Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

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Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

Canadian Journal of Forest Research ◽

10.1139/x26-162 ◽

1996 ◽

Vol 26 (8) ◽

pp. 1454-1462 ◽

Cited By ~ 31

Author(s):

Naoki Tani ◽

Nobuhiro Tomaru ◽

Masayuki Araki ◽

Kihachiro Ohba

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Phylogenetic Trees ◽

Genetic Relationships ◽

Natural Populations ◽

Group Method ◽

Stone Pine ◽

Arithmetic Means ◽

Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

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Genetic Diversity among Isolates of Phytophthora sojae in Anhui Province of China based on ISSR-PCR Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04398-18 ◽

2018 ◽

Vol 143 (4) ◽

pp. 304-309 ◽

Cited By ~ 2

Author(s):

Dong Liu ◽

Ping Li ◽

Jiulong Hu ◽

Kunyuan Li ◽

Zhenyu Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Genetic Relationships ◽

Inter Simple Sequence Repeat ◽

Phytophthora Sojae ◽

Anhui Province ◽

Population Variation ◽

Spatial Distance ◽

Similarity Coefficients

To explore genetic differentiation and the genetic relationships of Phytophthora sojae in Anhui Province, the inter-simple sequence repeat (ISSR) technique was used to analyze the genetic diversity of P. sojae. One hundred and sixty ISSR fragments were observed, including 129 (80.6%) polymorphic bands. This suggested that abundant genetic diversity existed among P. sojae in Anhui Province. The pairwise genetic similarity coefficients among the 62 strains ranged from 0.72 to 0.96, with a mean value of 0.85, indicating that there was a high level of genetic variation. Phytophthora sojae strains were divided into five clusters based on neighbor-joining (NJ) analysis, and the clustering was not related to geographic source, according to Mantel’s test (r = 0.3938). In addition, the clustering of strains from the same geographical source had little relationship to the year of collection. Analysis of molecular variance (AMOVA) showed that 16.65% of the genetic variation was derived from the collection area and 83.35% of the genetic variation was within-population variation. The genetic flow between different geographical sources ranged from 0.623 to 2.773, with a mean of 1.325, suggesting that gene exchange was frequent. Genetic distance and the genetic differentiation coefficient were not related to spatial distance.

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Genetic diversity of Matrinxã breeding stocks: implications for management and conservation

Semina Ciências Agrárias ◽

10.5433/1679-0359.2021v42n2p757 ◽

2021 ◽

Vol 42 (2) ◽

pp. 757-768

Author(s):

Angela Maria Urrea Rojas ◽

◽

Felipe Pinheiro de Souza ◽

Ed Christian Suzuki de Lima ◽

Claudete de Fátima Ruas ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Genetic Differentiation ◽

Genetic Drift ◽

Polymorphic Information Content ◽

Common Origin ◽

Null Alleles ◽

Mato Grosso ◽

Weinberg Equilibrium ◽

Hardy Weinberg Equilibrium

The formation of fish breeding stocks for fish farming or conservation programs is commonly carried out from the capture of fish in natural environments. Information on the geographic and genetic origin of these stocks is important to guide actions that allow correct management in captivity and, when lost, harm production and genetic conservation. In this sense, the objective of this study was to evaluate the genetic diversity and origin of two breeding stocks of matrinxã, Brycon amazonicus (INPA, Amazonas - INPA and Nova Motum, Mato Grosso - NM). A total of 68 caudal fin samples were collected, including 33 INPA samples and 35 NM samples. Twenty pairs of microsatellite primers were tested, but only seven primers showed satisfactory amplification, amplifying 41 alleles ranging from 187-318 bp. The polymorphic information content ranged from 0.135 (Borg25) to 0.782 (Bh6). Exclusive alleles were observed for both populations (INPA: 04 and NM: 18). Allelic richness results revealed that there was increased loss of genetic variation in NM, indicating a lower evolutionary potential of this stock. The average values of the observed heterozygosity corroborated this statement; however, there were high values for INPA (0.545) and NM (0.475), signifying an adequate genetic variability. An imbalance was found in the Hardy-Weinberg equilibrium at the Borg59 locus in INPA (P < 0.05), possibly due to the effect of null alleles, but was attributed to a founder effect. For NM, an imbalance in the Hardy-Weinberg equilibrium was observed at loci BoM13 and Bh6, which together with the results of the mean inbreeding coefficient values demonstrated the presence of genetic drift. The analysis of molecular variance showed greater variation within populations than between them, and was confirmed by the genetic differentiation value (0.086 - moderate genetic differentiation) and by the distance and genetic identity values (0.273 and 0.761, respectively). Bayesian analysis designated a value of K = 2, with the presence of structuring for NM and INPA; however, with correlated allelic frequencies, confirming a common origin. This origin was corroborated by the presence of gene flow through the number of migrants (5.691). Based on these results, there was a moderate genetic variability for INPA and NM and their common origin was confirmed. Recommendations are also included to minimize the probability of inbreeding processes or genetic drift in the studied stocks.

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Microsatelite diversity of Bosnian-Herzegovinian-Croatian shepherd dog Tornjak

Genetika ◽

10.2298/gensr1601049s ◽

2016 ◽

Vol 48 (1) ◽

pp. 49-56

Author(s):

Almira Softic ◽

Katica Velija ◽

Jasmin Ramic ◽

Kasim Bajrovic ◽

Gabrijela Radosavljevic ◽

...

Keyword(s):

Genetic Diversity ◽

Allele Frequency ◽

Bosnia And Herzegovina ◽

Microsatellite Loci ◽

Weinberg Equilibrium ◽

Major Allele Frequency ◽

Hardy Weinberg Equilibrium ◽

Major Allele ◽

High Level ◽

Diversity Studies

This paper presents the first estimation of polymorphism of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak in Bosnia and Herzegovina using 10 microsatellite loci, which are an integral part of StockMarks? for Canine Genotyping Kit (Applied Biosystems, Foster City, CA, USA). Ten microsatellite loci used in this study are appropriate for assessing the genetic diversity for this breed. Measures of genetic diversity were estimated based on allelic and genotypic calculations, observed (HO) and expected (HE) heterozygosities, deviations from Hardy-Weinberg equilibrium and polymorphism information content (PIC). The lowest genetic diversity was estimated for locus PEZ20, and the highest for PEZ6 locus. Observed and expected mean heterozygosities were 0.7261 and 0.7392, respectively. Statistically significant deviation (p<0.05) from Hardy-Weinberg equilibrium was found for PEZ1, PEZ12, PEZ3 and PEZ6 loci. The PIC values suggested that all markers (100%) are very informative (PIC > 0.5) in terms of their suitability for genetic diversity studies. When all observed parameters are taken into account (observed and expected heterozygosities, PIC, number of detective and effective alleles, number of detected and maximum possible genotypes, major allele frequency and major allele frequency index), we can conclude that PEZ6 locus shows the highest genetic diversity while PEZ3 displays the lowest. However, assuming values of observed and expected heterozygosities, as well as PIC, we consider loci PEZ20 to be the least diverse, but this locus has more effective alleles and more genotypes present than PEZ3. These preliminary results are the first genetic diversity survey of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak in Bosnia and Herzegovina and could be useful to the dog breeders in designing and managing breeding strategies. Summarizing the information above, we can conclude that the population of the Bosnian-Herzegovinian-Croatian Shepherd dog Tornjak from B&H is not affected by substantial loss of genetic diversity. Results of our study indicate presence of reasonably high level of genetic variability and lead to a better understanding of this dog breed.

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Assessing the relationship between height growth and molecular genetic variation in Douglas-fir (Pseudotsuga menziesii) provenances

10.1101/039818 ◽

2016 ◽

Author(s):

Charalambos Neophytou ◽

Anna-Maria Weisser ◽

Daniel Landwehr ◽

Muhidin Šeho ◽

Ulrich Kohnle ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Growth Performance ◽

Pseudotsuga Menziesii ◽

Phenotypic Variation ◽

Microsatellite Loci ◽

Variety Versus ◽

Height Growth ◽

Douglas Fir

Douglas-fir (Pseudotsuga menziesii) is a conifer tree native to western North America. In central Europe, it shows superior growth performance and is considered a suitable substitute for tree species impaired in vitality due to climate change. Maintenance and improvement of growth performance in a changing environment is a main challenge for forest tree breeders. In this context, genetic variation as a factor underlying phenotypic variation, but also as the basis for future adaptation, is of particular interest. The aims of this study were to analyse (i) genetic diversity of selected Douglas-fir provenances, (ii) variation in height growth among provenances, and (iii) to assess the link between genetic and phenotypic variation height growth. Genotyping was done on microsatellite loci. Effects of provenance, genotype, and site on height growth were assessed by fitting mixed linear models. The most significant genetic differentiation was observed between provenances of the coastal variety, versus a provenance of the interior variety originating from British Columbia. Although genetic differentiation among provenances of the coastal variety was lower, genetic structures within this variety were identified. Moreover, genetic diversity showed a latitudinal gradient with the southernmost provenances being more diverse, probably reflecting the species' evolutionary history. The modelling approach revealed that height growth differed significantly by provenance, site, and the interaction between site and provenance, demonstrating that height growth is under strong genetic control. Additionally, this analysis showed that genetic variation captured by the genotyped microsatellite loci was significantly related to variation in height growth, providing statistical evidence for a genetic component in the observed phenotypic variation.

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Genetic diversity in Tunisian horse breeds

Archives Animal Breeding ◽

10.5194/aab-60-153-2017 ◽

2017 ◽

Vol 60 (2) ◽

pp. 153-160 ◽

Cited By ~ 3

Author(s):

Bayrem Jemmali ◽

Mohamed Mezir Haddad ◽

Nawel Barhoumi ◽

Syrine Tounsi ◽

Faten Lasfer ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Genetic Differentiation ◽

Microsatellite Loci ◽

Genomic Dna ◽

Genetic Distances ◽

Jugular Veins ◽

Blood Samples ◽

Important Amount

Abstract. This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed) were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49), 7.35 (0.54), 6.3 (0.44), and 6 (0.38) for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03) in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02) in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p  <  0.05) and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.

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Development of 11 Polymorphic Microsatellite Loci from Primula amthystina Franchet. (Primulaceae)

HortScience ◽

10.21273/hortsci.45.1.148 ◽

2010 ◽

Vol 45 (1) ◽

pp. 148-149

Author(s):

Yuan Huang ◽

Xue-qin Wang ◽

Chun-yan Yang ◽

Chun-lin Long

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Loci ◽

Southwest China ◽

Herbaceous Plant ◽

Genetic Population ◽

Weinberg Equilibrium ◽

Perennial Herbaceous Plant ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite

Primula amethystina Franchet. is a beautiful perennial herbaceous plant locally endemic to the alpine area in southwest China. We isolated and characterized 11 polymorphic microsatellite primer pairs from this species. The number of alleles ranged from two to five. The observed and expected heterozygosities (HO and HE) were 0.25 to 0.875 and 0.223 to 0.691, respectively. Six loci were significantly deviated from Hardy-Weinberg equilibrium as a result of the heterozygote deficiency. These markers will have great potential to reveal the genetic population structure and genetic diversity of P. amethystina.

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Allele Frequencies of 15 AmpFISTR Identifiler loci in the Nepalese population

Scientific World ◽

10.3126/sw.v10i10.6856 ◽

2012 ◽

Vol 10 (10) ◽

pp. 20-23 ◽

Cited By ~ 5

Author(s):

Dinesh Kumar Jha ◽

Luis Javier Martinez Gonzalez ◽

Jiwan Prasad Rijal ◽

Bhinu Shova Tuladhar ◽

Nirajan Thapa Chhetri

Keyword(s):

Allele Frequencies ◽

Statistical Parameters ◽

Weinberg Equilibrium ◽

Allelic Frequencies ◽

Str Loci ◽

Scientific World ◽

Hardy Weinberg Equilibrium

Allele frequencies for the 15 STR loci in the AmpFlSTR® Identifiler® and statistical parameters were estimated from a sample of 233 unrelated individuals from different area of Nepal. A total of 161 alleles were found, with corresponding allelic frequencies ranging from 0.0021 to 0.4077. The MP, PD, PIC, PE, TPI, Ho and He ranged from 0.0282 to 0.1511, 0.8489 to 0.9717, 0.6478 to 0.8700, 0.4546 to 0.7631, 1.7651 to 4.3148, 0.7167 to 0.8841 and 0.7009 to 0.8833 respectively. Deviations from the Hardy–Weinberg Equilibrium were observed for D16S539, D18S51, D21S11 and TPOX Markers. One new allele has been detected in the process. Scientific World, Vol. 10, No. 10, July 2012 p20-23 DOI: http://dx.doi.org/10.3126/sw.v10i10.6856

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Genetic diversity and population structure of Tarek (Alburnus tarichi), an endemic species to the Lake Van basin, Turkey

Aquatic Living Resources ◽

10.1051/alr/2021005 ◽

2021 ◽

Vol 34 ◽

pp. 3

Author(s):

Yılmaz Çiftci ◽

Oğuzhan Eroğlu ◽

Şirin Firidin ◽

Hacı Savaş ◽

Yusuf Bektaş

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Relationships ◽

Significance Test ◽

Management Plan ◽

Lake Van ◽

Essential Information ◽

Low Level ◽

Lake Van Basin ◽

Sustainable Fishery

In this study, the genetic relationships of 804 tarek (Alburnus tarichi) samples from a total of 18 populations, including the potamodromus and resident individuals from Lake Van basin in eastern Turkey, were studied by using nine microsatellite loci. A total of 93 alleles was detected, and the average number of alleles per locus was 10.3 ± 3.39. The mean estimated observed and expected heterozygosity were 0.340 ± 0.016 and 0.362 ± 0.015, respectively, which indicated a low level of polymorphism. After Bonferroni correction (P < 0.0027), the multi-locus test applied to each population revealed that 12 out of 18 populations were in Hardy-Weinberg equilibrium (HWE) (P = 0.0120–0.9981). Analysis of molecular variance (AMOVA) showed more than 76% genetic variability within individuals and 19% among populations, which was significantly higher than zero (FST = 0.19), and furthermore, a low level of genetic variation was observed among individuals within populations (4.84%: FIS = 0.06). Bayesian clustering analysis indicated that the total genetic variation grouped into 3 clusters. Additionally, the significance test results revealed that 11 of the 18 populations are threatened with extinction due to recent bottleneck events.We conclude that the tarek populations from the Lake Van basin can be classified into distinct genetic groups, based on microsatellite information. In addition, our results provide essential information for the development of a management plan that conserves the tarek's genetic diversity and achieves a sustainable fishery.

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Genetic variation analysis of superior cotton varieties of Gossypium hirsutum through microsatellite markers

International Journal of Plant Biology ◽

10.4081/pb.2017.6996 ◽

2017 ◽

Vol 8 (1) ◽

Author(s):

Dede Nuraida ◽

Yusuf Abdurrajak ◽

Moh Amin ◽

Utami S. Hastutik

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gossypium Hirsutum ◽

Microsatellite Markers ◽

Size Range ◽

Allele Frequencies ◽

Variation Analysis ◽

Ctab Method

This study was conducted in order to obtain information on genetic variation in populations rated as superior cotton (Gossypium hirsutum L.) varieties in Balittas Malang, Indonesia. The samples used 10 varieties of cotton Kanesia series and 2 other superior varieties that are LRA 5166 and ISA 205A. Indicators of genetic diversity are the number of alleles per locus, allele frequencies, and heterozygosity values. DNA was isolated from the leaves of 3- week-old seedlings using the CTAB method. Amplification was performed using 5 SSRs primer pairs of the JESPR series. The results showed five microsatellite loci, yielding 12 alleles with a size range of 80–500 bp, with an average number of alleles per locus of 4.60. The average values of heterozygosity of the five loci was high, at 0.71. Based on the number of alleles, allele frequencies and heterozygosity values, the genetic variation sampled in the superior cotton varieties studied here is quite high.

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