Studying of genetic polymorphism of olive varieties of Azerbaijan and Turkey

In the article, genetic diversity of olive samples from Azerbaijan and Turkey, genotyping of natural populations and gene pools with molecular markers, associative mapping, genome analysis, carried out jointly genetic relationships between genotypes of olives and genetics originating from Azerbaijan and Turkey are studied by molecular analysis through their SSR markers. When the research work is successful, the results of this study will be demonstrated the presence of SSR markers to distinguish olive genotypes and further studies on olive production in both countries will be undertaken.

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Comparison of genetic diversity between cultivated and wild grape varieties originating from the Near-Caspian zone of Azerbaijan

OENO One ◽

10.20870/oeno-one.2010.44.4.1478 ◽

2010 ◽

Vol 44 (4) ◽

pp. 191

Author(s):

Samira Salayeva ◽

Stéphanie Decroocq ◽

Stéphanie Mariette ◽

Ellada Akhundova

Keyword(s):

Genetic Diversity ◽

Vitis Vinifera ◽

Ssr Markers ◽

Research Work ◽

Similarity Index ◽

Null Alleles ◽

Gene Pools ◽

Wild Grape ◽

Wild Accessions ◽

Grape Varieties

Aim: The Caucasus is considered as a possible primary centre of origin of grapevine. The aim of our research work was to study genetic diversity among cultivated Caucasian grape varieties and wild relatives originating from Near-Caspian areas of Azerbaijan on the basis of simple sequence repeat (SSR) markers.Methods and Results: Microsatellite allele data obtained in 31 local table grape varieties of Vitis vinifera L. ssp. sativa (Absheron region) and 34 wild varieties of Vitis vinifera L. ssp. sylvestris (Nabran, Davachi and Guba regions) were used to estimate population genetic parameters such as the polymorphism information content (PIC), the probability of identity (PI) and the frequency of null alleles (r). The genetic differences among the wild populations and between the wild and the cultivated gene pools were assessed using POPGENE, Arlequin and GENETIX programs. The selected fifteen microsatellite (SSR) markers revealed a high degree of polymorphism within and among the grape populations analyzed. The genetic similarity index ranged from 0.02 to 0.933.Conclusions: Among the selected markers, VVMD28 and VVMD36 displayed the highest diversity level regarding the expected heterozygosity and PIC (highest values) and PI (lowest values). In consequence, we postulate that these two markers are the most appropriate ones for the identification of grape accession and the determination of genetic diversity among cultivated and wild grape genotypes. Clustering analysis based on SSR markers data led to a good separation between cultivated and wild accessions and between wild accessions originating from different regions.Significance and impact of the study: The fifteen microsatellite markers used in this study were highly informative for the identification and analysis of genetic structure of Azerbaijan grapevine populations and clarified the relationships among grape accessions.

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Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

10.21203/rs.2.18928/v2 ◽

2020 ◽

Author(s):

Alemneh Mideksa Egu ◽

Kassahun Tesfaye ◽

Kifle Dagne New ◽

Xuebo Hu New

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Ssr Markers ◽

Polymorphic Information Content ◽

In Situ Conservation ◽

Germplasm Conservation ◽

Pharmaceutical Products ◽

Gene Pools ◽

Vernonia Galamensis ◽

Diversity Assessment

Abstract Background: Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidized oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. This study was initiated for the systematic and intensive genetic diversity assessment of V. galamensis accessions by SSR molecular markers to minimize the existing research gaps, provide a clue for germplasm conservation and further research. Results: Twenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified for the 20 loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations among populations which accounted for 11% of the variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. Since, the cluster and the STRUCTURE analyses did not group the populations into sharply distinct clusters, due to presence of gene flow and mode of reproduction of the plant. Conclusions: The SSR molecular markers used in this study are highly polymorphic. Among the ten populations, East Showa and East Hararghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

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Genetic diversity of Salvia tomentosa Miller (Lamiaceae) species using Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) molecular markers

Acta Biologica Szegediensis ◽

10.14232/abs.2019.2.135-141 ◽

2020 ◽

Vol 63 (2) ◽

pp. 135-141

Author(s):

Basel Saleh

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Sea Level ◽

Natural Population ◽

Polymorphic Information Content ◽

Genetic Relationships ◽

Natural Populations ◽

Mediterranean Species ◽

Marker Index ◽

Minisatellite Dna

Salvia tomentosa Miller (Lamiaceae) a Mediterranean species has an important role in various pharmacological applications. To reveal genetic relationships among S. tomentosa natural populations, 35 samples were collected from different regions of Syria. Touch-down Directed Amplification of Minisatellite DNA (Td-DAMD) markers have been investigated for this goal. Td-DAMD assay produced 158 total bands of which 131 (82.911%) were polymorphic with a mean polymorphic information content (PIC) value of 0.264 and a mean marker index (MI) value of 2.269. Clustering profile based on TdDAMD data showed that samples were grouped into two main clusters; the first cluster included Lattakia samples which split into two subclusters regardless their altitudes over the sea level. Whereas, the second cluster included Tartous and Hama samples. Td-DAMD assay successfully discriminate among the tested 35 samples belonged to the S. tomentosa natural population.

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Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2012000800009 ◽

2012 ◽

Vol 47 (8) ◽

pp. 1095-1102 ◽

Cited By ~ 6

Author(s):

Víctor Pecina‑Quintero ◽

José Luis Anaya‑López ◽

Alfredo Zamarripa‑Colmenero ◽

Noe Montes‑García ◽

Carlos Nuñez‑Colín ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Ssr Markers ◽

Sweet Sorghum ◽

Genetic Relationships ◽

Biofuel Production ◽

Germplasm Bank ◽

New Varieties ◽

Sorghum Genotypes ◽

Sorghum Germplasm

The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers revealed robust amplification profiles and were able to differentiate the 41 genotypes of sweet sorghum evaluated. Analysis of the frequency and distribution of polymorphic fragments allowed for the detection of unique (AFLP) and rare (SSR) alleles in several genotypes (RBSS‑8, RBSS‑9, RBSS‑25, RBSS‑32, and RBSS‑37), indicating that these markers may be associated with a feature that has not yet been determined or may be useful for the identification of these genotypes. The genetic relationships indicated the presence of at least two types of sweet sorghum: a group of modern genotypes used for sugar and biofuel production, and another group consisting of historic and modern genotypes used for the production of syrups. Sweet sorghum genotypes may be used to develop new varieties with higher sugar and juice contents.

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Cross Species/Genera Transferability of SSR Markers, Genetic Diversity and Population Structure Analysis in Gladiolus (Gladiolus × grandiflorus L.) Genotypes

10.21203/rs.3.rs-673512/v1 ◽

2021 ◽

Author(s):

Varun Hiremath ◽

Kanwar Pal Singh ◽

Neelu Jain ◽

Kishan Swaroop ◽

Pradeep Kumar Jain ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Structure Analysis ◽

Genetic Relationships ◽

Crop Improvement ◽

Test Analysis ◽

Average Value ◽

Population Structure Analysis ◽

Genetic Diversity And Structure

Abstract Genetic diversity and structure analysis using molecular markers is necessary for efficient utilization and sustainable management of gladiolus germplasm. Genetic analysis of gladiolus germplasm using SSR markers is largely missing due to scarce genomic information. In the present investigation, we report 66.66% cross transferability of Gladiolus palustris SSRs whereas 48% of Iris EST-SSRs were cross transferable across the gladiolus genotypes used in the study. A total of 17 highly polymorphic SSRs revealed a total 58 polymorphic loci ranging from two to six in each locus with an average of 3.41 alleles per marker. PIC values ranged from 0.11 to 0.71 with an average value of 0.48. Four SSRs were selectively neutral based on Ewens-Watterson test. Analysis of genetic structure of 84 gladiolus genotypes divided whole germplasm into two subpopulations. 35 genotypes were assigned to subpopulation 1 whereas 37 to subpopulation 2 and rest of the genotypes recorded as admixture. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations whereas 36.55% of variation observed among individuals within total population. Least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation of two subpopulations was observed. Grouping pattern of population structure was consistent with UPGMA dendrogram based on simple matching dissimilarity coefficient (ranged from 01.6 to 0.89) and PCoA. Genetic relationships assessed among the genotypes of respective clusters assist the breeders in selecting desirable parents for crossing. SSR markers from present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement.

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Assessment of genetic diversity in Indian Barnyard millet (Echinochloa spp. complex) using morphological and molecular markers

Journal of Applied and Natural Science ◽

10.31018/jans.v8i3.1016 ◽

2016 ◽

Vol 8 (3) ◽

pp. 1643-1648 ◽

Cited By ~ 1

Author(s):

M. P. Moharil ◽

Dipti Gawai ◽

N. Dikshit ◽

M.S. Dudhare ◽

P. V. Jadhav

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Improvement ◽

Molecular Diversity ◽

Genetic Relationships ◽

Barnyard Millet ◽

Clear Cut ◽

Cultivated Species ◽

High Degree

In the present study, morphological and molecular markers (RAPD primers) were used to analyze the genetic diversity and genetic relationships among 21 accessions of Echinochloa spp. complex comprising the wild and cultivated species collected from Melghat and adjoining regions of Vidarbha, Maharashtra. The availability of diverse genetic resources is a prerequisite for genetic improvement of any crop including barnyard millet. A high degree of molecular diversity among the landraces was detected. Among the 21 genotypes, two major groups (A and B) were formed, at 67.28 % similarity, which clearly encompasses 15 accessions of E. frumentacea and 6 accessions of E. colona. Higher similarity was observed in accessions of E. frumentacea. The accessions IC 597322 and IC 597323 also IC 597302 and IC 597304 showed more than 94% similarity among themselves. The classification of genetic diversity has enabled clear-cut grouping of barnyard millet accessions into two morphological races (E. frumentacea and E. colona).

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Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

Asian Journal of Biology ◽

10.9734/ajob/2021/v12i130156 ◽

2021 ◽

pp. 36-48

Author(s):

Farhana Afrin Vabna ◽

Mohammad Zahidul Islam ◽

Md. Ferdous Rezwan Khan Prince ◽

Md. Ekramul Hoque

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Molecular Diversity ◽

Genetic Relationships ◽

Group Method ◽

Diversity Analysis ◽

Average Value ◽

Rice Landraces ◽

Boro Rice ◽

Research Institute

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

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Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401189 ◽

2020 ◽

Vol 10 (5) ◽

pp. 1629-1637 ◽

Cited By ~ 2

Author(s):

Steven R. Eichten ◽

Akanksha Srivastava ◽

Adam J. Reddiex ◽

Diep R. Ganguly ◽

Alison Heussler ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Methylation ◽

Phenotypic Variation ◽

Genetic Relationships ◽

Natural Populations ◽

Epigenetic Inheritance ◽

Genetic Differences ◽

Linear Modeling ◽

Climate Conditions ◽

Joint Contribution

Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modeling revealed large genetic differences between families and a minor contribution of DNA methylation variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation toward heritable phenotypic variation relative to genetic differences.

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Genetic diversity among silkworm (Bombyx mori L., Lep., Bombycidae) germplasms revealed by microsatellites

Genome ◽

10.1139/g05-053 ◽

2005 ◽

Vol 48 (5) ◽

pp. 802-810 ◽

Cited By ~ 30

Author(s):

Muwang Li ◽

Li Shen ◽

Anying Xu ◽

Xuexia Miao ◽

Chengxiang Hou ◽

...

Keyword(s):

Genetic Diversity ◽

Bombyx Mori ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Group Method ◽

Sequence Repeat ◽

Bombyx Mori L ◽

Simple Sequence ◽

Silkworm Bombyx Mori

To determine genetic relationships among strains of silkworm, Bombyx mori L., 31 strains with different origins, number of generations per year, number of molts per generation, and morphological characters were studied using simple sequence repeat (SSR) markers. Twenty-six primer pairs flanking microsatellite sequences in the silkworm genome were assayed. All were polymorphic and unambiguously separated silkworm strains from each other. A total of 188 alleles were detected with a mean value of 7.2 alleles/locus (range 2–17). The average heterozygosity value for each SSR locus ranged from 0 to 0.60, and the highest one was 0.96 (Fl0516 in 4013). The mean polymorphism index content (PIC) was 0.66 (range 0.12–0.89). Unweighted pair group method with arithmetic means (UPGMA) cluster analysis of Nei's genetic distance grouped silkworm strains based on their origin. Seven major ecotypic silkworm groups were analyzed. Principal components analysis (PCA) for SSR data support their UPGMA clustering. The results indicated that SSR markers are an efficient tool for fingerprinting cultivars and conducting genetic-diversity studies in the silkworm.Key words: silkworm, Bombyx mori L., microsatellites, simple sequence repeat (SSR), genetic diversity.

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Genetic analysis of mango landraces from Mexico based on molecular markers

Plant Genetic Resources ◽

10.1017/s147926210932434x ◽

2009 ◽

Vol 7 (03) ◽

pp. 244-251 ◽

Cited By ~ 9

Author(s):

Didiana Gálvez-López ◽

Sanjuana Hernández-Delgado ◽

Maurilio González-Paz ◽

Enrique Noe Becerra-Leor ◽

Miguel Salvador-Figueroa ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Fragment Length Polymorphism ◽

Geographical Origin ◽

Genetic Recombination ◽

Genetic Relationships ◽

Mangifera Indica ◽

Aflp Analysis ◽

Significant Genetic Differentiation ◽

Simple Sequence

Genetic diversity and relationships among 112 mango (Mangifera indica) plants native to 16 states of Mexico and four controls [three mango cultivars (Ataulfo, Manila and Tommy Atkins) and one accession ofMangifera odorata] were evaluated based on amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) molecular markers. Mango germplasm shows broad dispersion through Mexico and genetically similar germplasm from different agroecological regions has previously been found by our group. Both AFLP and SSR analyses indicated high genetic similarity among mango populations that were clustered in two major groups: mangos from Gulf of Mexico coastline and mangos from Pacific Ocean coastline and locations far away from the sea. The highest genetic diversity was found within plants from each state, and significant genetic differentiation (FST = 0.1921, AFLPs and 0.1911, SSRs) was also observed among mango populations based on geographical origin and genetic status (cultivars versus landraces). Heterozygosity values ranged from low (0.38) to moderate (0.68), and no heterozygote deficits were found. The highest genetic variability was found in mango populations from Tabasco, Michoacán and Oaxaca. Data suggested that mangoes are subjected to natural or induced pollination, so segregation as well as genetic recombination plays major roles on genetic diversification of Mexican mangos. AFLP analysis was more robust than SSR for determining the genetic relationships among mango landraces from Mexico.

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