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

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.

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

PLoS ONE ◽

10.1371/journal.pone.0258714 ◽

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.

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Evaluation of genetic diversity and management of disease in Border Collie dogs

Scientific Reports ◽

10.1038/s41598-021-85262-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Pamela Xing Yi Soh ◽

Wei Tse Hsu ◽

Mehar Singh Khatkar ◽

Peter Williamson

Keyword(s):

Genetic Diversity ◽

Common Ancestor ◽

Neuronal Ceroid Lipofuscinosis ◽

Reference Population ◽

Pedigree Information ◽

Genotype Data ◽

Runs Of Homozygosity ◽

Effective Population ◽

Maximum Loss ◽

High Level

AbstractMaintaining genetic diversity in dog breeds is an important consideration for the management of inherited diseases. We evaluated genetic diversity in Border Collies using molecular and genealogical methods, and examined changes to genetic diversity when carriers for Trapped Neutrophil Syndrome (TNS) and Neuronal Ceroid Lipofuscinosis (NCL) are removed from the genotyped population. Genotype data for 255 Border Collies and a pedigree database of 83,996 Border Collies were used for analysis. Molecular estimates revealed a mean multi-locus heterozygosity (MLH) of 0.311 (SD 0.027), 20.79% of the genome consisted of runs of homozygosity (ROH ) > 1 Mb, effective population size (Ne) was 84.7, and mean inbreeding (F) was 0.052 (SD 0.083). For 227 genotyped Border Collies that had available pedigree information (GenoPed), molecular and pedigree estimates of diversity were compared. A reference population (dogs born between 2005 and 2015, inclusive; N = 13,523; RefPop) and their ancestors (N = 12,478) were used to evaluate the diversity of the population that are contributing to the current generation. The reference population had a Ne of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (f), 205.5 effective founders (fe), 28 effective ancestors (fa) and 10.65 (SD 2.82) founder genomes (Ng). Removing TNS and NCL carriers from the genotyped population had a small impact on diversity measures (ROH > 1 Mb, MLH, heterozygosity), however, there was a loss of > 10% minor allele frequency for 89 SNPs around the TNS mutation (maximum loss of 12.7%), and a loss of > 5% for 5 SNPs around the NCL mutation (maximum 5.18%). A common ancestor was identified for 38 TNS-affected dogs and 64 TNS carriers, and a different common ancestor was identified for 33 NCL-affected dogs and 28 carriers, with some overlap of prominent individuals between both pedigrees. Overall, Border Collies have a high level of genetic diversity compared to other breeds.

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

SPERMOVA ◽

10.18548/aspe/0009.22 ◽

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

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

Revista de Investigaciones Altoandinas - Journal of High Andean Research ◽

10.18271/ria.2016.178 ◽

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

RESUMENEl 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 (F), coeficiente de relación media (AR), tamaño efectivo de la población (Ne), de fundadores (fe) de ancestros (fa), 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. ABSTRACTThe 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 (F), coefficient average ratio (AR), effective population size (Ne), of founders (fe) of ancestors (fa), 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.<div><hr align="left" size="1" width="33%" /><div><div> </div></div></div>

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Pedigree analysis of Polish warmblood horses participating in riding performance tests

Canadian Journal of Animal Science ◽

10.4141/cjas-2014-006 ◽

2015 ◽

Vol 95 (1) ◽

pp. 21-29 ◽

Cited By ~ 5

Author(s):

Alicja Borowska ◽

Tomasz Szwaczkowski

Keyword(s):

Genetic Diversity ◽

Performance Test ◽

Pedigree Analysis ◽

Pedigree Information ◽

Performance Tests ◽

Effective Number ◽

Horse Population ◽

Inbreeding Coefficients ◽

Discrete Generation ◽

Inbreeding Rate

Borowska, A. and Szwaczkowski, T. 2015. Pedigree analysis of Polish warmblood horses participating in riding performance tests. Can. J. Anim. Sci. 95: 21–29. The aim of this study was to describe the population structure and genetic diversity in Polish warmblood horse population participating in the performance test. The reference population consisted of 596 stallions and 866 mares that participated in stationary performance tests conducted between 2002 and 2011 in Poland. The pedigree data contained 15 452 individuals. Completeness of pedigree information was assessed by two measures: percentage of animals with both parents known and discrete generation equivalent. Individual inbreeding coefficients, coancestry coefficient, individual increase in inbreeding, founder equivalent, founder genome equivalent, effective number of non-founders and genetic diversity loss were estimated to characterize the genetic diversity of the population. The average number of discrete generation equivalents reached 4.50 for observed stallions and 5.04 for mares, which shows good pedigree completeness. Pedigree analysis showed that 34% of the stallions and 44% of mares had inbreeding coefficients above zero. The average coancestry was 0.39% in the whole tested population. Average inbreeding rate of studied populations was very low (0.46%). The effective number of founders was 560. Generally, the inbreeding rate was low; genetic diversity was observed at a constant level for mares and only a small decrease was noticed for stallion. However, further studies are needed in this area.

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

Genetics Research ◽

10.1017/s0016672399004449 ◽

2000 ◽

Vol 75 (3) ◽

pp. 331-343 ◽

Cited By ~ 240

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.

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Genetic Variability of Cold-Blooded Horses Participating in Genetic Resources Conservation Programs, Using Pedigree Analysis

Annals of Animal Science ◽

10.2478/aoas-2018-0047 ◽

2019 ◽

Vol 19 (1) ◽

pp. 49-60 ◽

Cited By ~ 4

Author(s):

Grażyna Polak

Keyword(s):

Genetic Variability ◽

Genetic Resources ◽

Reference Population ◽

Pedigree Analysis ◽

Pedigree Information ◽

Effective Population ◽

Conservation Programs ◽

Data Set ◽

Genetic Resources Conservation ◽

Resources Conservation

AbstractTwo types of Polish local cold-blooded horses – Sztumski and Sokólski, covered by genetic resources conservation programs, were analyzed for founder’s contribution, genetic structure and inbreeding. In both populations, created in the early twentieth century, were used the same stallions, mainly Ardennes, Belgians and Bretons. The aim of the study was to analyze the genetic variability of Sztumski and Sokólski cold-blooded horses, using pedigree information. The reference population contained 2359 horses: 1129 Sztumski and 1230 Sokólski included in conservation programs in 2014. The data set consisted of a total of 12,821 ancestor pedigrees. The results showed that in the analyzed population the number of founders was 1139 for Sztumski and 1118 for Sokólski horses; effective population size and effective number of founders were 688.8; 156.9 and 704.5; 111.4, respectively. The mean coefficient of inbreeding was 1.54 for Sztumski and 1.56 for Sokólski horses. In the gene pool the most important contribution was of Ardennes horses (43.67% in Sztumski and 46.82% in Sokólski horses), followed by Belgian horses (18.32% and 9.3%, respectively). The most important ancestors in both populations were Ardennes sires Roll-tan 699 and Gustaw 2807, and German cold-blooded sires Elbgang 1504 and Bär.

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

Archives Animal Breeding ◽

10.7482/0003-9438-56-050 ◽

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.

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

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.18.0553 ◽

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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Genetic variability of a Criollo cattle population under conservation

The Journal of Agricultural Science ◽

10.1017/s0021859605005307 ◽

2005 ◽

Vol 143 (2-3) ◽

pp. 209-216 ◽

Cited By ~ 1

Author(s):

L. M. MELUCCI ◽

C. DÍAZ ◽

C. A. MEZZADRA

Keyword(s):

Genetic Variability ◽

Population Size ◽

Genetic Drift ◽

Germplasm Conservation ◽

Reference Population ◽

Effective Number ◽

Effective Population ◽

The Impact

The active germplasm Bank of the Integrated Unit (Facultad de Ciencias Agrarias, Unversidad Nacional de Mar del Plata and the Experimental Station of INTA) at Balcarce, keeps both in vivo (live herd) and in vitro Criollo Cattle (samples of semen and embryos cryogenically), with the aim of preserving genetic variability for potential future use. Parameters based on probable origin of genes, on population size and on the estimation of components of (co)variances for birth and weaning weights were estimated to evaluate the genetic variability of the material contained in the Bank. The information available came from 667 individuals, of which 84 had unknown parents, and 142 half-founders (only one parent known), having a mean number of births per year of 24 calves from four different sires. AI was performed during the mating season almost every year. The evolution of effective number of founders (fe), effective number of ancestors (fa), effective number of founder genomes (Ng) and the ratio fe/fa over different periods from the creation of the Bank, were analysed. Annual increase of inbreeding coefficient (F) was 0·2% and the effective population size (Ne) was estimated as 23, 14 and 25 individuals for the periods defined by years 1978–82, 1983–87 and 1993–97, respectively. The ratio fe/fa was higher in the years where the ratio number of sires/number of dams was lower, indicating that the impact of the effective number of sires is more important than the effective number of females in generating genetic bottlenecks. When the reference population was taken for the period 1989–97, 16·45 out of the 85·63 founders of the population made contributions not explained by other ancestors, but if possible losses of genomes due to genetic drift are considered, the number of genomes still present was reduced to 9·09 indicating a possible narrow genetic bottleneck in the last period. The Ng/fe ratio was 0·11, 0·10 and 0·11 for the reference populations defined by years 1989–92, 1993–97 and 1989–97, respectively. The main objective in germplasm conservation programmes should be the maintenance of genetic variability. Thus, matings in the population under conservation should be designed in order to mate those animals that maximize the effective number of genome founders (Ng) to avoid losses due to genetic drift.

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