scholarly journals Molecular Characterization of Persian Walnut Populations in Iran with Microsatellite Markers

HortScience ◽  
2010 ◽  
Vol 45 (9) ◽  
pp. 1403-1406 ◽  
Author(s):  
Rohollah Karimi ◽  
Ahmad Ershadi ◽  
Kourosh Vahdati ◽  
Keith Woeste
Keyword(s):  
Juglans Regia ◽  
Natural Populations ◽  
Genetic Distances ◽  
Group Method ◽  
Restricted Gene Flow ◽  
Pair Group ◽  
Hardy Weinberg Equilibrium ◽  
High Level ◽  
Genetic Structure And Diversity

The genetic structure and diversity of natural populations of Juglans regia L. in Iran were characterized using 11 microsatellite loci. A total of 105 individuals from seven populations were sampled. A high level of genetic diversity was observed within populations with the number of alleles per locus (A) ranging from three to 11 (average = 5.73), the proportion of polymorphic loci was 100%, and the expected heterozygosity ranged from 0.598 to 0.848 (average = 0.707). The proportion of genetic differentiation present among populations accounted for 12% of the total variation. Such considerable interpopulation differentiation detected in J. regia L. could have resulted from several factors, including restricted gene flow between populations. Significant departures from Hardy-Weinberg equilibrium were observed for WGA276, WGA32, and WGA321 loci. The deviations were primarily the result of the surplus of heterozygotes. The unweighted pair group method with arithmetic mean cluster analyses based on Nei's unbiased genetic distances separated the seven populations into two main groups.

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

scholarly journals Molecular characterization of oil seed Brassica using RAPD markers

2020 ◽  
Vol 55 (1) ◽  
pp. 1-8
Author(s):  
M Islam ◽  
A Habib ◽  
S Khan ◽  
S Akter ◽  
B Goswami ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Oil Seed ◽  
Pair Group ◽  
Brassica Spp ◽  
Breeding Programmes ◽  
High Level

Twelve varieties of oil seed Brassica spp. were characterized at molecular level using Random Amplified Polymorphic DNA (RAPD) primers to explore genetic diversity and to find out relationship among them. Twelve random primers used in the study generated 94 RAPD fragments and 53 (56.38%) of them were considered as polymorphic indicating high level of polymorphism within the materials. The size of amplified fragments ranged between 300-3000 bp. The values of pair-wise genetic distance ranged from 0.1613 to 0.5543. To find out phylogenetic relationships among the varieties, dendrogram based on Nei’s genetic distance was constructed using Unweighted Pair Group Method of Arithmetic Means (UPGMA) separating the 12 Brassica spp into two major clusters C1 and C2. This result will be useful for designing future breeding programmes for improvement of Brassica varieties. Bangladesh J. Sci. Ind. Res.55(1), 1-8, 2020

scholarly journals Genetic Variability Assay of Different Natural and Hatchery Populations of Rohu (Labeo rohita) in Bangladesh

2015 ◽  
Vol 9 (1) ◽  
pp. 30-36
Author(s):  
Shikder Saiful Islam ◽  
Md. Saifuddin Shah ◽  
Foyez Ibn Shams ◽  
Md. Rayhan Ali ◽  
Md. Lifat Rahi
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Labeo Rohita ◽  
Genetic Distances ◽  
Raw Material ◽  
Group Method ◽  
Pair Group ◽  
Fish Samples ◽  
Population Genetic Variation ◽  
High Level

The level of genetic variation determines the genetic status and provides the raw material for selective improvement of a stock. Randomly amplified polymorphic DNA (RAPD) technique was used to assess the genetic variability of 7 different natural (2) and hatchery (5) populations of Indian Major Carp, Labeo rohita (Rohu) in Bangladsh. In total, 140 fish samples were collected (20 from each of the populations). Genomic DNA was extracted from the muscle tissue, and 5 different oligonucleotide primers were used which revealed 80% polymorphic DNA bands. The polymorphic loci proportions were 0.71, 0.75, 0.75, 0.85, 0.84, 0.86 and 0.89 for Ma-Fatema hatchery, Chowdhuri hatchery, Niribili hatchery, Sonali hatchery, Kapotakha hatchery, the Halda river and the Baluhor Baor populations respectively. The pair-wise population differentiation (FST) values indicated a high level of genetic variation between different populations. The Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendogram based on Nei’s genetic distances also revealed high level of inter-population genetic variation among the populations. The populations were segregated into two groups: the Halda River and Baluhar Baor hatchery in one group and Kapotakha, Ma-Fatema, Chowdhuri, Niribili and Sonali hatcheries in another group. Overall, RAPD results clearly indicate the reduced genetic quality of the hatchery seeds.DOI: http://dx.doi.org/10.3126/ijls.v9i1.11923 International Journal of Life Sciences Vol.9(1) 2015 30-36

scholarly journals Genetic Diversity and Structure of Walnut Populations in Central and Southwestern China Revealed by Microsatellite Markers

2008 ◽  
Vol 133 (2) ◽  
pp. 197-203 ◽  
Author(s):  
Hua Wang ◽  
Dong Pei ◽  
Rui-sheng Gu ◽  
Bao-qing Wang
Keyword(s):  
Genetic Diversity ◽  
Juglans Regia ◽  
Central Area ◽  
Population Level ◽  
Genetic Distances ◽  
Mantel Test ◽  
Southwestern China ◽  
Group Method ◽  
Pair Group ◽  
Genetic Diversity And Structure

Molecular markers were used to study the genetic diversity, structure, and relationship of Juglans L. with nine populations (five from Juglans regia L. and four from Juglans sigillata Dode) in central and southwestern China. A moderate level of genetic diversity was observed at the population level with the number of effect alleles per locus (A E) ranging from 1.75 to 3.35 (average 2.39) and the proportion of polymorphic loci (P) equaling 100.0%. The expected heterozygosity (H E) within populations ranged from 0.389 to 0.687, and the average was 0.525. The proportion of genetic variation presented among populations accounted for 18.6% of the total genetic diversity. The overall gene flow (N m) among populations equaled 1.10. The unweighted pair-group method using arithmetic averages (UPGMA) clustering and the Mantel test showed that genetic distances among the nine populations are in a good agreement with their geographic distribution, supporting the viewpoint that J. regia and J. sigillata belong to one species. We suggest that the central area of the southwestern mountain regions of China could be considered as a priority for walnut genetic resource conservation.

High level of genetic diversity among spelt germplasm revealed by microsatellite markers

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1043-1052 ◽  
Author(s):  
P Bertin ◽  
D Grégoire ◽  
S Massart ◽  
D de Froidmont
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum L ◽  
Genetic Distances ◽  
Group Method ◽  
Germplasm Collections ◽  
Pair Group ◽  
Genetic Diversity And Structure ◽  
The Mean ◽  
High Level ◽  
Shared Alleles

The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 – proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 ± 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.Key words: spelt, SSR, microsatellites, genetic diversity, germplasm.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

Genetic Structure and Diversity among Species of Salacia: An Endangered Medicinal Herb of Western Ghats, India

2019 ◽  
Vol 9 (1) ◽  
pp. 23-33
Author(s):  
Chandrashekhar G Patil ◽  
Sheetal Ganapati Kamat ◽  
R Vasudeva
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Issr Marker ◽  
Group Method ◽  
Population Genetic Differentiation ◽  
Expected Heterozygosity ◽  
Marker Analysis ◽  
Endangered Medicinal Herb ◽  
High Level ◽  
Genetic Structure And Diversity

Salacia is one of the medicinally valuable genus, distributed throughout tropical areas which include India, Sri Lanka, Southern China and other Southern Asian Countries. The genus Salacia is represented by 21 species in India, among them eight species are recorded from the state of Karnataka in the Southern part of India. Despite its pharmaceutical importance, very little information exists about the genetic diversity of Salacia at molecular level. Hence the present study was carried out to evaluate the genetic among six species of Salacia namely S. chinensis, S. malabarica, S. oblonga, S. macrosperma, S. reticulata and S. gambleana with the help of ISSR marker analysis. Dendrogram and genetic distance were generated adopting Unweighted Paired Group Method with Arithmetic mean (UPGMA) in the NTSYS-pc software. Basic genetic parameters were calculated by analysing the genetic data with Pop gene 1.32 and GenAlEx 6.2 software. The overall polymorphism across the ten primers screened revealed 26 % polymorphism. A 60% polymorphism was scored for the primer UBC 841, whereas, no polymorphism was observed for primer UBC 840 and ISSR 6. The average observed heterozygosity was more than expected heterozygosity. Observed heterozygosity (Ho) ranged from 0.15 (UBC 841) to 0.38 (ISSR 6) with an average of 0.25, whereas expected heterozygosity (He) ranged from 0.10 (UBC 843) to 0.35 (ISSR 6) with an average of 0.23 for Salacia species. The higher heterozygosity pointed towards increased genetic diversity amongst the species. ISSR marker analysis showed high level of inter and intra population genetic differentiation.

scholarly journals Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

2000 ◽  
Vol 23 (4) ◽  
pp. 739-743 ◽  
Author(s):  
Mariana Pires de Campos Telles ◽  
José Alexandre Felizola Diniz-Filho
Keyword(s):  
Stochastic Process ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Small Sample ◽  
Group Method ◽  
Gene Frequencies ◽  
Exponential Relationship ◽  
Local Populations ◽  
Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

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