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Öğe Allelic variations of glutenin subunits and their association with quality traits in bread wheat genotypes(2017) Aktaş, Hüsnü; Baloch, Faheem ShehzadThe present study was conducted to evaluate the genotype × environment interaction of the yield and quality traits for five bread wheat varieties commonly grown in the Southeastern Anatolia Region of Turkey and 20 advanced lines developed within the framework of the International Winter Wheat Improvement Project. We also determined the allelic pattern of the Glu-1 and Glu-3 loci of these genotypes and examined whether these loci had an effect on the quality traits. There was a significant variation among the genotypes and environments in terms of grain yield, protein content, sedimentation volume (SV), and the extensograph dough energy value (EDEV). The results of the study indicated that genotypic effect was more influential on SV and EDEV than environmental effect; thus, both traits could be used in breeding programs to develop elite cultivars with better quality. Twelve different high-molecularweight (HMW) glutenin alleles were identified at the Glu-A1, Glu-B1, and Glu-D1 loci, resulting in 14 allelic combinations, and 17 different alleles were observed in 19 combinations for low-molecular-weight (LMW) subunits. Furthermore, among all the genotypes, 13 + 16 and 13 + 19 alleles at Glu-B1 and 5 + 12 at Glu-D1 were observed to have the lowest frequency. Our study indicated that the combinations of HMW glutenin alleles with 2* at Glu-A1, 17 + 18 and 13 + 16 at Glu-B1, and 5 + 10 at Glu-D1, as well as the combinations of LMW alleles with subunits c and d at Glu-A3; subunits d, b, c, and g at Glu-B3; and subunits a and b at Glu-D3 had positive effects on the quality traits.Öğe Ancient Wheats(Springer International Publishing, 2022) Zencirci, Nusret; Ulukan, Hakan; Baloch, Faheem Shehzad; Mansoor, Shahid; Rasheed, AwaisWheat (Triticum L.), an annual herbaceous plant in Poacae (Gramineae) family, settles in the Triticeae (Hordeae) subfamily. The grasses (Poaceae Barnhart) are the fifth largest (monocotyledonous flowering) plant family and of great importance for human civilization and life. Cereal crops such as maize, wheat, rice, barley, and millet are the domesticated ones in the family. It is still the most vital economical plant family in modern times, providing food, forage, building materials (bamboo, thatch), and fuel (ethanol). Wheat has many accessions in national and international gene banks. The estimated number of wheats by FAO in 2010 is 856,000, and, followed by rice (774,000), and barley (467,000). However, the recent consumer's (misdirected) focus on gluten content and nutritional value urges scientists to reexamine their knowledge about wheat (i.e., origin, evolution, and general and special quality characteristics), as well as their wild relatives and landraces for newer possible genetic resources. Cultured or non-cultured ancestral wheats: einkorn, emmer, wild emmer, spelt, macha, and vavilovii are still limitedly grown on the higher areas in Turkey, Italy, Germany, Morocco, Israel, and Balkan countries. They are exploited mostly for their desired agronomic, and specific quality. In some cultures, wheat species are believed to be therapeutic, with bioactive compounds that reduce and inhibit stubborn illnesses such as diabetes, cancer, Alzheimer, and cardiovascular diseases. In this book, we summarize the importance of ancestral wheat species, and provide a prospect for their future with special considerations in terms of species conservation and improvement. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022.Öğe Assessing genetic diversity of potato genotypes using inter-PBS retrotransposon marker system(Cambridge Univ Press, 2018) Demirel, Ufuk; Tındaş, İlknur; Yavuz, Caner; Baloch, Faheem Shehzad; Çalışkan, Mehmet EminHaving knowledge on genetic similarity and DNA profile of potato genotypes facilitates a breeder's decision for parent selection and provides accurate variety identification. Fingerprinting and identification of genetic similarity among 151 potato genotypes were achieved using an inter-primer-binding sites (iPBS) retrotransposon marker system. Our study is the first application of iPBS markers for fingerprinting and distinguishing large numbers of Solanum tuberosum genotypes. Initially, 16 potato genotypes were screened using 45 iPBS retrotransposon markers to identify polymorphisms. Seventeen of these primers were selected for fingerprinting the whole set of accessions due to strong, reproducible and polymorphic bands. The 17 iPBS primers produced 290 scorable bands of which 224 were polymorphic. The number of bands per primer ranged from 10 to 26 with an average of 17.1. The number of polymorphic bands per primer was between 6 and 21. The polymorphism percentage per primer ranged from 46.2 to 100.0% with an average of 77.2% per primer. The mean polymorphism information content (PIC) values of iPBS primers varied from 0.12 to 0.31 per primer. Genetic similarity based on Jaccard's coefficient of potato genotypes ranged from 0.61 to 0.93 with an average of 0.73. The data produced herein may be used for selection of appropriate parents and variety description in the future. The findings of the present study suggest that iPBS retrotransposons are powerful and easy DNA markers for fingerprinting the large samples of potato germplasm.Öğe Characterization of cellulose synthase A (CESA) gene family in eudicots(Springer/Plenum Publishers, 2019) Nawaz, Muhammad Amjad; Lin, Xiao; Chan, Ting-Fung; Imtiaz, Muhammad; Rehman, Hafiz Mamoon; Baloch, Faheem ShehzadCellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms. Duplications have played an important role in expansion of CESA gene family members in eudicots. Co-expression networks showed that primary and secondary cell wall modules are duplicated in eudicots. We also identified 230 simple sequence repeat markers in 103 eudicot CESAs. The 13 identified conserved motifs in eudicots will provide a basis for gene identification and functional characterization in other plants. Furthermore, we characterized (in silico) eudicot CESAs against senescence and found that expression levels of CESAs decreased during leaf senescence.Öğe 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, VahdettinTurkey 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.Öğe Development of a competent and trouble free dna isolation protocol for downstream genetic analyses in glycine species(2016) Nawaz, Muhammad Amjad; Baloch, Faheem Shehzad; Rehman, Hafiz Mamoon; Le, Bao; Akther, FahimaExtraction of deoxyribose nucleic acid (DNA) from plants is preliminary step in molecular biology. Fast and cost effective genomic DNA isolation from Glycine species for downstream application is a major bottleneck. Here we report a high throughput and trouble free method for genomic DNA extraction from leaf and seeds of Glycine species with high quality and quantity. Protocol reports the optimization by employing different concentrations of CTAB and PVP in extraction buffer. Efficiency of optimized protocol was compared with frequently used DNA extraction methods. Wide adoptability and utility of this protocol was confirmed by DNA extraction from leaves as well as seeds of G. max, G. soja, G. tomentella and G. latifolia. Extracted DNA was successfully subjected to PCR amplification of five microsatellite markers and four putative glycosyltransferase genes. DNA extraction protocol is reproducible, trouble free, rapid and can be adopted for plant molecular biology applications.Öğe Development of a Competent and Trouble Free DNA Isolation Protocol for Downstream Genetic Analyses in Glycine Species(2016) Nawaz, Muhammad Amjad; Baloch, Faheem Shehzad; Rehman, Hafiz Mamoon; Le, Bao; Akther, Fahima; Yang, Seung Hwan; Chung, GyuhwaExtraction of deoxyribose nucleic acid (DNA) from plants is preliminary step in molecular biology. Fast and cost effective genomic DNA isolation from Glycine species for downstream application is a major bottleneck. Here we report a high throughput and trouble free method for genomic DNA extraction from leaf and seeds of Glycine species with high quality and quantity. Protocol reports the optimization by employing different concentrations of CTAB and PVP in extraction buffer. Efficiency of optimized protocol was compared with frequently used DNA extraction methods. Wide adoptability and utility of this protocol was confirmed by DNA extraction from leaves as well as seeds of G. max, G. soja, G. tomentella and G. latifolia. Extracted DNA was successfully subjected to PCR amplification of five microsatellite markers and four putative glycosyltransferase genes. DNA extraction protocol is reproducible, trouble free, rapid and can be adopted for plant molecular biology applications.Öğe Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome(Springer Heidelberg, 2019) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Ercişli, Sezai; Baloch, Faheem ShehzadTianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.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 DNA fingerprinting and genetic diversity analysis of world quinoa germplasm using iPBS-retrotransposon marker system(Tubitak Scientific & Technical Research Council Turkey, 2020) Barut, Muzaffer; Nadeem, Muhammad Azhar; Karaköy, Tolga; Baloch, Faheem ShehzadQuinoa is an important staple food crop for millions of impoverished rural inhabitants of the Andean region. Quinoa is considered a good source of protein,vitamins, minerals, and antioxidants. This study aimed to investigate the genetic diversity and population structure of world quinoa gennplasm originating from 8 countries through the iPBS-retrotransposon marker system. Molecular characterization was performed using the 11 most polymorphic primers. A total of 235 bands were recorded, of which 66.8% were polymorphic. Mean polymorphism information content (PIC) was 0.410. Various diversity indices including mean effective number of alleles (1.269), mean Shannon's information index (0.160) and gene diversity (0.247) revealed the existence of sufficient amount of genetic diversity in studied germplasm. Bolivia-17 and Mexico-1 were found to be genetically distinct accessions and can be suggested as candidate parents for future breeding activities. Various diversity indices were also calculated among germplasm collection counries and the results clearly showed the existence of higher genetic diversity in Bolivian and Peruvian accessions. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) grouped quinoa germplasm according to their collection country. Analysis of molecular variance (AMOVA) revealed that most of the variations (69%) in world quinoa germplasm are due to differences within populations. Findings of this study can be used for deeper understanding of the genetic relationship and in the determination of appropriate breeding and conservation strategies for quinoa.Öğe Effects of different priming applications on seed germination and some agromorphological characteristics of bread wheat (Triticum aestivum L.)(Turkiye Klinikleri Journal of Medical Sciences, 2015) Toklu, Faruk; Baloch, Faheem Shehzad; Karaköy, Tolga; Özkan, HakanThis study was conducted to determine the effects of some priming treatments on seed germination properties, grain yield, and several agromorphological characteristics of bread wheat. Two commonly grown bread wheat varieties, namely Adana-99 and Pandas, were selected for experimentation conducted during the 2007–08 and 2008–09 growing periods. The seeds of the Adana-99 and Pandas wheat varieties were primed with the following: (1) distilled water, (2) 100 ppm indole-3-acetic acid (IAA), (3) 2.5% potassium chloride (KCl), (4) 1% potassium dihydrogen phosphate (KH2 PO4), (5) 10% polyethylene glycol (PEG-6000), or (6) gibberellic acid (GA3, used only for field experiments). Nonprimed seeds were used as the control group. First 1000 mL of priming media was prepared for each priming treatment, and seeds of both varieties were rinsed in the solution for 12 h at room temperature. Germination percentage at two different temperatures (10 °C and 20 °C), coleoptile length, seedling emergence percentage, and seedling growth rate were evaluated under laboratory conditions. Primed seeds of both varieties were sown on two different dates under field conditions to evaluate certain agromorphological characteristics. PEG, IAA, and distilled water treatments increased seed germination percentage, seedling emergence percentage, and seedling growth rate. PEG, KCl, and hydropriming treatments increased grain yield compared to the control. Among the different priming agents used in the study, PEG, KCl, and hydropriming were the most effective treatments to attain higher germination percentage and grain yield. © TÜBİTAK.Öğe Effects of trimethylamine oxide (TMAO) and loading duration on the shoot tip cryopreservation of loquat (Eriobotrya Japonica)(2018) Huang, Tian Qi; Shahıd, Muhammad Qasim; Baloch, Faheem Shehzad; Lın, Shun Quan; Yang, Xiang HuiTwo cryoprotectant solutions, including trimethylamine oxide (TMAO) and dimethyl sulfoxide (DMSO), and several loading durations were used to evaluate the cryopreservation of the shoot tip of Eriobotrya plants. The best results for regrowth (59.91%) were obtained from 10% TMAO compared to 10% DMSO as cryoprotectant, although nonsignificant differences were found for survival between the two cryoprotectants. We detected pronounced effects of loading duration on survival and regrowth rates of shoot tips. The maximum regrowth (56.36%) was observed at 9 h of loading duration. The cryoprotectants and loading durations greatly affected the regrowth of Eriobotrya shoot tips, and TMAO could be introduced as a nontoxic and efficient cryoprotectant. These results could lay a foundation for the cryopreservation of Eriobotrya.Öğe Evaluation of the geographical pattern of genetic diversity of Glycine soja and Glycine max based on four single copy nuclear gene loci : for conservation of soybean germplasm(Pergamon-Elsevier Science Ltd, 2015) Wang, Yunsheng; Shahid, Muhammad Qasim; Ghouri, Fozia; Baloch, Faheem Shehzad; Wang, YingGenetic diversity and its geographical patterns play a very important role in species conservation and exploitation. Here, nucleotide polymorphism patterns of four single copy nuclear gene loci in wild (Glycine soja) and cultivated soybean (Glycine max) populations from different geographical regions as well as their demographic history were analyzed. The results showed that: (1) Southern subpopulation has the highest, while central subpopulation revealed the lowest genetic diversity among three Chinese G. soja subpopulations. (2) Northern Chinese G. max subpopulation depicted higher genetic diversity than other two Chinese, Korean, Japanese and American G. max subpopulations. (3) Significant genetic differentiation (P < 0.001) was observed among Chinese G. soja subpopulations from three ecological zones. There was also a significant genetic differentiation ( P < 0.01) between three Chinese and Japanese subpopulations of G. max. (4) The demographic dynamics revealed that effective population size of G. soja is expanding, while it was constant in G. max. G. soja is a useful germplasm resource to widen the genetic diversity of G. max. This study suggests that native populations of G. soja from different geo-ecological regions should be protected to conserve the genetic diversity. (C) 2015 Elsevier Ltd. All rights reserved.Öğe 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, GokselBean 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.Öğe Exploring Genetic Diversity and Population Structure of Turkish Black Sea Region Maize (Zea mays L.) Germplasm using SSR Markers(2022) Baran, Nurettin; Nadeem, Muhammad Azhar; Yilmaz, Abdurrahim; Andirman, Mehtap; Kurt, Fırat; Temiz, M. Gültekin; Baloch, Faheem ShehzadPlant landraces are heterogeneous plant populations that have adapted to local environmental conditions and serve as a source of genetic variations that can be used for the breeding perspectives. Studies regarding genetic diversity assessment are very important as they provide an opportunity for the scientific community to investigate novel genetic variations for the genetic improvement of crops. Maize is one of the most important cereal crops and provides daily calories to millions of people all over the world. This study aimed to investigate the genetic diversity and population structure of 32 local maize genotypes collected from the Black Sea Region of Turkey using SSR markers. Molecular characterization was performed using the 14 most polymorphic primers that yielded a total of 42 bands. An average of 3 alleles per SSR primer was detected, and the number of alleles varied from 1 (phi022) to 6 (umc1571). The unweighted pair-group method with arithmetic means (UPGMA) clustering divided maize accessions into three main populations. According to Nei's genetic distances, DZ-M-145 (Corum) and DZ-M-20 (Trabzon) genotypes were the closest (0.03) genetically related populations, while DZ-M-68 (Artvin) and DZ-M-55 (Rize) were the most genetically distant (0.63) populations. The study identified molecular genetic diversity not mentioned for maize plants from the Black Sea. On this occasion, new opportunities have been created for hybrid maize products.Öğe Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers(Agricultural Research Communication Centre, 2019) Aydın, Muhammet Fatih; Baloch, Faheem ShehzadPresent study was aimed to investigate the genetic diversity and population structure of Turkish common bean germplasm. A total of 96 bean genotypes were characterized with iPBS-retrotansposons that yielded a mean polymorphism information contents of 0.8. Mean gene diversity and Shannon information index were 0.14 and 0.25, respectively. Neighbor joining analysis divided the bean genotypes into two main group (A and B) according to their geographical regions, growth habits and seed size. Bingol-17, Sivas-14 and Hakkari-11 genotypes were found very distinct and can be used as candidate parents for the bean breeding. The higher efficiency and reproducibility of iPBS-retrotransposons was witnessed in common bean as compared to earlier studies using the same marker system. Results of this study will boost up the investigators for genotyping the larger germplasm of common bean with minimum laboratory infrastructure in developing and least developed countries.Öğe Genetic characterization of rheum ribes (wild rhubarb) genotypes in lake Van basin of Turkey through Issr and ssr markers(Friends Science Publ, 2019) Ekincialp, Aytekin; Erdinç, Çeknas; Turan, Sibel; Çakmakçı, Özlem; Nadeem, Muhammad Azhar; Baloch, Faheem Shehzad; Şensoy, SuatRheum ribes L. (wild rhubarb) is one of the less known plants to the world and the only species from the Rheum genus present in Turkey. In this study, one R. rhabarbarum (as check genotype) and 80 R. ribes genotypes were collected from different geographical locations of Turkey for the investigation of diversity and genetic structure using ISSR (Inter Simple Sequence Repeat) and SSR (Simple Sequence Repeats) markers. SSR markers reflected higher (100%) polymorphism as compared to the ISSR marker. However, ISSR markers produced higher average Polymorphism Information Content (PIC) value (0.805) than the SSR markers (0.724). A Similar range of (PIC) values with ISSR markers was found greater (0.935-0.395) as compared to the range of SSR makers (0.88-0.47). Using Jaccard similarity index, genetic distance was measured for both markers and average genetic distance was found to be higher with ISSR markers as compared to the SSR markers. Neighbor-joining analysis clustered genotypes into 3 groups for both marker systems. During this study some distinct genotypes like R. rhabarbarum, YYUERC19, YYUERCO9 and YYUNIER65 were investigated that can be used as candidate parents for the development of R. ribes L. varieties. Structure analysis grouped the genotypes according to altitude by clustering genotypes having at more than 2000 m in one group and genotypes less than 2000 m altitude in another group. Genetic variations observed in this study can be applied to investigate various traits of interest for the R. ribes L. breeding. (C) 2019 Friends Science PublishersÖğe Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers(Inst Nacional Pesquisas Amazonia, 2020) Vasquez Guizado, Stalin Juan; Nadeem, Muhammad Azhar; Ali, Fawad; Barut, Muzaffer; Habyarimana, Ephrem; Pacheco Gomez, Tedi; Vargas Santillan, Jhon Antoni; Baloch, Faheem ShehzadRosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.Öğe Genetic diversity and population structure of Korean wild soybean (Glycine soja Sieb. and Zucc.) inferred from microsatellite markers(Pergamon-Elsevier Science Ltd, 2017) Nawaz, Muhammad Amjad; Yang, Seung Hwan; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad; Lee, Jeong DongKorea is considered one of the centers of genetic diversity for cultivated as well as wild soybeans. Natural habitats of wild soybeans are distributed across the Korean mainland and the islands surrounding the Korean peninsula. In this study, the genetic diversity of 100 mainland Korean wild soybean accessions was evaluated by using 42 simple sequence repeat markers covering 17 soybean chromosomes. All analyzed loci were polymorphic and a total of 114 alleles were found. The observed average genetic diversity was low (0.4). The results showed that the 100 selected accessions did not exactly follow the geographical distribution. These results were further confirmed by the phylogeny inferred from five morphological characteristics (i.e., leaf shape, leaf area, plant shape, seed area, and 100-seed weight). Together, the genetic and morphological evaluations suggested conclusively that the selected population did not follow the geographical distribution pattern. The present study could provide useful information for the ex situ conservation and exploitation of wild soybean accessions in soybean improvement stratagems, and will aid in further understanding about the phylogeography of the species in the Korean center of diversity. (C) 2017 Elsevier Ltd. All rights reserved.Öğe The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences(Pergamon-Elsevier Science Ltd, 2017) Wang, Yunsheng; Ghouri, Fozia; Shahid, Muhammad Qasim; Naeem, Muhammad; Baloch, Faheem ShehzadGlycine sofa, also called wild soybean, is the wild ancestor of domesticated soybean (Glycine max), and one of the world's major cultivated crops. Wild soybean is a valuable resource for the breeding of cultivated soybean and harbors useful genes or agronomic traits. To use and conserve this valuable resource, we conducted a study to evaluate the genetic diversity and population structure of wild soybean using the sequencing data of two nuclear loci (AF105221 and PhyB) and one chloroplast locus (trnQ-rps16) of more than 600 individuals representing 53 populations throughout the natural distribution range. The results showed that most of the variation was found within the populations and groups, but significant genetic differentiation was also detected among different eco-geographical groups. Correlations between genetic and geographical distance at all the loci were consistent with the isolation by distance gene flow model. G. sofa exhibited the highest genetic diversity in middle and downstream of Yangzi River (MDYR) region, followed by North East China (NEC), and was the lowest in North West China (NWC). We concluded that both in situ and ex situ conservation strategies required for wild soybean populations, especially which are native to MDYR and NEC regions. (C) 2017 Elsevier Ltd. All rights reserved.
