scholarly journals A Significant Genetic Admixture in Farmed Populations of the Noble Scallop Chlamys nobilis Revealed by Microsatellite DNA Analysis in Southern China

2021 ◽  
Vol 8 ◽  
Author(s):  
Haitao Ma ◽  
Dongmei Yu ◽  
Shu Xiao ◽  
Yanping Qin ◽  
Yang Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Analysis ◽  
Wild Population ◽  
Southern China ◽  
Genetic Admixture ◽  
Chlamys Nobilis ◽  
Weinberg Equilibrium ◽  
Artificial Breeding ◽  
Hardy Weinberg Equilibrium ◽  
Bayesian Assignment

The noble scallop, Chlamys nobilis, is an important bivalve mollusk with high commercial value and is usually farmed in the waters of southern China. To date, very little is known about the genetic diversity and population structure of C. nobilis. In this study, 10 microsatellite loci of four farmed C. nobilis populations were compared with one another and compared wild population in southern China. A total of 83 alleles were found. Surprisingly, the level of genetic diversity of the farmed C. nobilis populations was higher than that of the wild population. Although the population genetic of wild population was completely in the Hardy–Weinberg equilibrium, due to heterozygote deficiency, significant deviations from the Hardy–Weinberg equilibrium were found in all farmed populations, suggesting a genetic admixture caused by the mixing of seeds from various hatcheries. The Fst and AMOVA values showed significant genetic differences between wild and farmed populations. The Bayesian assignment also confirmed that genetic admixture was significant and widespread in artificial breeding of C. nobilis. Furthermore, the UPGMA tree topology and PCA demonstrated that the genetic diversity of wild population can be clearly distinguished from farmed populations. In a nutshell, the findings of this study not only fill the knowledge gaps in genetic diversity of wild and farmed C. nobilis populations, but also serve as a guide for maintaining the genetic diversity of C. nobilis in both farmed and wild populations.

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

2004 ◽  
Vol 52 (3) ◽  
pp. 259-265
Author(s):  
Daniela Šátková-Jakabová ◽  
J. Trandžík ◽  
Ľudmila Hudecová-Kvasňáková ◽  
Erika Hegedüšová-Zetochová ◽  
A. Bugarský ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
International Society ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Allele Frequencies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

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.

Microsatellite marker-based estimation of the genetic diversity of cattle in Chongqing

2018 ◽  
Author(s):  
Weiwei Ni ◽  
An Jiang ◽  
Jian Zhang ◽  
Guangxin E ◽  
Yongfu Huang
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Marker ◽  
Weinberg Equilibrium ◽  
The Future ◽  
Hardy Weinberg Equilibrium ◽  
The Mean ◽  
Coefficient Of Inbreeding

Cattle are the main source of meat in Chongqing. This study investigated the genetic diversity of cattle native to Chongqing and 4 introduced breeds. A total of 96 individuals from 5 breeds were genotyped using six microsatellite markers. Five markers were highly polymorphic within the breed populations, and one marker had moderate levels of polymorphism. Heterozygosity ranged from 0.5379±0.0434 in Simmental to 0.6667±0.0559 in Charolais. The heterozygosity deficit was significant in all populations analyzed compared with the expected level of heterozygosity. In addition, two microsatellite markers (TGLA53 and OarFCB20) deviated from Hardy-Weinberg equilibrium across populations (except in cattle native to Chongqing). The mean number of alleles ranged from 6.00±2.37 in Angus to 7.17±2.14 in Droughtmaster across six markers. The coefficient of inbreeding ranged from 0.0017 in Simmental and Droughtmaster to 0.0367 in Angus. Pairwise difference analyses revealed that Simmental and Droughtmaster were the most differentiated (FST= 0.06861) from each other, whereas cattle native to Chongqing and Charolais were the least differentiated (FST= 0.00557). In summary, this study showed that cattle native to Chongqing and 4 introduced breeds were genetically well protected in Chongqing, and information from this study would be helpful for guiding hybridization and genetic improvements in the future.

scholarly journals Genetic Polymorphism of Calpastatin (CAST) Gene in Pasundan Cattle

2018 ◽  
Vol 42 (4) ◽  
Author(s):  
Slamet Diah Volkandari ◽  
Aina Nadila ◽  
Nani Radiastuti ◽  
Endang Tri Margawati
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Fresh Blood ◽  
Weinberg Equilibrium ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Pcr Method ◽  
Variant Alleles ◽  
Cast Gene

The aim of this study was to determine genetic diversity of Calpastatin gene (CAST) in Pasundan cattle. Forty-four fresh blood samples were collected from UPTD BPPT Beef Cattle Ciamis West Java. Genomic DNA samples were extracted using High Salt method. A 523 bp fragment of Calpastatin gene was successfully amplified using PCR method. Genotyping of CAST gene was conducted by PCR-RFLP method using RsaI restriction enzyme (GT^AC). Genotypes and alleles were analyzed using software Cervus 3.0.7. Parameters were observed i.e genotypes and alleles frequencies, heterozygosity observed (Ho) and expected (He), Hardy Weinberg Equilibrium (HWE), and Polymorphic Information Content (PIC). Result showed that three variant genotypes of GG, GC and CC were found and two variant alleles of G and C. Allele G was found higher (0.77) than allele C (0.23). Population of Pasundan cattle was found polymorphism and in the Hardy Weinberg Equilibrium. Polymorphic Information Content (PIC) value showed in a moderate (0.290) condition. Values of Heterozygosity observed and expected were 0.409 and 0.355 respectively. This research concludes that there is polymorphism of CAST gene in Pasundan cattle population and has genetic diversity. This result could be used as early genetic information in exploration of Pasundan cattle.

scholarly journals Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1067
Author(s):  
Emel Özkan Ünal ◽  
Raziye Işık ◽  
Ayşe Şen ◽  
Elif Geyik Kuş ◽  
Mehmet İhsan Soysal
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Water Buffalo ◽  
Polymorphic Information Content ◽  
Breeding Strategy ◽  
Weinberg Equilibrium ◽  
Expected Heterozygosity ◽  
Genetic Diversity And Structure ◽  
Hardy Weinberg Equilibrium ◽  
The Mean

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy–Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy–Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.

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

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.

scholarly journals Microsatelite diversity of Bosnian-Herzegovinian-Croatian shepherd dog Tornjak

Genetika ◽  
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.

scholarly journals Genetic diversity detection of the domestic horse (Equus caballus) by genes associated with coat color

2015 ◽  
pp. 4779-4789
Author(s):  
Luz Correa A ◽  
Cindy Reyes E ◽  
Enrique Pardo P ◽  
Teodora Cavadia M
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Distance ◽  
Coat Color ◽  
Equus Caballus ◽  
Phenotypic Characterization ◽  
Domestic Horse ◽  
Global Level ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

ABSTRACT Objective. To assess the population structure and genetic diversity in populations of domestic horse (Equus caballus) in the municipality Cienaga de Oro-Córdoba (Colombia). Materials and methods. Random sampling were conducted between August and October 2013, in adult animals on farms seven districts, which was carried out phenotypic characterization of each animal, based on autosomal markers encoding morphological Extension (E) , Agouti (A), Cream (C), White (W), Gray (G), Tobiano (TO), Overo (O) and Roan (RN). Population genetic parameters: allele frequency, genetic diversity, gene flow, Hardy-Weinberg equilibrium and genetic distance were calculated through the program POPGENE 1.31; the genetic structure was assessed using the program FSTAT v. 2.9.3.2. Results. 341 individuals were analyzed in the seven populations studied, where the Extension gene Was the MOST faq frequently as the Overo and Tobiano genes showed the lowest values. Insignificant values of genetic variability and population recorded a global level, likewise, low genetic differentiation among populations, accompanied by a high gene flow was obtained; an excess of heterozygotes at population and global level was observed; to this is added the presence of Hardy-Weinberg equilibrium in all populations relative to the markers studied and low genetic distance values were reported. Conclusions. The populations are highly genetically related, a situation that may result from the existing geographical proximity between them, favoring genetic exchange and the establishment of a metapopulation.

Genetic variability of sheep populations of Saudi Arabia using microsatellite markers

2018 ◽  
Author(s):  
Ahmed H. Mahmoud ◽  
Faisal M. Abou Tarboush ◽  
Ahmed Rady ◽  
Khalid M. Al-Anaz Mohammad Abul Farah ◽  
Osama B. Mohammed
Keyword(s):  
Genetic Diversity ◽  
Saudi Arabia ◽  
Genetic Variability ◽  
Microsatellite Markers ◽  
Population Differentiation ◽  
Genomic Dna ◽  
Mean Value ◽  
Weinberg Equilibrium ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium

The present study was conducted to know the genetic diversity of three Saudi sheep populations; Naeimi (NM), Herri (H) and Najdi (NJ). Genomic DNA was extracted from 156 animals of sheep comprising 47 Naeimi, 47 Herri and 62 Najdi breeds using 18 microsatellite markers. A total of 212 alleles were generated with a mean value of 11.80 alleles per locus, with a range of observed and expected heterozygosity of 0.505 to 0.875 and 0.595 to 0.854, respectively. Eleven of the microsatellites loci studied in NM, three loci in H and fifteen loci in NJ were observed to be deviated from Hardy-Weinberg equilibrium. The fixation genetic indices (Fst) among the three sheep populations were very low, ranging from 0.017 (between NJ and H) to 0.033 (between NJ and NM), indicating low population differentiation among the three sheep populations studied. The present study showed that the microsatellite markers are powerful tool in determining genetic diversity among sheep populations.

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

HortScience ◽  
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.

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

2002 ◽  
Vol 78 (4) ◽  
pp. 539-549 ◽  
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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