Effective Number Of Ancestors Research Articles

Pedigree diversity and implications for genetic selection of Katahdin sheep.

The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.

Genealogical structure of the Colombian Romosinuano Creole cattle

The Romosinuano cattle breed is one of the most important Creole genetic resources in Colombia, and interesting traits like adaptation or reproductive efficiency have promoted its use in different countries in America. To consolidate the genealogical historical records, the review of very first yield records in this population was used to reconstruct the genealogy of the breed since the first animals incorporated to the in vivo germplasm bank and estimate different demographic parameters. The complete genealogy comprises 17,136 animals with 5.8 years of generation interval for two pathways. The estimated average inbreeding for the population and inbred animals was 2.53% and 6.32% respectively, with a progressive increase of inbred animals across the generations. Almost 48% of the total animals presented some level of consanguinity. Effective population size (Ne) based on the inbreeding rate estimated by regression in all generations was 120 animals whereas Ne estimated by equivalent generations was 69 animals. Effective number of founders (Fe), effective number of ancestors (Fa), and ancestors explaining 50% of variability were 75, 48, and 22, respectively. The relation between Fa/Fe of 64% indicates a genetic bottleneck effect in the population studied.

Population dynamics of a long-term selection experiment in White Plymouth Rock chickens selected for low or high body weight

The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selection horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 individuals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was available. Inbreeding (F) and average relatedness (AR) coefficients were computed. Average F per generation and AR coefficients were 1.3 (SD 0.8) % and 0.53 (SD 0.001) for LWS, and 1.5 (SD 1.1) % and 0.66 (SD 0.001) for HWS. Mean F for the entire pedigree was 0.26 (0.16) and 0.33 (0.19), and maximum F was 0.64 and 0.63, in LWS and HWS, respectively. Based on Wright's fixation index, at generation 59, substantial genetic differences were established between lines. The effective population size was 39 in LWS and 33 in HWS. The effective number of founders was 17 and 15, effective number of ancestors were 12 and 8, and genome equivalents were 2.5 and 1.9 in LWS and HWS, respectively. About 30 founders explained the marginal contribution to both lines. By generation 59, only 7 male and 6 female founders contributed to both lines. Moderately high levels of inbreeding and low effective population sizes were inevitable, as this was a closed population. However, effects on the fitness of the population were expected to be less substantial because founders were a combination of 7 lines. The effective numbers of founders and ancestors were relatively low compared to the actual number of founders, as few ancestors contributed to descendants. Based on these evaluations, it can be inferred that LWS and HWS had similar population structures. Comparisons of selection responses in the 2 lines therefore should be reliable.

Análise de informações genealógicas de bovinos Gir e Nelore da Costa Rica

ABSTRACT: The objectives were to analyze the genealogical information of Gyr (GY) and Nelore (NL) cattle from Costa Rica. Analyzed: pedigree integrity (GY, 13272; NL, 18153); number of complete, maximum traced and equivalent complete generations; inbreeding (FI); generation interval (GI) through four selection routes; average additive genetic ratio (AGR); effective number of founders (fe); effective number of ancestors (fa); effective population size (Ne). The analysis was performed with the ENDOG software. The maximum proportion of unknown parents, grandparents, and great-grandparents was 18.6%, 39.9%, and 59.3%, respectively. The average FI for NL was 8.87% and 2.85% in GY. The average consanguineous population (%) and FI was 53.9 and 16.5% in NL, 28.9 and 9.9% in GY. The average and maximum values of AGR for NL were 3.5 and 12.8, 1.4 and 5.6 in GY. The fe and fa for NL were 65.0 and 38.0, in GY 145.7 and 59.0. The Ne indicated increases in FI in the range of 1 to 2% in GY, for NL greater than 2%, with a status of care to monitor the evolution of F and AGR and their possible implications in genetic improvement. The GI ranged from 6.3 to 7.9 years with a general average of 6.9 years. These results show a summary of the genetic and reproductive management those breeders have carried out.

[Variabilidade genética do gado Guzerat criado no norte do Brasil, com base na análise do pedigree]

ABSTRACT Genealogical data comprised 45,711 animals born between 1901 and 2016, with 48,127 animals in the pedigree file. Population structure was analyzed in terms of pedigree completeness, individual inbreeding coefficient (F), generation interval (L), rate of inbreeding (ΔF), effective population size (Ne), effective number of founders (ff), and effective number of ancestors (fa). The herd initially consisted of 13 bulls and 14 cows, and there were variations in the number of selected bulls and cows throughout the analyzed period, with 2,575 bulls, 13,691 cows, and 45,711 births recorded at the end of 2016. In total, 48.81% of the cows had only one progeny. Most dams (47.59%) were between three and seven years old, with a mean L in the population of 7.9 years. According to the results, 52.75% of the cows, 44.92% of the bulls, and 63.71% of the calves of the Guzerat breed in the northern region of Brazil showed some degree of inbreeding, with small-magnitude coefficients (0.56, 0.83, and 0.71% for cows, bulls, and calves, respectively). This fluctuation did not hinder the genetic evolution of the herd in the region. The effective population size does not seem to compromise the maintenance of genetic variability in the breed.

Genetic and Population Structure of Croatian Local Donkey Breeds

The two native Croatian donkey breeds (Littoral-Dinaric donkey and Istrian donkey) were marginalized in the second half of the 20th century and were on the verge of biological extinction. The aim of this study was to analyze the demographic and genetic status of two donkey breeds, two decades after the start of protection by analyzing their pedigrees and genetic structure. The average generation interval was higher for the Istrian donkey (7.73) than for the Littoral-Dinaric donkey (7.27). The rate of the effective number of founders compared with the effective number of ancestors in the Littoral-Dinaric donkey (1.03; 325/316) and in the Istrian donkey (1.08; 70/65) revealed no evidence of a genetic bottleneck. The inbreeding coefficient (F) and the average relatedness coefficient (AR) was lower in the Littoral-Dinaric donkey population (0.99%; 0.13%) than in the Istrian donkey population (1.77%; 1.10%). Genetic microsatellite analysis showed relatively high genetic diversity in Littoral-Dinaric donkey and Istrian donkey breeds, expressed by mean allele number (5.92; 5.85) and expected heterozygosity (0.650; 0.653). Genetic differentiation between the Littoral-Dinaric donkey and the Istrian donkey has not significantly increased in the last two decades (FST = 0.028). Genetic analysis also showed no evidence of high inbreeding or genetic bottleneck in both breeds. A total of 11 haplotypes including 28 polymorphic sites were found in 30 samples. Analysis of mtDNA has shown that the Littoral-Dinaric donkey and Istrian donkey breeds belong to the Equus asinus africanus group. The study confirms the need to use different analytical approaches to get a regular and complete insight into the situation and trends within and between breeds, so that the existing diversity can be fully preserved.

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

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.

Genetic diversity and the application of runs of homozygosity-based methods for inbreeding estimation in German White-headed Mutton sheep.

The German White-headed Mutton (GWM) sheep is a monitoring population believed to have been improved through crosses with other breeds, e.g., Texel (TXL) and French Berrichone du Cher (BDC). The primary aim of the study was to analyse genetic diversity and breed composition of GWM sheep. Furthermore, different measures of computing inbreeding from the runs of homozygosity (ROH) were investigated. Data for GWM consisted of pedigree information on 19,000 animals and 40,753 quality filtered SNPs on 46 individuals. Additionally, publicly available genotype data on 209 individuals belonging to nine sheep breeds were included in the analysis. Due to evenness of SNPs spacing and proportionality of the number of SNPs in each autosome to autosome length, a high correlation (rp = 0.99) was found between genomic inbreeding coefficients computed based on the length of ROH (FROH_L) and those computed relative to the number of SNPs in ROH (FROH_N). Total inbreeding was partitioned into values for individual chromosomes revealing the highest levels of inbreeding on chromosomes 1, 2 and 3. Correlations between the ROH-based inbreeding measures and pedigree inbreeding reached 0.82. The observed heterozygosity estimate in GWM was high (0.39), however, the breed suffered low level of effective population size (~50) from a genomic viewpoint. Moreover, effective number of founders (186), and effective number of ancestors (144) implied disequilibrium of founder contribution and a genetic bottleneck in the breed. Multidimensional scaling and network visualisation analyses revealed close connectedness of GWM to BDC and German Texel (GTX). A model-based admixture analysis consistently indicated the flow of genes from other breeds, particularly BDC to GWM. Our analyses highlight the mixed genetic background of GWM sheep and furthermore, suggest a close monitoring of the breed to consolidate its genetic diversity while averting further reduction in the effective population size.

Analysis of the population structure of a cattle conservation nucleus Curraleiro Pé Duro

ABSTRACT The objective of this research was to study the population structure of the Cattle Conservation Nucleos Curraleiro Pé Duro of the Instituto Nacional do Semiárido (NCP_INSA) based on pedigree data. Genealogical information from 338 animals registered in the period from 1991 to 2019 was used. The number of founding animals (Nf), the effective number of founders (fe), effective number of ancestors (fa), inbreeding coefficient (F), and average relatedness coefficient (AR), in addition to Fis, Fit and Fst were estimated. It was possible to identify ancestors up to the third generation, with an increase in information over the generations. Of the total pedigree information evaluated, 90.53% had the identification of the father and mother. The effective size of the population was smaller than those proposed by FAO, suggesting the need to redefine the herd management and genetic management plan strategies, promoting gene flow and breed expansion.

Assessment of the genetic diversity of Two Czech autochthonous sheep breeds

Based on pedigree information, the population structure, within-breed genetic variability and causes of genetic variability losses in Wallachian sheep (WS), and Sumava sheep (SS) were studied. The maximum number of generations observed in both WS and SS was 16, and the equivalent number of complete generations 5.66 and 4.35, respectively. The average generation intervals were in WS and SS 4.33 and 4.72 years, respectively. A span of four years, 2015–2018, was used as the reference population (animals from the last generation). The average inbreeding coefficient and average relatedness coefficient were 5 % and 9 % for WS, while both were 3 % for SS. The rate of the inbreeding coefficient was 0.5 % in WS and 1 % in SS. The effective number of founders, effective number of ancestors and effective number of founder genomes were 104, 50 and 22.8 for SS and 39, 21 and 10.28 for WS. The effective population size based on an increase in the inbreeding coefficient and computed based on average coancestry were 50.61 and 64.5 in WS and 99.56 and 166.14 in SS. These results indicate a low value of genetic diversity in Wallachian sheep. The loss of variability was caused by the bottleneck effect and partly also genetic drift and the unequal contribution of the founders.

Genetic Variability of Bharat Merino Sheep Derived from Pedigree Information

Background: The genetic variability in a population is the raw material for selection, because the estimation of genetic parameters depends on the variability present within the population. The pedigree analysis is a method to assess population genetic variability. An increase in the level of inbreeding disturbs the production performance of the animals. Hence, it is essential to assess the effect of inbreeding on production performance of the animals at regular intervals. The present study was conducted on data of Bharat Merino (BM) sheep with twin objectives of evaluating the population structure by pedigree analysis and possible effect of inbreeding on lamb growth and heritability estimates. Methods: The study was conducted on data consisting of a total of 9688 pedigree records of BM sheep born from 1975 to 2018 (43 years), out of which 9050 formed population reference (with both the parents known). ENDOG ver 4.8 program was used to generate different measures of genetic diversity. General Linear Model of SPSS 25.0 was used to ascertain the effect of inbreeding (Fi) or change in inbreeding (ÄFi) on the lamb live weights. Using animal model with software WOMBAT, single trait linear mixed model analyses were performed. The heritability estimates and breeding values were obtained by including or excluding the inbreeding coefficient in the model to observe how the estimates of heritability varied with inclusion or exclusion of the inbreeding coefficient. Result: Effective number of founders (fe) was 56, constituting 11.39% founders in the population reference, while the effective number of ancestors (fa) was 43.The genetic contribution of the 15 most influent ancestors explained 50% of the genetic variability in the dataset. The ratio fe/fa, representing the effect of population bottleneck, was 1.302. The average inbreeding coefficients for the whole pedigree was 2.36%, while it was 3.84% for inbred animals. It was found that the inbreeding coefficient (Fi) increased with the addition of each generation to the pedigree. The average relatedness coefficient was 4.53% between members of the population.The effect of individual inbreeding (Fi) or the change in inbreeding (DFi) was not significant on the lamb live weights, except the effect of individual inbreeding (Fi) on three-month body weight and average daily gain (0-3month) and of change in inbreeding (DFi) on three-month body weight. From the analysis of the pedigree data of Bharat Merino sheep, it was found that the most of the measures of genetic diversity were within acceptable limits and the pedigree data was reasonably well maintained. When inbreeding was accounted for in the model, there were reductions in h2 estimates as well as the estimates of breeding values for both 3WT and ADG1 and consequently there were changes in ranking of animals for both 3WT and ADG1.

Population structure and effect of inbreeding on milk yield of Saanen goats in Brazilian production systems

• The aim of this study was to investigate the population structure and effect of inbreeding of Saanen goats under Brazil. • The effective number of ancestors in the present study was 101 animals. • The average inbreeding and relatedness coefficients are under control. The aim of this study was to evaluate the history of a population of Saanen goats based on the population structure and the effect of inbreeding on accumulated 305-d milk yield ( MY305 ) and lactation length ( LL ). Pedigree records of 7640 individuals born between 1997 and 2014 were analyzed and population parameters were estimated based on the probability of gene origin, effective population size ( Ne ), average inbreeding coefficient ( F ), flock classification according to origin and use of breeding animals, average relatedness coefficient ( AR ), pedigree completeness and number of generations using the ENDOG v4.8 program. A total of 79.57 %, 50.73 %, 29.10 % and 11.60 % of the examined individuals had pedigrees in the first, second, third and fourth ascendancy, respectively. The total number of founders and ancestors was 123 and 101, respectively, and 39 of the latter explained 50 % of the genetic variability in the population, which indicates a loss of original genes. The AR and F coefficients were 0.78 % and 1.48 %, respectively. There was no significant inbreeding effect on LL . The MY305 was significantly affected by inbreeding, with a reduction of 2.31 kg per 1% increase in the individual inbreeding coefficient. The LL and MY305 exhibited heritability of 0.03 and 0.18 respectively, with a genetic correlation of 0.97.

Genetic diversity, admixture and the effect of inbreeding on milk performance in two autochthonous goat breeds

For the development of an appropriate program for the conservation of animal genetic resources, careful evaluation of the current genetic diversity in endangered breeds was performed. Pedigree data from a total of 38,288 animals registered in studbooks between 1970 and 2017 from two autochthonous Czech goat breeds, White and Brown Shorthair goats, were analysed to identify factors that may have affected the genetic variability of the breeds. Because the populations of both breeds are closed, there is concern about the loss of genetic variation. The average numbers of equivalent complete generations were 10 and 11 for White Shorthair goat and Bowen Shorthair goat, respectively. The effective numbers of founders contributing to the current genetic pool were 323 and 45, and the effective numbers of ancestors were 90 and 24, respectively. The average inbreeding and relatedness coefficients for the reference populations of the two breeds were 2% and 5.3%, respectively, for White Shorthair goats and 3.7 and 11.5% for Brown Shorthair goats. The corresponding estimates of the effective population size based on an increase in inbreeding or coancestry were 244 and 311, respectively, for White Shorthair goats and 82 and 87 for Brown Shorthair goats. Three kinds of inbreeding coefficients, the classical inbreeding coefficient, the new inbreeding coefficient and the ancestral inbreeding coefficient, were used to quantify the effects of inbreeding and purging on milk production in both analysed breeds. All tested inbreeding coefficients (FX, Fnew) showed a significantly negative influence on milk performance in the White Shorthair goat breed. The purging effect was confirmed based on the difference between FX and Fnew in White Shorthair goats and on the suitability of the statistical model in Brown Shorthair goats. These statistics suggest that genetic variability has decreased and inbreeding depression has occurred and that without changes in the breeding strategy, genetic variability might continue to decline.

Monitoring of genetic diversity in autochthonous Czech poultry breeds assessed by genealogical data

Czech local poultry breeds face high risks of extinction. Because these populations are closed, they are more likely to lose genetic diversity. The aim of this analysis was to determine the loss of genetic diversity in three Czech autochthonous poultry breeds. Pedigree data from a total of 1 932 Czech Gold Speckled Hens, 325 Czech White Geese and 111 Czech Crested Geese registered in studbooks between 2000 and 2018 were evaluated. Data were analysed to determine the major factors that affect the genetic variability of these breeds. The average numbers of equivalent complete generations ranged from 2.53 to 4.82. The effective numbers of founders were from 29 to 59, representing from 43% to 62% of the total number of founders. The effective number of ancestors was estimated in the range of 21 to 41. The average inbreeding coefficient and relatedness coefficient (in parentheses) for the reference populations were 2.0% (6.5%), 1.9% (4.9%) and 2.1% (9.3%), respectively. The results showed that the effective population size derived from the rate of inbreeding ranged from 46 to 108 and if derived from the rate of coancestry it ranged from 35 to 74. With regard to these results, the analysed breeds showed a high probability of allele loss and consequent loss of genetic diversity.

Population structure and genetic diversity of Mangalarga Marchador horses

Mangalarga Marchador (MM) is the most numerous horse breed in Brazil. The aim of this study was to analyze the genetic structure of the MM horses population of Brazil based on pedigree analysis and identify factors that may affect its genetic variability. Pedigree data from 1906 to 2015 was used and the inbreeding and probability of gene origin parameters were obtained, considering the total population (TP, n = 514,282) and a reference population (RP, n = 172,508) from 2005 to 2015. The generation interval was 10.43 in the TP and 9.48 in the RP. The inbreeding coefficient (F) was 1.02% in the TP and 1.10% in the RP. The effective population size was 1,471 for the TP and 959 for the RP. The effective number of ancestors, founders, and founder genomes were 1,038, 1,062, and 150 in the TP, and 198, 225, and 133 in the RP, respectively. The numbers of founders that exhibit 50% of the current gene pool of the breed represented 7.94% of the total founders of the TP and 19.09% of the RP. The analysis of probability of gene origin alert for a small loss of genetic diversity in the recent population. However, the Mangalarga Marchador population does not exhibit relevant factors that may seriously affect your genetic variability and that would impair the evolution of the breed in Brazil.

Genetic diversity and population structure of Boer and Nubian goats in Mexico

In Mexico, since 2010 the Asociación Mexicana de Criadores de Ganado Caprino de Registro has been undertaking annual national genetic evaluations for the Boer and Nubian goat breeds. Mexican pedigree goat farmers are concerned with maintaining a reasonable high genetic diversity and a low level of inbreeding without loss of genetic gain. This study aimed to assess the genetic diversity and to describe the population structure of the Boer and Nubian goat breeds in Mexico using pedigree analyses to support the development of strategies for breeding programs. Herdbook information collected between 1994–2017 for Boer and from 1991 to 2017 for Nubian were utilized. The information included pedigree records on 18,947 animals for Boer (141 flocks) and 13,744 animals for Nubian (99 flocks). The effective number of founders ( f e ) were 504 and 203, and the effective number of ancestors ( f a ) were 253 and 88, for Boer and Nubian, respectively. The ratio f a / f e was 0.50 for Boer and 0.43 for Nubian, indicating the existence of population bottlenecks. The average inbreeding and relatedness coefficients were 1.02 and 0.28 % for Boer and, 1.39 and 1.04 % for Nubian. The number of most influential ancestors that explained 50 % of the genetic diversity in the population were 109 for Boer and 38 for Nubian. The average generation interval estimated through the four gametic paths was 3.27 ± 0.03 yr for Boer and 4.63 ± 0.06 yr for Nubian. Realized effective population size, computed from the individual increase in inbreeding, was 61.3 ± 24.5 for Boer and 69.3 ± 22.8 for Nubian (kids born from 2013 to 2017 were considered as the reference population for both breeds). The average equivalent completed generations, as a measure of pedigree completeness, were 2.02 for Boer and 2.88 for Nubian. The pedigree completeness index increased over time for both breeds. The results revealed the loss of genetic diversity and the presence of genetic bottlenecks for both populations. The study of the genetic diversity on these populations must continue to prevent the decrease in genetic progress and genetic variability. Additionally, a mating policy that simultaneously allows low levels of inbreeding, high levels of genetic diversity and maximum genetic progress, must be designed.

Population structure and inbreeding of Holstein cattle in southern Brazil

ABSTRACT The present investigation aimed to evaluate the population structure and inbreeding of Holstein herds in southern Brazil. To carry out the analysis, the Associacao Paranaense de Criadores de Bovinos da Raca Holandesa (APCBRH) in Brazil provided the data, which consisted of a pedigree file of 206,796 animals born between 1970 and 2014. Results regarding the following parameters were determined: pedigree integrity, effective number of founders, effective number of ancestors, generation interval, inbreeding coefficient, realized effective population size, and average [...]

Population structure of Lori-Bakhtiari sheep in Iran by pedigree analysis

The objective of this study was to describe the population genetic structure and evaluate the state of conservation of genetic variability of Lori-Bakhtiari sheep in Iran. As such, pedigree information of 10,644 lambs lambed from 1989 through 2016 in the stud flock of Lori-Bakhttiari sheep was included in the analysis. Our first goal was to estimate mean and variance of family size across sires and dams using pedigree data. Our second goal was to estimate population structure in Lori-Bakhtiari sheep including estimation of pedigree completeness (PC), genetic conservation index (GCI), effective population size (Ne), effective number of founders (fe), effective number of ancestors (fa), generation interval (L), individual inbreeding coefficient (F) and average relatedness coefficient (AR) using the ENDOG software. The results showed that the average number of progenies per ram and ewe in their lifetime were 26.44 (15–152) and 3.6 (1–15), respectively. The mean and variance of family size of sires differ across years. The pedigree completeness (PC) was equal to 0.61. The fe and fa were 109 and 98, respectively with a ratio of 1.11. The number of ancestors explaining 50% of genetic diversity was 30. The Ne also varied from 142.68 to 144.13 during the study period. The average generation interval was 4.11 years. The mean inbreeding coefficient was 2.5% in inbred lambs and 1.26% in whole population with an annual increase of 0.09% per year and 0.87% per generation. The AR of the total population was estimated to 2.27% with an incremental trend of 0.10% per year and 0.59% in each generation. The average GCI was 11.75 units with an incremental trend of 0.76 per year. The effects of birth type and year of birth were found to be significant on most of the studied demographic parameters. Though there is an increasing inbreeding coefficient trend over a number of generations, it is still lower than the maximum acceptable recommendation of 1% per generation. This provides us an opportunity for maintaining genetic diversity and implementation of the improvement breeding program. However, unbalanced use of rams led to the creation of family size variation over years. Therefore, this study warrants a comprehensive mating plan with minimum inbreeding rate to maintain genetic variability in Lori-Bakhtiari sheep.

Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure, genetic variability and inbreeding

The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the ‘Endog v 4.8’ program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the most important one was the population of the 12 368 Maremmano horses officially registered in the National Studbook. The pedigree completeness of this population was very good because it was more than 90% at the third parental generation and more than 70% at the fifth generation; the pedigree traced back to a maximum of 10.50 generations with an average of 3.30 complete generations and 5.70 equivalent complete generations. The average generation interval was 10.65±4.72 years, with stallions used for longer periods than mares. The intervals ranged from 10.15±4.45 (mother–daughter) to 10.99±4.93 (father–daughter). The effective number of founders (fe) was 74 and the effective number of ancestors (fa) was 30 so that the ratio fe/fa was 2.47. The founder genome equivalents (fg) was 13.72 with a ratio fg/fe equal to 0.18. The mean of the genetic conservation index was 5.55±3.37, and it ranged from 0.81 to 21.32. The average inbreeding coefficient was 2.94%, with an increase of 0.1%/year, and the average relatedness coefficient was 5.52%. The effective population size (Ne) computed by an individual increase in inbreeding was 68.1±13.00; the Ne on equivalent generations was 42.00, and this value slightly increased to 42.20 when computed by Log regression on equivalent generations. The analysis confirmed the presence of seven traditional male lines. The percentage of Thoroughbred blood in the foals born in 2015 was 20.30% and has increased 0.21%/year since 1980; in particular, it increased more than twice (0.51%/year) until 1993 and afterwards slightly fluctuated. The pedigree analysis confirmed the completeness of genealogical information and the traditional importance that breeders gave to the male lines; although the genetic diversity of Maremmano seemed to be not endangered by the selection program, some effects on the population structure were found and a more scientific approach to genetic conservation should be incorporated in the selection plans.

Assessing genetic diversity of various Canadian sheep breeds through pedigree analyses

The loss of genetic variability in a population will drastically affect the success of a breeding program by reducing selection response and fitness and, consequently, affecting reproduction, resilience, and production efficiency. The objective of this study was to perform an in-depth analysis of the pedigree of the Canadian sheep breeds to assess the levels of inbreeding, effective population size, and other metrics of genetic diversity, which included the five most important sheep breeds in Canada: Dorset, Polypay (PO), Rideau-Arcott, Romanov (RV), and Suffolk, using a large dataset (1 336 926 animals). As measures of genetic diversity, effective population size, inbreeding coefficient, effective number of founders, effective number of founder genomes, effective number of nonfounders, and effective number of ancestors were estimated. The completeness and depth of the Canadian sheep pedigree datasets were reasonably high, with <20% parental information missing. More attention should be given to PO breed, which was found to have the smallest effective population size (55), and RV breed, which had the highest average level of inbreeding (4.8%). Techniques such as optimum contribution selection and minimum coancestry mating could be used to minimize the inbreeding of future generations, while maintaining genetic progress at a desirable level.