scholarly journals Genealogical analyses in open population of Silla Argentino horses belonging to the national police of Colombia

SPERMOVA ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 166-172
Author(s):  
Jeisson León Rubio ◽  
◽  
Ricardo da Silva Faria ◽  
John Infante Gonzalez ◽  
Yuly Rincón Lozano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Total Population ◽  
Reference Population ◽  
Genetic Contribution ◽  
Effective Number ◽  
Population Parameters ◽  
Pedigree Data ◽  
Effective Population ◽  
Open Population ◽  
National Police

This study aimed to evaluate population parameters, genetic diversity and identify the ancestors with the highest genetic contribution of an open population of Silla Argentino horses in Colombia using pedigree data. 508 horses born between 1998 and 2018 were evaluated, called reference population (RP). The ancestors of the RP were added, defining the total population (TP) whit 1,861 horses born since 1905. Population parameters were estimated, including inbreeding coefficient (F), effective population size (Ne), effective number of founders (fe), ancestors (fa), and founder genomes (fg) and generation interval (GIN). The GIN was 10.1 (TP) and 7.7 (RP) years. The estimate of F for the RP was 0.3%, indicating control in mattings. The Ne was 317 (RP) and 179 (TP). The probability of genes origin indicated values for fe, fa and fg of 386, 187 and 351 (TP), and 161, 64 and 56 (RP), respectively, evidencing a reduction of genetic variability in the RP. Half of the genetic variation in the equine population studied was explained by 40 ancestors. The results show loss of genetic diversity in the RP and the genetic contribution of the ancestors suggests the need to increase the number of stallions for breeding and guide mating to increase genetic diversity in the new generations of Silla Argentino horses of the Colombian National Police

scholarly journals Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0258714
Author(s):  
Kristina Lehocká ◽  
Simon A. Black ◽  
Adrian Harland ◽  
Ondrej Kadlečík ◽  
Radovan Kasarda ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
North Africa ◽  
Reference Population ◽  
Captive Population ◽  
Effective Number ◽  
Pedigree Data ◽  
Effective Population ◽  
Loss Of Diversity

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

scholarly journals Using pedigree information to study genetic diversity and re-evaluating a selection program in an experimental flock of Afshari sheep

2012 ◽  
Vol 55 (4) ◽  
pp. 375-384 ◽  
Author(s):  
F. Ghafouri-Kesbi
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Selection ◽  
Reference Population ◽  
Pedigree Information ◽  
Selection Experiment ◽  
Founder Population ◽  
Effective Number ◽  
Effective Population ◽  
Breeding Values ◽  
Closed Population

Abstract. The purpose of this paper was to evaluate the inbreeding consequences of a short-term selection experiment which was initiated in 1998 in an Afshari sheep flock. Moreover, the conducted selection experiment was re-evaluated through assessing change in ranking of the first 10 influential ancestors when their genetic contributions were replaced with their breeding values. A total of 1714 animals were registered in the herdbook with a founder population comprised of 243 animals. The average coancestry (f) and inbreeding (F) in the reference population were 2.1% and 1.2%, respectively. Estimated value of the effective population size (Ne) was 50. The effective number of founders (fe) was estimated to be 40 and the effective number of ancestors (fa) was 34. Estimates of breeding values revealed that owing to phenotypic selection some ancestors with lower breeding values had greater contribution to the reference genome than those with greater breeding values and, for this reason, the population has been deprived from the maximum genetic improvement that could be achieved if selection was based on breeding values. The effective number of founder genomes (fg) was computed to be 23 and the effective number of non-founder genomes (fne) was 55. The index of genetic diversity decreased by almost 2.2% over the period studied. In general, decrease in genetic variability was low and Ne was not very low for a small-closed population under selection, indicating even in populations which undergo selection, besides achieving genetic gain, the rate of inbreeding is controllable if matings carefully planned.

scholarly journals Population Structure Analysis of the Border Collie Dog Breed in Hungary

Animals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 250 ◽  
Author(s):  
Virág Ács ◽  
Árpád Bokor ◽  
István Nagy
Keyword(s):  
Genetic Diversity ◽  
Reference Population ◽  
Inbreeding Coefficient ◽  
Pedigree Data ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Population Structure Analysis ◽  
Dog Breed ◽  
Fixation Indices ◽  
Mixed Line

Pedigree data of the Border Collie dog breed were collected in Hungary to examine genetic diversity within the breed and its different lines. The database was based on available herd books dating from the development of the breed (in the late 1800s) to the present day. The constructed pedigree file consisted of 13,339 individuals, of which 1566 dogs (born between 2010 and 2016) composed the alive reference population which was active from breeding perspective. The breed is subdivided by phenotype, showing a thicker coat, harmonic movement, a wide skull, and heavier bones for the show type, and a thinner or sometimes short coat and smaller body for the working line, while the mixed line is quite heterogeneous (a combination of the above). Thus, the reference population was dissected according to the existing lines. The number of founders was 894, but eight individuals were responsible for contributing 50% of the genetic variability. The reference population had a pedigree completeness of 99.6% up to 15 generations and an inbreeding coefficient of 9.86%. Due to the changing breed standards and the requirements of the potential buyers, the effective population size substantially decreased between 2010 and 2016. Generation intervals varied between 4.09 and 4.71 years, where the sire paths were longer due to the later initial age of breeding in males compared to females. Genetic differences among the existing lines calculated by fixation indices are not significant; nonetheless ancestral inbreeding coefficients are able to show contrasts.

scholarly journals Genetic Diversity and the Impact of the Breed Proportions of US Brown Swiss in German Brown Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 152
Author(s):  
Anna Wirth ◽  
Jürgen Duda ◽  
Ottmar Distl
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Reference Population ◽  
Pedigree Data ◽  
Effective Population ◽  
Brown Swiss ◽  
Inbreeding Coefficients ◽  
Loss Of Genetic Diversity ◽  
The Impact

Increase of inbreeding and loss of genetic diversity have large impact on farm animal genetic resources. Therefore, the aims of the present study were to analyse measures of genetic diversity as well as recent and ancestral inbreeding using pedigree data of the German Brown population, and to identify causes for loss of genetic diversity. The reference population included 922,333 German Brown animals born from 1990 to 2014. Pedigree depth and completeness reached an average number of complete equivalent generations of 6.24. Estimated effective population size for the German Brown reference population was about 112 with a declining trend from 141 to 95 for the birth years. Individual inbreeding coefficients increased from 0.013 to 0.036. Effective number of founders, ancestors and founder genomes of 63.6, 36.23 and 20.34 indicated unequal contributions to the reference population. Thirteen ancestors explained 50% of the genetic diversity. Higher breed proportions of US Brown Swiss were associated with higher levels of individual inbreeding. Ancestral inbreeding coefficients, which are indicative for exposure of ancestors to identical-by-descent alleles, increased with birth years but recent individual inbreeding was higher than ancestral inbreeding. Given the increase of inbreeding and decline of effective population size, measures to decrease rate of inbreeding and increase effective population size through employment of a larger number of sires are advisable.

Analysis of genetic diversity in four Canadian swine breeds using pedigree data

2010 ◽  
Vol 90 (3) ◽  
pp. 331-340 ◽  
Author(s):  
M G Melka ◽  
F. Schenkel
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Relative Proportion ◽  
Random Genetic Drift ◽  
Pedigree Data ◽  
Effective Population ◽  
Animal Genetic Resources ◽  
Loss Of Genetic Diversity

Conservation of animal genetic resources entails judicious assessment of genetic diversity as a first step. The objective of this study was to analyze the trend of within-breed genetic diversity and identify major causes of loss of genetic diversity in four swine breeds based on pedigree data. Pedigree files from Duroc (DC), Hampshire (HP), Lacombe (LC) and Landrace (LR) containing 480 191, 114 871, 51 397 and 1 080 144 records, respectively, were analyzed. Pedigree completeness, quality and depth were determined. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness indexes of the four breeds were 90.4, 52.7, 89.6 and 96.1%, respectively. The estimated percentage of genetic diversity lost within each breed over the last three decades was approximately 3, 22, 12 and 2%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in DC, HP, LC and LR was 74.5, 63.6, 72.9 and 60.0%, respectively. The estimated current effective population size for DC, HP, LC and LR was 72, 14, 36 and 125, respectively. Therefore, HP and LC have been found to have lost considerable genetic diversity, demanding priority for conservation. Key words: Genetic drift, effective population size

scholarly journals Estructura Genética de la Población de Llamas (Lama glama del Banco de Germoplasma del Instituto Nacional de Innovación Agraria -Perú

2016 ◽  
Vol 18 (1) ◽  
pp. 55
Author(s):  
Rubén Mamani Catoa ◽  
Roberto Gallegos Acero ◽  
Teodosio Huanca Mamani ◽  
Juan P Ablo Gutiérrez
Keyword(s):  
Genetic Structure ◽  
Reference Population ◽  
Critical Value ◽  
Inbreeding Coefficient ◽  
Gene Bank ◽  
Effective Number ◽  
Effective Population ◽  
Generation Interval ◽  
Average Ratio ◽  
Lama Glama

<p><strong>RESUMEN</strong></p><p>El objetivo del  estudio fue evaluar la estructura genética de la población de llamas, del Banco de Germoplasma  de  Quimsachata Estación Experimental Illpa-Puno del Instituto Nacional de Innovación Agraria, durante el año 2015<a href="#_msocom_1">[h1]</a> <a href="#_msocom_2">[h2]</a> . Se analizó el archivo de pedigrí de 4698 animales nacidos en el periodo 1993 al 2014, de los cuales 2075 fueron machos y 2623 hembras<a href="#_msocom_3">[h3]</a> . Para el cálculo de los coeficientes individuales de consanguinidad (<em>F</em>), coeficiente de relación media (<em>AR</em>), tamaño efectivo de la población (<em>N<sub>e</sub></em>), de fundadores (<em>f<sub>e</sub></em>)  de ancestros (<em>f<sub>a</sub></em>), intervalo generacional (IG) y la profundidad de pedigrí se ha utilizado el programa ENDOG v.4.8. Los resultados para coeficiente de consanguinidad media y el promedio de relación media de la población de llamas fueron 0.11 y 0.25% respectivamente. Del total de 906 ancestros que dieron origen a la población de referencia, 102 explican el 50% de la variabilidad genética de la población. El número efectivo de fundadores fue 508 y de ancestros 284. El intervalo generacional medio fue  5.65 años, siendo mayor en las vías gaméticas padre-hijo y padre-hija. Para el grado de profundidad de pedigrí fueron identificados 65.88% de animales con información sobre los padres y 83.95% sobre las madres. El tamaño efectivo de la población  fue de 281.81, este valor está por encima del valor crítico. En conclusión la consanguinidad en la población de llamas del banco de germoplasma fue de pequeña magnitud y que las prácticas de apareamiento fueron adecuadas durante el periodo evaluado.</p><p> </p><p><strong>ABSTRACT</strong></p><p>The objective of the study was to describe the genetic structure of the population of llama’s gene bank National Institute of Innovation Agrarian INIA-Puno. The pedigree file of 4698 animals born in the period 1993 to 2014, of which 2075 were males and 2623 females were analyzed. For the calculation of individual coefficients of inbreeding (<em>F</em>), coefficient average ratio (<em>AR</em>), effective population size (<em>N<sub>e</sub></em>), of founders (<em>f<sub>e</sub></em>)  of ancestors (<em>f<sub>a</sub></em>), generation interval (IG) and depth of pedigree has been used ENDOG v.4.8 program. The results for inbreeding coefficient average and average mean ratio of the population were 0.11 and 0.25 flames% respectively. Of the total of 906 ancestors that gave rise to the reference population, 102 account for 50% of the genetic variability of the population. The effective number of founders and ancestors was 508 284. The average generation interval was 5.65 years, being higher in the gametic roads father-son and father-daughter. For the degree of depth of pedigree they were identified 65.88% of animals with information about parents and 83.95% on mothers. The effective size of the population was 281.81, this value is above the critical value. In conclusion inbreeding in the population of llamas gene bank was small in magnitude and mating practices were adequate during the period evaluated.</p><div><hr align="left" size="1" width="33%" /><div><div><p> </p></div></div></div>

scholarly journals Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1520
Author(s):  
Paula Wiebke Michels ◽  
Ottmar Distl
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Ductus Arteriosus ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Data ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Candidate Loci

Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients FPed based on pedigree data and FROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.

scholarly journals Interrelations between effective population size and other pedigree tools for the management of conserved populations

2000 ◽  
Vol 75 (3) ◽  
pp. 331-343 ◽  
Author(s):  
ARMANDO CABALLERO ◽  
MIGUEL A. TORO
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Parameters ◽  
Effective Number ◽  
Effective Population ◽  
Clear Cut ◽  
Captive Populations ◽  
Practical Recommendations

Genetic parameters widely used to monitor genetic variation in conservation programmes, such as effective number of founders, founder genome equivalents and effective population size, are interrelated in terms of coancestries and variances of contributions from ancestors to descendants. A new parameter, the effective number of non-founders, is introduced to describe the relation between effective number of founders and founder genome equivalents. Practical recommendations for the maintenance of genetic variation in small captive populations are discussed. To maintain genetic diversity, minimum coancestry among individuals should be sought. This minimizes the variances of contributions from ancestors to descendants in all previous generations. The method of choice of parents and the system of mating should be independent of each other because a clear-cut recommendation cannot be given on the latter.

scholarly journals Management of genetic diversity using gene dropping method based on pedigree information

2013 ◽  
Vol 56 (1) ◽  
pp. 518-526
Author(s):  
M. Khaldari ◽  
A. N. Javaremi ◽  
A. Pakdel ◽  
H. M. Yeganeh ◽  
P. Berg
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Low Frequency ◽  
Pedigree Analysis ◽  
Simulation Software ◽  
Pedigree Information ◽  
Genetic Contribution ◽  
Effective Population ◽  
Management Plans

Abstract. Preservation of genetic diversity in populations is an important task to ensure a possible longterm response to selection in animal breeding. The purpose of this study was to consider how pedigree analysis and gene dropping method could be used for management plans in order to maintain genetic variation in a population under selection of Japanese quail. Therefore, the distributions of alleles frequencies originated from founders were estimated on an actual pedigree using gene dropping simulation software. Then, genetic contribution of founders to the current population, components such as the F-statistics and effective population size were estimated. The results show that from 156 founders there are only 64 of them (22 males and 42 females) in the last generation. The average genetic contribution of a founder male and female contributing to the last generation were 1.87 and 1.40 %, respectively. A total of 87 and 95 % of the genome in the last generation were constituted by 34 and 42 founders, respectively. The effective population size decreased as inbreeding increases. The allele frequency averaged over replicates agreed with the genetic contribution. Some useful information regarding the management of genetic diversity such as the probability of allele extinction, the probability of alleles surviving at a critically low frequency and risk of future allele extinction were derived by using these distributions. Results show that pedigree analysis and gene dropping are valuable tools in optimizing decisions to preserve genetic variability.

scholarly journals Evaluation of selection program by assessing the genetic diversity and inbreeding effects on Nellore sheep growth through pedigree analysis

2020 ◽  
Vol 33 (9) ◽  
pp. 1369-1377
Author(s):  
Satish Kumar Illa ◽  
Gangaraju Gollamoori ◽  
Sapna Nath
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Selection Process ◽  
Reference Population ◽  
Inbreeding Coefficient ◽  
Research Station ◽  
Effective Population ◽  
Generation Interval ◽  
Nellore Sheep ◽  
Reference Cohort

Objective: The main objectives of the present study were to assess the genetic diversity,population structure and to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd of Nellore sheep through pedigree analysis.Methods: Information utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from 1989 to 2016. Genealogical parameters like generation interval, pedigree completeness, inbreeding level, average relatedness among the animals and genetic conservation index were estimated based on gene origin probabilities. Lambs born during 2012 and 2016 were considered as reference population. Two animal models either with the use of Fi or ∆Fi as linear co-variables were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep.Results: Average generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10 and 91.56±1.58, respectively and the average inbreeding coefficient for reference population was 3.32%. Similarly, the effective number of founders, ancestors and founder genome equivalent of the reference population were observed as 47, 37, and 22.48, respectively. Fifty per cent of the genetic variability was explained by 14 influential ancestors in the reference cohort. The ratio fe/fa obtained in the study was 1.21, which is an indicator of bottlenecks in the population. The number of equivalent generations obtained in the study was 4.23 and this estimate suggested the fair depth of the pedigree.Conclusion: Study suggested that the population had decent levels of genetic diversity and a non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, small portion of genetic diversity was lost due to a disproportionate contribution of founders and bottlenecks. Hence, breeding strategies which improve the genetic gain, widens the selection process and with optimum levels of inbreeding are recommended for the herd.

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