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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 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, AhmadAgricultural 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.Öğe DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum Sativum) germplasm from Turkey(Pergamon-Elsevier Science Ltd, 2015) Baloch, Faheem Shehzad; Alsaleh, Ahmad; Saenz de Miera, Luis E.; Hatipoğlu, Rüştü; Çiftçi, VahdettinRetrotransposons have been highly studied in monocots; however retrotransposon diversity in dicot crops has not been well documented. Our objective was to assess the diversity harbored by field pea landraces using retrotranposon markers. In this research, molecular characterization of 104 landraces and 34 field pea breeding lines was assessed using newly developed iPBS-retrotransposon markers. The 12 iPBS-retrotransposon primers generated a total 106 scorable bands, and 81 of these were found to be polymorphic (76.4%), with an average of 6.75 polymorphic fragments per primer. Polymorphism information content (PIC) ranged from 0.33 to 0.84 with an average of 0.61. It was evident that field pea landraces from the same geographical region were often placed in different groups in the neighbor joining analysis, indicating that grouping based on genetic parameters was not closely related to the geographical origin. The population structure was determined by using STRUCTURE software, and three populations at K = 3 and five populations at K = 5 were identified among landraces. The plentiful diversity present in Turkish field pea landraces could be used as genetic resource in designing breeding program, and may also contribute to worldwide pea breeding programs. Our data also suggested a role of iPBS-retrotransposons as 'a universal marker' for molecular characterization of pea germplasm. (C) 2015 Elsevier Ltd. All rights reserved.Öğe High levels of segregation distortion in the molecular linkage map of bread wheat representing the West Asia and North Africa region(Tubitak Scientific & Technical Research Council Turkey, 2016) Baloch, Faheem Shehzad; Alsaleh, Ahmad; Andeden, Enver Ersoy; Hatipoğlu, Rüştü; Nachit, MiloudiThe Fertile Crescent is a primary center of wheat domestication and diversity. Despite its importance for bread wheat breeding, few efforts have been made to fully understand the genetic structure of the Anatolian bread wheat. A lack of information regarding the genetic structure of the bread wheat from this region is evident. Therefore, this study aimed to provide new insights into the genetic structure of bread wheat from Anatolia. A genetic linkage map was constructed based on recombinant inbred lines derived from a cross between the Turkish cultivar Gerek-79 and the Moroccan cultivar Arrehane, by using DArT markers anchored with simple sequence repeat markers. This map consisted of 54 linkage groups belonging to 21 bread wheat chromosomes, spanning a total of 935.629 cM. The total number of mapped markers varied from 5 to 87, depending on the chromosome. Seventy-seven DArT markers with unpublished chromosomal locations were mapped on different chromosomes, whereas 23 were mapped onto chromosomes that deviated from those detailed in the literature. This linkage map represents a key starting point towards our understanding of the genome structure of Anatolian bread wheat, which would, in turn, permit us to genetically dissect important agromorphological and quality characteristics. This linkage map will be useful for the identification of QTL for biotic and abiotic stresses, and for important agronomic traits that are valuable for Anatolian wheat.Öğe Identification of chromosomal regions in the genetic control of quality traits in durum wheat (Triticum Turgidum L.) from the Fertile Crescent(2019) Alsaleh, Ahmad; Baloch, Faheem Shehzad; Azrak, Mohamad; Hamwıeh, Aladdin; Cömertpay, Gönül; Hatipoğlu, Rüştü; Nachıt, Miloudi; Özkan, HakanDurum wheat genetic resources from Turkey and Syria are expected to harbor novel alleles for most traits that are of interest to breeders and consumers. However, there have not been sufficient efforts to investigate the genetic structure of this gene pool. In this study, cultivar Kunduru-1149 (selected from one of the unique landraces, Kunduru) from Anatolia was crossed with a Syrian cultivar, Cham1, to produce recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. The RIL population was genotyped with simple sequence repeats, amplified fragment length polymorphism, and seed storage protein markers and analyzed for 9 different important quality traits of durum wheat in 8 different environments in Turkey, Syria, and Lebanon. We identified 59 QTLs of various quality and rheology traits using single-marker analysis. Some of the QTLs were also reported in earlier studies; however, new major QTLs were also identified in our QTL mapping population. In future studies, after validation, the markers linked with these QTLs can be used in marker-assisted durum wheat breeding.Öğe Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species(Pergamon-Elsevier Science Ltd, 2015) Baloch, Faheem Shehzad; Derya, Muazzez; Andeden, Enver Ersoy; Alsaleh, Ahmad; Cömertpay, Gönül; Kilian, Benjamin; Özkan, HakanEven though lentil has been an important food legume for centuries, genetic studies in lentil are still in their infancy. Genetic diversity and relationships among wild Lens species from Turkey has seldom been investigated. Additionally, a limited number of simple sequence repeat (SSR) markers have been developed for use in breeding and genetic studies of lentil crop. In this study, molecular characterization of 50 accessions mostly from Turkey, belonging to 6 wild and 1 cultivated Lens species, was performed using newly developed inter-primer binding site (iPBS) retrotransposons and inter-SSR (ISSR) markers. The 10 iPBS primers generated a total of 151 scorable bands, of which 150 were polymorphic (99.3%) with an average of 15.0 polymorphic fragments per primer. The 10 ISSR primers detected 138 scorable bands showing 100% polymorphism, with an average of 13.5 bands per primer. The average polymorphism information content (PIC) value for ISSR markers (0.97) was higher than that for iPBS markers (0.90). Lens orientalis was found to be the most diverse species, raising the possibility of wide crosses with cultivated species Lens culinaris. Cultivated varieties also showed high level of polymorphism, at 82.92% and 51.92% with ISSR and iPBS markers, respectively. Lens lamottei and Lens tomentosus were found as the least polymorphic species using both marker systems. The grouping of accessions and species within clusters were almost similar when iPBS and ISSR graphs were compared. Our data also suggested the role of iPBS-retrotransposons as 'a universal marker' for molecular characterization of wild and cultivated Lens species. (C) 2014 Elsevier Ltd. All rights reserved.Öğe Phenotypic and genotypic intra-diversity among Anatolian durum wheat "Kunduru" landraces(Pergamon-Elsevier Science Ltd, 2016) Alsaleh, Ahmad; Baloch, Faheem Shehzad; Nachit, Miloudi; Özkan, HakanKunduru is an important Anatolian landrace having peculiar traits that are appreciated by farmers and breeders. 33 accessions known as Kunduru collected by ICARDA from six geographical provinces of Turkey, were used to study the phenotypic and genotypic intra-diversity. Kunduru landraces exhibited high intra-diversity for most of the studied morphological traits. GPC (12.10-14.90%), vitreousness (75-100%), TKW (31.80-56.70 g), YP (4.70-8.00 ppm), b*-value (1430-19.50), ash content (1.60-2.0%) and gluten strength (14-60 ml) showed marked variations. Gliadin and glutenin banding patterns showed high polymorphism. 65 alleles were detected with 14 SSR markers, giving a mean of 6.77 alleles per locus. The average PIC value was 0.44 and ranged from 0.11 to 0.70. The average genetic distance between pairs of landraces was 0.47 and ranged between 0.11 and 0.72. This study showed that Kunduru landraces maintains high allelic variation. PCoA indicated that eco-geographical variables have a significant effect on SSR diversity as well as morphological traits. Many of the landraces studied are in danger of disappearing from the local farmers' fields; this study demonstrates the importance of maintaining and conserving this precious genetic resources. (C) 2016 Elsevier Ltd. All rights reserved.Öğe Population structure of rice varieties used in Turkish rice breeding programs determined using simple-sequence repeat and inter-primer binding site-retrotransposon data(Funpec-Editora, 2016) Cömertpay, Gönül; Baloch, Faheem Shehzad; Derya, Muazzez; Andeden, Enver Ersoy; Alsaleh, AhmadEffective breeding programs based on genetic diversity are needed to broaden the genetic basis of rice (Oryza sativa L.) in Turkey. In this study, 81 commercial varieties from seven countries were studied in order to estimate the genomic relationships among them using nine interprimer binding site (iPBS)-retrotransposon and 17 simple-sequence repeat (SSR) markers. A total of 59 alleles for the SSR markers and 96 bands for the iPBS-retrotransposon markers were detected, with an average of 3.47 and 10.6 per locus, respectively. Each of the varieties could be unequivocally identified by the SSR and iPBS-retrotransposon profiles. The iPBS-retrotransposon-and SSR-based clustering were identical and closely mirrored each other, with a significantly high correlation (r = 0.73). A neighbor-joining cluster based on the combined SSR and iPBS-retrotransposon data divided the rice varieties into three clusters. The population structure was determined using the STRUCTURE software, and three populations (K = 3) were identified among the varieties studied, showing that the diversity harbored by Turkish rice varieties is low. The results indicate that iPBS-retrotransposon markers are a very powerful technique to determine the genetic diversity of rice varieties.Öğe Stripe rust resistance gene Yr15 in Turkish and Kazakhstan wheat germplasms and the potential of Turkish wild emmer for stripe rust breeding(Springer Nature, 2024) Baloch, Faheem Shehzad; Ali, Amjad; Tajibayev, Daniyar; Nadeem, Muhammad Azhar; Ölmez, Fatih; Aktaş, Hüsnü; Alsaleh, AhmadPuccinia striiformis f. sp. tritici (Pst) is a devastating obligate fungal biotroph that causes stripe rust disease in wheat in temperate and cooler regions, especially in Kazakhstan and Turkey. Chemical control of Pst is not a sustainable or economic strategy in these countries. Therefore, a suitable alternative to these pesticides, such as the development of resistant wheat cultivars, is needed. During the present investigation, a large set of wheat germplasms was characterized to determine the presence of the broad-spectrum resistance Yr15 gene using Y15K1_F2/uhw30_1R primers. This collection contained 360 accessions including 233 durum and bread wheat collected from KASIB cultivars and advanced lines that were developed by eight breeding programs within the Kazakhstan-Siberia Wheat Improvement Network and Turkey, and 127 wild emmer collected from Turkey only. The positive control was wild emmer IDs WEW 83-1, WEW 84-1, and WEW-85, which previously showed positive amplification of the Yr15 gene with these primers. Yr15, a broad-spectrum R-gene derived from wild emmer wheat encoding a putative kinase-pseudokinase protein designated as wheat tandem kinase 1, comprises a unique R-gene structure in wheat against the yellow (stripe) rust. None of the tested cultivated wheat germplasms from 174 durum wheat of the KASIB Network or 59 of bread wheat from Turkey showed positive amplification, but 89 of 127 (70.07%) wild Triticum dicoccoides showed positive amplification. The collection from the Karacadağ regions showed the maximum number of genotypes (46) with positive amplification for Yr15, followed by Eruh (10), Şırnak (5), Malazgir-Tunceli (4), Tunceli (4), Şırnak-Uludere yol (3), Tunceli-Pülümür (3), and Karacadağ/Kerteş Köyü –Siverek (3). We conclude that wild wheat cultivars are a good source of the Yr15 gene and that introgression of this gene into the cultivated wheat germplasm of both countries should be performed to manage the Pst pathogen in the future. © The Author(s), under exclusive licence to Springer Nature B.V. 2023.Öğe A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from Central Fertile Crescent(Public Library Science, 2017) Baloch, Faheem Shehzad; Alsaleh, Ahmad; Shahid, Muhammad Qasim; Çiftçi, Vahdettin; de Miera, Luis E. Saenz; Nadeem, Muhammad AzharUntil now, little attention has been paid to the geographic distribution and evaluation of genetic diversity of durum wheat from the Central Fertile Crescent (modern-day Turkey and Syria). Turkey and Syria are considered as primary centers of wheat diversity, and thousands of locally adapted wheat landraces are still present in the farmers' small fields. We planned this study to evaluate the genetic diversity of durum wheat landraces from the Central Fertile Crescent by genotyping based on DArTseq and SNP analysis. A total of 39,568 DArTseq and 20,661 SNP markers were used to characterize the genetic characteristic of 91 durum wheat land races. Clustering based on Neighbor joining analysis, principal coordinate as well as Bayesian model implemented in structure, clearly showed that the grouping pattern is not associated with the geographical distribution of the durum wheat due to the mixing of the Turkish and Syrian landraces. Significant correlation between DArTseq and SNP markers was observed in the Mantel test. However, we detected a non-significant relationship between geographical coordinates and DArTseq (r = -0.085) and SNP (r = -0.039) loci. These results showed that unconscious farmer selection and lack of the commercial varieties might have resulted in the exchange of genetic material and this was apparent in the genetic structure of durum wheat in Turkey and Syria. The genomic characterization presented here is an essential step towards a future exploitation of the available durum wheat genetic resources in genomic and breeding programs. The results of this study have also depicted a clear insight about the genetic diversity of wheat accessions from the Central Fertile Crescent.
