Morphometric analysis in different geographical populations of Varroa destructor (Acari: Varroidae) associated with Apis mellifera colonies in Iran

2018 ◽  
Vol 23 (10) ◽  
pp. 1915
Author(s):  
Mahsa Farjamfar ◽  
Alireza Saboori ◽  
Jamasb Nozari ◽  
Vahid Hosseininaveh
Keyword(s):  
Apis Mellifera ◽  
Morphometric Analysis ◽  
Varroa Destructor ◽  
Principal Component ◽  
Group Method ◽  
Dorsal Shield ◽  
Pair Group ◽  
Geographical Regions ◽  
Geographical Populations ◽  
And Cluster Analysis

Varroa destructor is a major ectoparasitic mite which feeds on the western honey bee, Apis mellifera hemolymph. Morphometric analysis of V. destructor in Iran was performed in order to detect differences within some populations of the species. Totally, 145 female mites were collected from A. mellifera colonies in different geographical regions in Iran and Europe (Spain and France). Eight morphological variables were measured: 1) length of dorsal shield (LDS), 2) width of dorsal shield (WDS), 3) length of genital shield (LGS), 4) width of genital shield (WGS), 5) length of metapodal shield (LMS), 6) width of metapodal shield (WMS), 7) length of anal shield (LAS) and 8) width of the anal shield (WAS). The ratios of LDS/WDS, WDS/LDS, LGS/WGS and LAS/WAS were also calculated. Multivariate analyses demonstrated significant differences in means of body length (LDS) and body width (WDS) between populations. Using principal component analysis (PCA) and cluster analysis with pair group method, five morphological groups were established. PCA analyses were also shown one morphotype, A3, between samples. Collectively, our findings suggest a wide phenotypic plasticity within the populations of Varroa mite in Iran.

Palynological observations on the genus Gundelia L. (Asteraceae) growing in Turkey

Phytotaxa ◽  
2021 ◽  
Vol 502 (1) ◽  
pp. 51-66
Author(s):  
MEHMET FIRAT ◽  
SELAMI SELVİ
Keyword(s):  
Pollen Morphology ◽  
Pollen Grains ◽  
Principal Component ◽  
Polar Axis ◽  
Morphological Characters ◽  
Group Method ◽  
Pair Group ◽  
Equatorial Diameter ◽  
Polar Diameter ◽  
And Cluster Analysis

The pollen morphology of 17 taxa of Gundelia, of which 13 taxa are endemic to Turkey, was investigated by light microscopy (LM) and scanning electron microscopy (SEM). In this study, the pollen morphology of 16 taxa except G. tournefortii was investigated for the first time. The quantitative data were analyzed by descriptive statistics and multivariate statistics. The pollen grains are oblate spheroidal and prolate spheroidal in shape with the polar diameter of 37.01–61.2 μm and the equatorial diameter of 31.2–63.4 μm. The smallest pollen grains were observed in G. anatolica, G. rosea and G. tournefortii, while the largest pollen grains were observed in G. vitekii, G. komagenensis and G. colemerikensis. Pollen ornamentation is echinate in LM and echinate-microperforate in SEM. Statistically, the relationships between pollen characters of the examined taxa were identified using Principal Component Analysis (PCA) and Clustering Analyzis. In addition, a dendrogram was constructed by applying UPGMA based on the determined 15 pollen morphological characters, and the degree of their relationship was discussed. Polar axis, equatorial diameter and colpus length were the major explanations of the pollen morphological characters’ total variation in PCA. Pair group method was used to divide the main pollen taxa into three groups based on the pollen morphology by using arithmetic averages analysis (PCA scatterplot and cluster analysis). As a result, the pollen shape, polar axis, equatorial diameter and spine length were important characters distingushing the taxa from each other. We found some matches and mismatches between pollen and morphological characters, whose significance requires further study.

scholarly journals Morphologic and Agronomic Diversity of Brassica napus Crops

2008 ◽  
Vol 133 (1) ◽  
pp. 48-54 ◽  
Author(s):  
Pilar Soengas ◽  
Maria Elena Cartea ◽  
Pablo Velasco ◽  
Guillermo Padilla ◽  
Amando Ordás
Keyword(s):  
Cluster Analysis ◽  
Brassica Napus ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Winter Season ◽  
Principal Component ◽  
Group Method ◽  
Pair Group ◽  
Total Variability ◽  
And Cluster Analysis

A Brassica napus L. crop called nabicol traditionally has been grown by farmers in northwestern Spain for many years and is an important horticultural product during the winter season. The relationship of nabicol to other B. napus crops has been studied based on simple sequence repeat (SSR) data. However, molecular and morphologic classifications often disagree. The objectives of this research were to study the morphologic and agronomic relationships of nabicol landraces to other B. napus crops and to compare those relationships with the ones already known, based on SSR data. Thirty-five B. napus populations from different geographic origins and uses were evaluated. Data were recorded on 17 morphologic and agronomic traits. Principal component analysis and cluster analysis were performed to classify the populations. Eight principal components (94% of the total variability) were standardized to produce the Mahalanobis' generalized distances, and a cluster analysis was conducted using the unweighted pair group method with arithmetic averages. There are no major differences between B. napus var. pabularia (DC.) Rchb. (nabicol, couve-nabiça, forage rape) and B. napus var. oleifera DC. (oilseed rape), and they probably share a common origin. Rape kale (B. napus var. pabularia) and rutabaga [B. napus var. napobrassica (L.) Rchb.] cultivars are separated from the rest and probably they have an independent origin or domestication. Molecular and morphologic classifications are complementary, and both are necessary to classify germplasm correctly and to clarify genetic relationships among B. napus crops.

Genetic diversification of local onion populations under different production systems in Uruguay

2014 ◽  
Vol 13 (3) ◽  
pp. 238-246 ◽  
Author(s):  
Eliana Monteverde ◽  
Guillermo A. Galván ◽  
Pablo Speranza
Keyword(s):  
Production Systems ◽  
Genetic Material ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Male Sterile ◽  
Pair Group ◽  
Cytoplasm Type ◽  
Low Degree ◽  
European Immigrants ◽  
And Cluster Analysis

In Uruguay, onion (Allium cepa L.) germplasm is mainly derived from the genetic material introduced by several waves of European immigrants and subsequently multiplied by household farmers, resulting in a wealth of locally adapted populations. This study examined the genetic diversity in a collection of 27 local onion populations and two cultivars derived from them. A total of 843 onion plants were fingerprinted, and 83 inter-simple sequence repeat polymorphic bands were generated. Analysis of molecular variance showed high diversity within the populations (66% of the total variation). Some short-day populations from different geographical origins were grouped together by the unweighted pair-group method using arithmetic averages, principal coordinate analysis and cluster analysis, while the more extensively sampled long- and intermediate-day populations showed a widespread distribution, with no significant subgrouping among them. This weakly structured gene pool is probably the consequence of seed and bulb exchange between farmers and natural inter-pollination. Nevertheless, a Bayesian analysis allowed the distinction of four genetic backgrounds of alleles in the whole collection, and populations were predominately assigned to each genetic background. In addition, mitochondrial variants determining normal (N) pollen fertility or the sterile S or T types were analysed for the same set of plants using specific primers. Most accessions showed a proportion of male-sterile individuals. Cytoplasm type T was the most represented (26 out of 29 accessions), and cytoplasm type S was found in a low proportion of individuals in seven populations. Uruguayan onion germplasm maintains a low degree of genetic differentiation despite the small cultivated area and intense seed exchange, probably due in part to different market purposes based on the growing cycle.

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods

Genome ◽  
2013 ◽  
Vol 56 (5) ◽  
pp. 295-302 ◽  
Author(s):  
Kaan Yilancioglu ◽  
Selim Cetiner
Keyword(s):  
Vitis Vinifera ◽  
Fragment Length ◽  
Genetic Relatedness ◽  
Genetic Erosion ◽  
Principal Component ◽  
Distinct Group ◽  
Group Method ◽  
Local Cultivars ◽  
Pair Group ◽  
Selected Subset

Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region.

scholarly journals Description and analysis of genetic diversity among squash accessions

2009 ◽  
Vol 52 (2) ◽  
pp. 271-283 ◽  
Author(s):  
Athanasios L. Tsivelikas ◽  
Olga Koutita ◽  
Anastasia Anastasiadou ◽  
George N. Skaracis ◽  
Ekaterini Traka-Mavrona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Molecular Data ◽  
Optimal Number ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

scholarly journals Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

2018 ◽  
Vol 5 (2) ◽  
pp. 77
Author(s):  
Budi Martono ◽  
Syafaruddin Syafaruddin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Similarity ◽  
Binary Data ◽  
Rapd Markers ◽  
Group Method ◽  
Breeding Programs ◽  
Pair Group ◽  
Monomorphic Band ◽  
And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

scholarly journals Selection of the Most Discriminating Morphological Qualitative Variables for Characterization of Fig Germplasm

2010 ◽  
Vol 135 (3) ◽  
pp. 240-249 ◽  
Author(s):  
Esther Giraldo ◽  
Margarita López-Corrales ◽  
José Ignacio Hormaza
Keyword(s):  
Principal Components ◽  
Principal Component ◽  
Group Method ◽  
Germplasm Collections ◽  
Pair Group ◽  
Morphological Studies ◽  
Production Type ◽  
Qualitative Variables ◽  
Total Variability

Most descriptor lists for the characterization of genetic resources in plants include a large number of traits whose evaluation is a lengthy and expensive process making the characterization of large germplasm collections difficult. Consequently, to facilitate the study and the conservation of germplasm, it is important to select carefully the most informative variables for each species. In this work, we applied sequential statistical procedures to select the most discriminant variables in fig (Ficus carica L.) from the initial 134 qualitative variables studied. A total of 34 variables was finally selected and broken down in 97 characters that were grouped by principal component analysis in 11 principal components that explain 93.34% of the total variability. The unweighted pair group method with arithmetic mean dendrogram derived from a similarity matrix generated using the Pearson's correlation coefficient among the 11 principal components selected classifies the cultivars in four main groups mainly based in the production type. These results show that redundant information can be obtained in morphological studies with a large number of variables resulting from correlation between variables. Consequently, a carefully selected and reduced number of highly discriminating variables can allow efficient fig germplasm characterization and discrimination resulting in significant savings of time and resources.

scholarly journals Forensic characteristics and population construction of two major minorities from southwest China revealed by a novel 37 Y-STR loci system

2021 ◽  
Vol 8 (7) ◽  
pp. 210447
Author(s):  
Li Luo ◽  
Lilan Yao ◽  
Siyu Chai ◽  
Hao Zhang ◽  
Min Li ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Tandem Repeats ◽  
Principal Component ◽  
Guizhou Province ◽  
Group Method ◽  
Reference Database ◽  
Arithmetic Means ◽  
Asian Populations ◽  
Pair Group ◽  
Haplotype Data

Y-chromosome short tandem repeats (Y-STRs) have become important supplementary evidence in forensic science. Nowadays, the Y-chromosome STR haplotype reference database (YHRD) contains abundant Y-STR haplotype data from all over the world, while haplotype data of Guizhou Miao and Tujia are scarce. Hence, genetic polymorphisms of 37 Y-STRs were investigated in 446 unrelated males (206 Miao males and 246 Tujia males) residing in Guizhou Province. A total of 206 and 242 unique haplotypes with the highest diversity value of 0.9665 and 0.9470 were obtained. The heatmap, multidimensional scaling (MDS), the unweighted pair-group method with arithmetic means (UPGMA) tree and principal component analysis (PCA) based on the genetic distance (Rst) value within our studied populations and other 26 populations indicated that population structures follow the boundary of the continent. Guizhou Miao and Guizhou Tujia populations have intimate relationships with East Asian populations, especially the geographically close, similar history and the same language family populations.

scholarly journals Barrier to Gene Flow Between Eastern and Western Populations of Cronartium ribicola in North America

2000 ◽  
Vol 90 (10) ◽  
pp. 1073-1078 ◽  
Author(s):  
R. C. Hamelin ◽  
R. S. Hunt ◽  
B. W. Geils ◽  
G. D. Jensen ◽  
V. Jacobi ◽  
...  
Keyword(s):  
Gene Flow ◽  
New Mexico ◽  
North America ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Genetic Distances ◽  
Group Method ◽  
Cronartium Ribicola ◽  
Western North America ◽  
Pair Group

The population structure of Cronartium ribicola from eastern and western North America was studied to test the null hypothesis that populations are panmictic across the continent. Random amplified polymorphic DNA markers previously characterized in eastern populations were mostly fixed in western populations, yielding high levels of genetic differentiation between eastern and western populations (φst = 0.55; θ = 0.36; P < 0.001). An unweighted pair-group method, arithmetic mean dendro-gram based on genetic distances separated the four eastern and four western populations into two distinct clusters along geographic lines. Similarly, a principal component analysis using marker frequency yielded one cluster of eastern populations and a second cluster of western populations. The population from New Mexico was clearly within the western cluster in both analyses, confirming the western origin of this recent introduction. This population was completely fixed (Hj = 0.000; n = 45) at all loci suggesting a severe recent population bottleneck. Genetic distances were low among populations of western North America (0.00 to 0.02) and among eastern populations (0.00 to 0.02), indicating a very similar genetic composition. In contrast, genetic distances between eastern and western populations were large, and all were significantly different from 0 (0.07 to 0.19; P < 0.001). Indirect estimates of migration were high among western populations, including the number of migrants among pairs of populations (Nm > 1) between New Mexico and British Columbia populations, but were smaller than one migrant per generation between eastern and western populations. These results suggest the presence of a barrier to gene flow between C. ribicola populations from eastern and western North America.

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