesi Ve Fonksiyonel Karakterizasyonu(2020) Baloch, Faheem Shahzad; Karaköy, TolgaMetal tolerans proteini olarak adlandırılan MTP gen ailesi ile ilgili çalısmalar birçok bitki türünde yapılmasına ragmen fasulye için henüz mevcut bir çalısma bulunmamaktadır. Bu nedenle bu çalısmada MTP genlerinin fasulye tohumlarında ve baklalarında olan çinko (Zn) birikimindeki fonksiyonel rolüne odaklanılmıstır. Çalısmada iki çesit fasulye kültüvarı BN-16 ve SV-18 kullanılmıstır. Çinko (0/Kontrol, 5 ?M ZnCl2 ve 10 ?M ZnCI2), hidroponik kosullarda yetistirilen kültüvarlara uygulanmıs, ekspresyon seviyeleri ve Zn içerigi tohumlarda ve baklalarda belirlenmistir. MTP gen ailesinin üç geni PvMTP1, PvMTP4 ve PvMTP12 incelenmistir. Çinko uygulaması altında SV-18 kültüvarında yalnızca PvMTP1 geninin ekspresyon seviyesinin arttıgı ve tohumlarında ve baklalarında yüksek Zn içerigine sahip oldugu gözlenmistir. Daha sonraki çalısmada PvMTP1'in fonksiyonel karakterizasyonuna odaklanılmıstır. Kompozit fasulye bitkileri yetistirilmis ve kompozit bitkilerin köklerinde yüksek PvMTP1 ekspresyonu dogrulanmıstır. Çinko 0/Kontrol, 5 ?M ZnCl2 ve 10 ?M ZnCI2 uygulanan kompozit fasulye bitkilerinin tohumlarında ve baklalarında Zn içerigi belirlenmistir. Zn içerigi tohumlarda ve baklalarda Zn birikim aktivitesinin rolünü destekleyerek kompozit bitkilerin baklalarında ve tohumlarında daha yüksek bulunmustur. PvMTP1'in hücre altı lokalizasyonu, Zn içeriginin tohumda birikmesindeki rolünü dogrulayarak tonoplastta lokalize olan protein oldugunu göstermistir. Tüm veriler degerlendirildiginde, PvMTP1 tonoplastta lokalize olarak Zn tasımasını düzenlemekte ve fasulye bitkilerinin tohumlarında Zn birikiminde rol oynamaktadır. PvMTP1, tohumlarda çinko verimli genotiplerinin taranması için fonksiyonel bir isaretleyici olarak kullanılabilmesinin yanı sıra çinko ile biyolojik olarak zenginlestirilmis/biyofortifike genotiplerin gelistirilmesinde potansiyel olabilir. Ileride bu gen, kompozit bitkilerden faydalanılarak Zn ile kirlenmis maden alanlarının temizlenmesinde de kullanılabilir. Bu nedenle PvMTP1, biyofortifikasyon ve fitoremediasyon amaçları için büyük bir potansiyele sahip olabilir.Öğe Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposonbased markers(2020) Yıldız, Mehtap; Koçak, Metin; Nadeem, Muhammad Azhar; Cavagnaro, Pablo; Barboza, Karina; Baloch, Faheem Shahzad; Argün, Duygu; Keleş, DavutCapsicum 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 ~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 (UPGMA, 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 germplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.Öğe Genome-wide association mapping of total antioxidant capacity, phenols, tannins, and flavonoids in a panel of Sorghum bicolor and S. bicolor x S. halepense populations using multi-locus models(Public Library Science, 2019) Habyarimana, Ephrem; Dall'Agata, Michela; De Franceschi, Paolo; Baloch, Faheem ShahzadSorghum is widely used for producing food, feed, and biofuel, and it is increasingly grown to produce grains rich in health-promoting antioxidants. The conventional use of grain color as a proxy to indirectly select against or for antioxidants polyphenols in sorghum grain was hampered by the lack of consistency between grain color and the expected antioxidants concentration. Marker-assisted selection built upon significant loci identified through linkage disequilibrium studies showed interesting potential in several plant breeding and animal husbandry programs, and can be used in sorghum breeding for consumer-tailored antioxidant production. The purpose of this work was therefore to conduct genome-wide association study of sorghum grain antioxidants using single nucleotide polymorphisms in a novel diversity panel of Sorghum bicolor landraces and S. bicolor x S. halepense recombinant inbred lines. The recombinant inbred lines outperformed landraces for antioxidant production and contributed novel polymorphism. Antioxidant traits were highly correlated and showed very high broad-sense heritability. The genome-wide association analysis uncovered 96 associations 55 of which were major quantitative trait loci (QTLs) explaining 15 to 31% of the observed antioxidants variability. Eight major QTLs localized in novel chromosomal regions. Twenty-four pleiotropic major effect markers and two novel functional markers (Chr9_1550093, Chr10_50169631) were discovered. A novel pleiotropic major effect marker (Chr1_61095994) explained the highest proportion (R-2 = 27-31%) of the variance observed in most traits evaluated in this work, and was in linkage disequilibrium with a hotspot of 19 putative glutathione S-transferase genes conjugating anthocyanins into vacuoles. On chromosome four, a hotspot region was observed involving major effect markers linked with putative MYB-bHLH-WD40 complex genes involved in the biosynthesis of the polyphenol class of flavonoids. The findings in this work are expected to help the scientific community particularly involved in marker assisted breeding for the development of sorghum cultivars with consumer-tailored antioxidants concentration.Öğe Identification, phylogenetic analysis, and expression patterns of the SAUR gene family in loquat (Eriobotrya Japonica)(2020) Gan, Xiaoqing; Jing, Yi; Shahid, Muhammad Qasim; He, Yehua; Baloch, Faheem ShahzadSmall auxin-up RNAs (SAURs) are the most frequent and primary auxin responsive genes, and they are commonly used as early auxin-responsive markers. Until now, no SAUR gene has been identified in Eriobotrya plants. In this study, we used Arabidopsis SAUR sequences as a query to search against the loquat genome sequence. In total, we obtained 57 SAUR genes in loquat, hereafter referred to as Eriobotrya japonica SAUR (EjSAUR) genes, which ranged from 267 to 735 bp in the coding sequence with predicted proteins of 88–244 aa. A total of 47 EjSAUR genes were distributed on 11 chromosomes of the loquat genome. Based on their physical positions, 80.9% (38 of 47) of the EjSAUR genes were clustered together on the loquat chromosomes, suggesting that tandem duplicate genes might be the major mechanism for the expansion of this family. The expression analysis displayed high expression divergence among the different organs, which suggested that EjSAUR genes may play an important role in different organs. These results laid a foundation for the functional validation of EjSAUR genes in Eriobotrya plants.Öğe Phenotypic characterization of 183 Turkish common bean accessions for agronomic, trading, and consumer-preferred plant characteristics for breeding purposes(Mdpi, 2020) Nadeem, Muhammad Azhar; Karaköy, Tolga; Yeken, Mehmet Zahit; Habyarimana, Ephrem; Hatipoğlu, Rüştü; Çiftçi, Vahdettin; Nawaz, Muhammad Amjad; Sönmez, Ferit; Baloch, Faheem ShahzadPlant landraces represent a repository of a gene pool, local adaptation of their domestic species, and thereby are considered a great source of genetic variations. Such genetic variation can be helpful to mitigate the current and future food challenges. A total of 183 common bean accessions including three commercial varieties collected from 19 Turkish provinces were grown to record their morpho-agronomic variations and to evaluate the best performing accessions under multi-environmental conditions. Plant height, days to maturity, pods weight, seed length, and 100-seed weight were used to evaluate the best performing accessions under different environmental conditions. A wide range of variations for traits like days to maturity (99-161), plant height (21-168.7 cm), seed length (7.41-16.4 mm), seeds per plant (17.8-254.4), and 100-seeds weight (24.97-73.8 g) were observed and can be useful for breeding purposes. The analytic results derived from the first three eigenvectors suggested that plant height, plant weight, 100-seed weight, and days to flowering were biologically significant bean traits. Seed yield per plant was positively and significantly correlated with plant weight and pods weight. Genotype x environment biplot discriminated the studied common bean accessions based on their plant height and growth habit. Plant height, days to maturity, seed width, and first pod height were found highly heritable traits and were least affected by environmental forces. Among 19 provinces, accessions of Bilecik showed maximum pods per plant, seed yield per plant and 100-seed weight, while Erzincan and Sivas provinces reflected the prevalence of bushy and early maturing accessions. Information provided herein comprehensively explored the occurrence of genotypic variations which can be used for the development of candidate varieties responding to breeder, farmer, and consumer preferences.Öğe Phylogenetic and taxonomic relationship of Turkish wild and cultivated emmer (triticum turgidum ssp. dicoccoides) revealed by ipbs-retrotransposons markers(Friends Science Publ, 2019) Arystanbekkyzy, Meerim; Nadeem, Muhammad Azhar; Aktaş, Hüsnü; Yeken, Mehmet Zahit; Zencirci, Nusret; Nawaz, Muhammad Amjad; Ali, Fawad; Baloch, Faheem ShahzadWild emmer (Triticum turgidum ssp. dicoccoides) is the progenitor of cultivated wheat. Turkey is the main center of wheat and plays a vital role in the spread of various crops among the continents. Karacadag region is considered as the domestication center of wheat and still, hundreds of landraces are prevalent. A total of 29 wild emmer landraces, 4 cultivated emmer wheat (T. turgidum ssp. dicoccum) and five durum wheat (T. turgidum ssp. durum) cultivars were investigated for the genetic diversity and phylogenetic relationship using the iPBS-retrotransposons markers. Mean polymorphism and polymorphic information contents (PIC) were 87.85% and 0.660, respectively. Mean effective numbers of alleles (1.961), Shannon's Information Index (0.682) and gene diversity (0.489) reflected the occurrence of a great level of variations. T17 and Chermik-1 genotypes were found much distinct and breeding valuable genotypes for wheat breeding. The unweighted pair-group method with arithmetic means (UPGMA) divided all genotypes by their genetic makeup and geographical locations. Among 3 species, UPGMA based clustering clearly separated the durum wheat from wild emmer and cultivated emmer wheat. Results are clearly supported by the principal coordinate analysis (PCoA) and model-based structure algorithm. Information provided herein comprehensively reflected the power of iPBS-retrotransposons for the diversity and phylogenetic relationship investigation and reflected that this marker system can be effectively applied to investigate phylogenetic and taxonomic relationship in any crop due to its universal nature. (C) 2019 Friends Science PublishersÖğe Türkiye'deki Fasulye Gen Kaynaklarının Önemli Agronomik, Fiziko-Kimyasal, Mineral, Antioksidan ve Pişirme Özelliklerinin Genomik Bölgelerinin Genom Çapı İlişkilendirme Çalışmaları (GWAS) ile Belirlenmesi(2019) Baloch, Faheem Shahzad; Kantar, Faik; Sönmez, Ferit; Karaköy, Tolga; Gündoğdu, MüttalipYemeklik baklagiller içerisinde yer alan fasulye (Phaseolus vulgaris L.), gerek dünya gerekse ülke tarımında önemli bir yere sahip olup, birçok ülkede olduğu gibi Türkiye?de de yaygın olarak tüketilmektedir. Mineral maddeler, vitaminler ve protein (%18-31.6) bakımından oldukça zengin olan fasulye, insan beslenmesinde önemli bir yere sahiptir. Ülkemizde kuru fasulye ıslahı genelde klasik ıslah yöntemleri kullanılarak gerçekleştirilmiştir. Bununla birlikte dünyada abiyotik ve biyotik faktörlere karşı çok sayıda gen ve bunlarla ilişkili moleküler markör tespit edilmiş olup, bunlar ıslah çalışmalarında yaygın olarak kullanılmaktadır. Klasik ıslah yöntemlerinde karşılaşılan problemleri elemine etmek için Markör Destekli Seleksiyon (MAS) yönteminin yapılan ıslah çalışmalarına dahil edilmesi oldukça önem taşımaktadır. Bu çalışma, Bolu Abant İzzet Baysal Ziraat ve Doğa Bilimleri Fakültesi, Tarla Bitkileri Bölümü yürütücülüğünde, aynı fakültenin Bahçe Bitkileri Bölümü ve Tohum Bilim ve Teknolojisi Bölümü, Sivas Cumhuriyet Üniversitesi, Meslek Yüksekokulu ve Akdeniz Üniversitesi, Ziraat Fakültesi, Tarla Bitkileri Bölümü iş birliği ile gerçekleştirilmiştir. Çalışma sonucunda, Türk yerel fasulye popülasyonlarında yüksek düzeyde hem fenotipik hem de genotipik çeşitlilik gözlemlenmiştir. Çiçeklenme gün saysı, bakla bağlama gün sayısı, bitki boyu, olgunlaşma gün sayısı, bitkideki bakla sayısı, ve 100 tane ağırlığı gibi özelikler Türk yerel fasulye popülasyonlarında var olan fenotipik çeşitlilikte önemli rol oynamışlardır. Fasulye genomunda, 11 kromozom boyunca dağılım gösteren toplamda 15.608 DArTseq marköründen en iyi olan 11.839 DArTseq markörü kullanılmış ve bunlardan %24.14?ünün yeni markör olduğu belirlenmiştir. Fasulye genomunda, 11 kromozom boyunca dağılım gösteren toplamda 14.290 SNP marköründen 12.871 SNP markörü kullanılmış ve bu markörlerden %9.93?ünün yeni markör olduğu belirlenmiştir. Çalışmada, 37 farklı özellik (agronomik, mineral, kalite ve pişirme) çalışılmış, DArTseq markörleriyle yapılmış GWAS analizinde 20 özellikte önemli ilişki tespit edilmiş, SNP markörleriyle yapılmış analizde 26 özellikte önemli ilşki tespit edilmiştir. SNP markörünün DArTseq ile kıyaslandığında daha bilgi verici olduğu saptanmıştır. SNP- 3384591, SNP-8205001, SNP-1312148, SNP-3368865, SNP-3381021, SNP-3382392, SNP- 8205132 ve DArTseq 8214418 markörlerinin farklı birkaç özellik ile önemli ilişkisi olduğu tespit edilmiştir. Bunların fasulye ıslahında etkin bir şekilde kullanılması tavsiye edilmektedir. Tanımlanan bağlantılı markörlerin çok lokasyonlu veya çok yıllık denemeler yoluyla doğruluğunun test edilmesi gerekmektedir. Doğruluğu kesinleşmiş markörlerin KASP sistemine dönüştürülerek fasulye ıslahında kullanılması mümkündür. Proje ekibi olarak, projede yer alan tüm kurumlara ve özellikle de TUBİTAK?a (Proje No:215O630) destekleri için teşekkürlerimizi sunuyoruz.
