Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers

2018 ◽  
Author(s):  
Muhammet Fatih Aydin ◽  
Faheem Shehzad Baloch
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Developed Countries ◽  
Least Developed Countries ◽  
Information Index ◽  
Geographical Regions ◽  
Group A ◽  
Growth Habits

Present 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-l7, 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.

scholarly journals Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 647 ◽  
Author(s):  
Ünal Karık ◽  
Muhammad Azhar Nadeem ◽  
Ephrem Habyarimana ◽  
Sezai Ercişli ◽  
Mehtap Yildiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Diversity Indices ◽  
Primer Binding Site ◽  
Neighbor Joining ◽  
Marker System ◽  
Information Index ◽  
Geographical Regions ◽  
The World

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon’s information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant.

scholarly journals Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

2021 ◽  
Vol 34 (2) ◽  
Author(s):  
MUHAMMAD FORHAD ALI ◽  
◽  
MD. RAFIQUL ISLAM SARDER ◽  
MOHAMMAD MATIUR RAHMAN ◽  
MD. FAZLUL AWAL MOLLAH ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Genetic Difference ◽  
Information Index ◽  
Hardy Weinberg Equilibrium ◽  
High Gene ◽  
High Level ◽  
Dna Microsatellite

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

scholarly journals Genetic Diversity, Population Structure, and Andean Introgression in Brazilian Common Bean Cultivars after Half a Century of Genetic Breeding

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1298
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Sérgio Augusto Morais Carbonell ◽  
Alisson Fernando Chiorato ◽  
Qijian Song ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Common Bean ◽  
Gene Diversity ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Association Mapping Approach

Brazil is the largest consumer and third highest producer of common beans (Phaseolus vulgaris L.) worldwide. Since the 1980s, the commercial Carioca variety has been the most consumed in Brazil, followed by Black and Special beans. The present study evaluates genetic diversity and population structure of 185 Brazilian common bean cultivars using 2827 high-quality single-nucleotide polymorphisms (SNPs). The Andean allelic introgression in the Mesoamerican accessions was investigated, and a Carioca panel was tested using an association mapping approach. The results distinguish the Mesoamerican from the Andean accessions, with a prevalence of Mesoamerican accessions (94.6%). When considering the commercial classes, low levels of genetic differentiation were seen, and the Carioca group showed the lowest genetic diversity. However, gain in gene diversity and allelic richness was seen for the modern Carioca cultivars. A set of 1060 ‘diagnostic SNPs’ that show alternative alleles between the pure Mesoamerican and Andean accessions were identified, which allowed the identification of Andean allelic introgression events and shows that there are putative introgression segments in regions enriched with resistance genes. Finally, genome-wide association studies revealed SNPs significantly associated with flowering time, pod maturation, and growth habit, showing that the Carioca Association Panel represents a powerful tool for crop improvements.

scholarly journals Diversity and phylogeny of saffron (Crocus sativus L.) accessions based on iPBS markers

Genetika ◽  
2018 ◽  
Vol 50 (1) ◽  
pp. 33-44 ◽  
Author(s):  
Mahdi Bayat ◽  
Reza Amirnia ◽  
Hakan Özkan ◽  
Aysun Gedik ◽  
Duygu Ates ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Diversity ◽  
Low Cost ◽  
Crocus Sativus ◽  
Phylogenetic Structure ◽  
Information Index ◽  
Geographical Regions ◽  
High Efficient ◽  
Crocus Sativus L

This study sought to measure genetic diversity and phylogenetic structure among 196 individuals of saffron from 20 geographically separate accessions from Iran, Spain and Turkey using retrotransposon derived iPBS markers. Twenty-eight primers amplified a total of 179 polymorphic alleles with an average of 6.4 bands per primer. The average of parameters shannon's information index, genetic distance and gene diversity was 0.483, 0.286 and 0.841 respectively. Polymorphic information index ranged from 0.407 to 0.953 with an average of 0.824. Primers 2298, 2229 and 2393 with 0.953, 0.943 and 0.943 PIC respectively, identified as the most informative primers in this study. The results of phylogenetic trees showed that twenty saffron accessions were placed into four major clusters that matched with their geographical locations completely. These results are supported by principal coordinate analysis. Overall, we can confirm that iPBS markers as low cost and high efficient molecular markers are a powerful DNA fingerprinting for assessing genetic diversity and phylogenetic analysis among saffron accessions originating from different geographical regions.

scholarly journals Genetic Relationships and Diversity Analysis in Turkish Laurel (Laurus Nobilis L.) Germplasm Using ISSR and SCoT Markers

2021 ◽  
Author(s):  
Abdurrahim YILMAZ ◽  
Vahdettin Ciftci
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Laurus Nobilis ◽  
Information Index ◽  
Geographical Regions ◽  
Polymorphism Rate ◽  
Amova Analysis ◽  
Breeding Techniques

Abstract Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 94.04% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 76.07% polymorphism rate, and Nei's distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting the average Shannon's information index (ISSR:0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (%96). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distance matrices was 0.88. The results of the study put forward resources for advanced breeding techniques, and contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.

scholarly journals Genetic diversity and population structure of rice stripe virus in China

2009 ◽  
Vol 90 (4) ◽  
pp. 1025-1034 ◽  
Author(s):  
Tai-Yun Wei ◽  
Jin-Guang Yang ◽  
Fu-Long Liao ◽  
Fang-Luan Gao ◽  
Lian-Ming Lu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Yunnan Province ◽  
Southwest China ◽  
Eastern China ◽  
Rice Stripe Virus ◽  
Genetic Distances ◽  
Geographical Regions ◽  
Strong Negative Selection ◽  
Recent Outbreak

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

Genetic Divergence among Populations of Invasive Alien Species Lantana camara L. from Selected Areas of Bangladesh

2021 ◽  
Vol 1 (01) ◽  
pp. 9-14
Author(s):  
SAILA KABIR ◽  
MD ABUL KASHEM ◽  
MOHAMMAD ZABED HOSSAIN
Keyword(s):  
Genetic Diversity ◽  
Alien Species ◽  
Invasive Alien Species ◽  
Gene Diversity ◽  
Lantana Camara ◽  
Native Plant ◽  
High Genetic Diversity ◽  
Native Plant Species ◽  
Information Index ◽  
Genetic Clustering

Lantana camara L., a well-known invasive alien species causing invasion and posing threat to native plant species community in different regions of Bangladesh. The present study aimed to investigate the genetic diversity of L. camara populations in different regions of Bangladesh. Eight RAPD markers were used in order to probe into its genetic variability. Total number of bands (202), polymorphic loci (104), per-centage of polymorphism (97.20%), average Shanon’s information index (0.3051±0.115), Nei’s gene diversity (0.4733±0.144) was found and in different populations and multiple divergent genetic clustering along with presence of unique alleles (4) for RAPD revealed high genetic diversity among the populations of L. camara in different regions of Bangladesh.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

scholarly journals The genetic diversity and population structure of common bean (Phaseolus vulgaris L) germplasm in Uganda

2014 ◽  
Vol 13 (29) ◽  
pp. 2935-2949 ◽  
Author(s):  
Okii Dennis ◽  
Tukamuhabwa Phinehas ◽  
Kami James ◽  
Namayanja Annet ◽  
Paparu Pamela ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Phaseolus Vulgaris L

scholarly journals Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

2012 ◽  
Vol 4 (3) ◽  
pp. 757-767 ◽  
Author(s):  
M. M. Hassan ◽  
A. K. M. Shamsuddin ◽  
M. M. Islam ◽  
K. Khatun ◽  
J. Halder
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Allele Number ◽  
Rice Landraces ◽  
Efficient Management ◽  
Ssr Loci ◽  
Pattern Of Variation ◽  
Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

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