MLVA25-Typed Yersinia pestis ssp. central asiatica biovar altaica Genotype Structure in Gorno-Altai Mountain Natural Plague Focus

The aim of the work was to study the genetic diversity and spatial-temporal genotype structure of Yersinia pestis subspecies central asiatica biovar altaica in the Gorno-Altai natural plague focus, using MLVA25-typing.Materials and methods. MLVA25-typing of 330 strains of Y. pestis ssp. central asiatica bv. altaica, isolated in the Gorno-Altai mountain natural plague focus during 1961–2015 was carried out. The phylogenetic tree was constructed with the help of UPGMA and MST algorithms.Results and discussion. The analyzed strains have been differentiated into 34 MLVA types based on cluster analysis. The formed major groups of strains show pronounced spatial confinedness. Three chorological groupings of the plague agent with peculiar genotype characteristics have been identified. Each of the groupings is circulating among the main carrier (Ochotona pallasi) population and within the limits of the similarly-named mesofocus, respectively (Ulandryksky, Tarkhatynsky and Kuraisky). MLVA25 structure of Y. pestis in Ulandryksky and Kuraisky mezofoci show stability over time; there are no significant changes from the time of their first detection in 1961 and 1999, respectively. The dramatic changes in MLVA25 structure are observed in Tarkhatynsky mesofocus, which is known from 1972. Mass expanding of the MLVA25 types which were very rare before took place there from the beginning of 1990-s, along with elimination of the types absolutely dominant up to 1980s. Most likely the changing of dominating genotypes is attributable to the bottleneck effect, arising from the sharp decline of the focal epizootic activity in the mid 1980s.

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PRRSV2 genetic diversity defined by RFLP patterns in the United States from 2007 to 2019

Journal of Veterinary Diagnostic Investigation ◽

10.1177/10406387211027221 ◽

2021 ◽

pp. 104063872110272

Author(s):

Giovani Trevisan ◽

Aditi Sharma ◽

Phillip Gauger ◽

Karen M. Harmon ◽

Jianqiang Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Difference ◽

The United States ◽

Respiratory Syndrome Virus ◽

Control Programs ◽

Geographic Space ◽

Different Strains ◽

Orf5 Sequences ◽

Over Time

The genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) increases over time. In 1998, restriction-fragment length polymorphism (RFLP) pattern analysis was introduced to differentiate PRRSV wild-type strains from VR2332, a reference strain from which a commercial vaccine (Ingelvac PRRS MLV) was derived. We have characterized here the PRRSV genetic diversity within selected RFLP families over time and U.S. geographic space, using available ISU-VDL data from 2007 to 2019. The 40,454 ORF5 sequences recovered corresponded to 228 distinct RFLPs. Four RFLPs [2-5-2 (21.2%), 1-7-4 (15.6%), 1-4-4 (11.8%), and 1-8-4 (9.9%)] represented 58.5% of all ORF5 sequences and were used for cluster analysis. Over time, there was increased detection of RFLPs 2-5-2, 1-7-4, 1-3-4, 1-3-2, and 1-12-4; decreased detection of 1-4-2, 1-18-4, 1-18-2, and 1-2-2; and different detection trends for 1-8-4, 1-4-4, 1-26-1, 1-22-2, and 1-2-4. An over-time cluster analysis revealed a single cluster for RFLP 2-5-2, supporting that sequences within RFLP 2-5-2 are still relatively conserved. For 1-7-4, 1-4-4, and 1-8-4, there were multiple clusters. State-wise cluster analysis demonstrated 4 main clusters for RFLP 1-7-4 and 1-8-4, and 6 for RFLP 1-4-4. For the other RFLPs, there was a significant genetic difference within them, particularly between states. RFLP typing is limited in its ability to discriminate among different strains of PRRSV. Understanding the magnitude of genetic divergence within RFLPs helps develop PRRSV regional control programs, placement, herd immunization strategies, and design of appropriate animal movements across borders to minimize the risk of PRRSV transmission.

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Thinning in mature eastern white pine: 43-year case study

The Forestry Chronicle ◽

10.5558/tfc78539-4 ◽

2002 ◽

Vol 78 (4) ◽

pp. 539-549 ◽

Cited By ~ 3

Author(s):

Paul D Anderson ◽

John C Zasada ◽

Glen W Erickson ◽

Zigmond A Zasada

Keyword(s):

Genetic Diversity ◽

Dna Analysis ◽

Large Diameter ◽

White Pine ◽

Thinning Intensity ◽

Pine Regeneration ◽

Volume Production ◽

Pine Stands ◽

Over Time

A white pine (Pinus strobus L.) stand at the western margin of the species range, approximately 125 years of age at present, was thinned in 1953 from 33.5 m2 ha-1 to target residual basal areas of 18.4, 23.0, 27.5, and 32.1 m2 ha-1 . Repeated measurement over the following 43-years indicated that the greatest total volume production and the greatest number of large diameter trees occurred in the unit of highest residual density. Over time, the distribution of stems was predominantly random although mortality between 1979 and 1996 resulted in a tendency for clumping in the 23.0 and 27.5 m2 ha-1 treatments. DNA analysis indicated that thinning intensity had little effect on the genetic diversity of residual white pine. This study suggests that mature white pine stands in northern Minnesota may be managed at relatively high densities without loss of productivity. However, regardless of overstory density, there was little or no white pine regeneration occurring in this stand. Key words: thinning, growth, genetic diversity, molecular markers, spatial pattern, regeneration

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Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers

Genome ◽

10.1139/g01-096 ◽

2001 ◽

Vol 44 (6) ◽

pp. 995-999 ◽

Cited By ~ 25

Author(s):

H I Amadou ◽

P J Bebeli ◽

P J Kaltsikes

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Geographic Origin ◽

Bambara Groundnut ◽

International Institute ◽

Tropical Agriculture ◽

Vigna Subterranea ◽

Ibadan Nigeria

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.

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Evaluation of Genetic Diversity in Castor (Ricinus communis L.) using RAPD Markes

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.343-344.981 ◽

2011 ◽

Vol 343-344 ◽

pp. 981-987

Author(s):

Feng Juan Li ◽

Chang Lu Wang ◽

Dong He ◽

Ya Qiong Liu ◽

Mian Hua Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Genetic Distance ◽

Oil Content ◽

Rapd Markers ◽

Rapd Analysis ◽

Ricinus Communis ◽

Major Group ◽

Ricinus Communis L ◽

Polymorphic Bands

RAPD markers are used to study the genetic diversity of the main planting on 37 castor varieties widely cultivated in china according to the oil content and other characteristic of different castor varieties. Genetic distance of 37 Chinese castor varieties is studied by RAPD markers analysis. RAPD analysis shows that a total of 122 bands are amplified from random primers of 20 S series, including 71 polymorphic bands with polymorphic rate of 58.20%. 37 castor beans are divided into four major groups in the phylogenetic tree. One castor germplasm is included in1, 2, 3 groups respectively, and two sub-groups are included in the 4 major group.

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Statistical analysis in support of maintaining a healthy traditional Siamese cat population

Genetics Selection Evolution ◽

10.1186/s12711-020-00596-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Arthur M. A. Pistorius ◽

Ineke Blokker

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Companion Animals ◽

Hereditary Diseases ◽

Small Scale ◽

Genetic Traits ◽

Inbreeding Coefficients ◽

A Value ◽

Siamese Cat ◽

Line Breeding

Abstract Background For many years, breeders of companion animals have applied inbreeding or line breeding to transfer desirable genetic traits from parents to their offspring. Simultaneously, this resulted in a considerable spread of hereditary diseases and phenomena associated with inbreeding depression. Results Our cluster analysis of kinship and inbreeding coefficients suggests that the Thai or traditional Siamese cat could be considered as a subpopulation of the Siamese cat, which shares common ancestors, although they are considered as separate breeds. In addition, model-based cluster analysis could detect regional differences between Thai subpopulations. We show that by applying optimal contribution selection and simultaneously limiting the contributions by other breeds, the genetic diversity within subpopulations can be improved. Conclusion In principle, the European mainland Thai cat population can achieve a genetic diversity of about 26 founder genome equivalents, a value that could potentially sustain a genetically diverse population. However, reaching such a target will be difficult in the absence of a supervised breeding program. Suboptimal solutions can be obtained by minimisation of kinships within regional subpopulations. Exchanging animals between different regions on a small scale might be already quite useful to reduce the kinship, by achieving a potential diversity of 23 founder genome equivalents. However, contributions by other breeds should be minimised to preserve the original Siamese gene pool.

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ANALYSIS OF GENETIC DIVERSITY OF 26 CASSAVA VARIETIES (Manihot esculenta CRANTZ) WITH DIFFERENT RESPONSES TO WATERLOGGING CONDITIONS BY USING RAPD MARKERS

Journal of Science Natural Science ◽

10.18173/2354-1059.2021-0058 ◽

2021 ◽

Vol 66 (3) ◽

pp. 170-179

Author(s):

Sengsoulichan Dethvongsa ◽

Vu Nguyen Anh ◽

Van Tran Khanh

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Manihot Esculenta ◽

Rapd Markers ◽

Flood Tolerance ◽

Randomly Amplified Polymorphic Dna ◽

Manihot Esculenta Crantz ◽

Rapd Pcr ◽

Cassava Production ◽

Cassava Varieties

RAPD (Randomly Amplified Polymorphic DNA) is an indicator for high and stable polymorphism, widely used in the study of the diversity of cassava. In this paper, the results of using 20 polymorphic primers OPK combined with the establishment of the phylogenetic tree to analyze the genetic diversity of 26 cassava varieties with different responses to waterlogging conditions by using the RAPD-PCR technique were presented. The purpose of this experiment was to show the genetic relevance of the studied cassava varieties. The results showed that the flood tolerance of cassava was not related to the polymorphism and branching characteristics of the stem. This information may be use as a basis for selecting flood-tolerant cassava varieties for cassava production, as well as the basis for selecting genetically different parents for breeding.

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Genetic Diversity Assessment in Dolichos Bean (Lablab purpureus L.) Based on Principal Component Analysis and Single Linkage Cluster Analysis

Legume Research - An International Journal ◽

10.18805/lr-4561 ◽

2021 ◽

Author(s):

S.R. Singh ◽

S. Rajan ◽

Dinesh Kumar ◽

V.K. Soni

Keyword(s):

Genetic Diversity ◽

Principal Component Analysis ◽

Cluster Analysis ◽

Principal Component ◽

Component Analysis ◽

Single Linkage ◽

Pod Yield ◽

Diversity Assessment ◽

Single Linkage Cluster ◽

Linkage Cluster

Background: Dolichos bean occupies a unique position among the legume vegetables of Indian origin for its high nutritive value and wider climatic adaptability. Despite its wide genetic diversity, no much effort has been undertaken towards genetic improvement of this vegetable crop. Knowledge on genetic variability is an essential pre-requisite as hybrid between two diverse parental lines generates broad spectrum of variability in segregating population. The current study aims to assess the genetic diversity in dolichos genotypes to make an effective selection for yield improvement.Methods: Twenty genotypes collected from different regions were evaluated during year 2016-17 and 2017-18. Data on twelve quantitative traits was analysed using principal component analysis and single linkage cluster analysis for estimation of genetic diversity.Result: Principal component analysis revealed that first five principal components possessed Eigen value greater than 1, cumulatively contributed greater than 82.53% of total variability. The characters positively contributing towards PC-I to PC-V may be considered for dolichos improvement programme as they are major traits involved in genetic variation of pod yield. All genotypes were grouped into three clusters showing non parallelism between geographic and genetic diversity. Cluster-I was best for earliness and number of cluster/plant. Cluster-II for vine length, per cent fruit set, pod length, pod width, pod weight and number of seed /pod, cluster III for number of pods/cluster and pod yield /plant. Selection of parent genotypes from divergent cluster and component having more than one positive trait of interest for hybridization is likely to give better progenies for development of high yielding varieties in Dolichos bean.

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Differential Aging: An Exploratory Approach Using Cluster Analysis

The International Journal of Aging and Human Development ◽

10.2190/jpmy-mk3l-7e4a-418k ◽

1984 ◽

Vol 18 (2) ◽

pp. 141-157 ◽

Cited By ~ 3

Author(s):

Graeme Ford ◽

Rex Taylor

Keyword(s):

Cluster Analysis ◽

Longitudinal Data ◽

Random Sample ◽

Successful Aging ◽

Elderly Population ◽

Structural Data ◽

Exploratory Approach ◽

Aging Well ◽

Well Elderly ◽

Over Time

This article uses cluster analysis to identify different patterns of personal resources within a random sample of the well, elderly population. Ten such patterns or natural groupings are identified and their implications for coping and successful aging are discussed. It is apparent that there are a number of ways both of aging well and aging badly, and that these patterns cannot be predicted solely on the basis of structural data. The article poses a number of questions on the performance of cluster members over time and draws attention to the importance of longitudinal data.

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