Average Relatedness Coefficient 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.

Population structure and genetic diversity of Boer goat breed in Brazil

Information about population structure of domestic breeds is essential to provide effective guidelines in order to increase productivity based on genetic improvement programs. Therefore, the purpose of this study was to describe and analyze the genetic diversity and population structure of Boer goat breed in Brazil. A pedigree data from 22,650 individuals born between 1980 and 2019 and recorded by the Brazilian Association of Goat Breeders was analyzed in terms of completeness, average generation interval, gene origin probability, average kinship coefficient, inbreeding coefficient, and genetic conservation index, using the software ENDOG 4.8. The ancestry was known for 84.06 %, 77.38 %, 72.43 %, 68.00 % and 59.34 % of samples in the first, second, third, fourth and fifth parentage, respectively. The average number of complete, equivalent and maximum generations over a 40-year period was equal to 2.79, 4.86 and 8.22, respectively. The mean interval between generations was 3.27 (+/−2.13). A total of 2013 founders and 1881 ancestors was determined, while the effective number of founders and ancestors were established in 262 and 68, respectively. The 44 main ancestors were responsible for 50.02 % of the total genetic variance in Boer breed. The average relationship coefficient was determined in 1.61 % while the average inbreeding coefficient was equal to 3.41 %. Both parameters were higher (2.09 and 4.96, respectively) in populations composed of two or more complete generations. The average genetic conservation index was 22.90, including seven animals with values above 100. The high quantity (75.31) of inbred individuals from two or more generations requires particular attention. On the other hand, the identification of animals that descend from a high quantity of founders in their pedigree indicate they can be used to keep or increase the genetic diversity in further generations.

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.

Long-term pedigree analysis: An effective tool for managing congenital malformations in cattle

Controlling congenital defects is an important aspect of breeding for genetic health; however, whether malformations are caused by genetic or nongenetic factors may not be clear. This study aims to analyse the incidence of aplasia genitalis, atresia ani et recti and hernia cerebralis in the Czech cattle population, analyse the relatedness of affected calves by a relationship matrix, and assess the potential future threat. The sires fathering affected calves were born in the Czech Republic or imported from 1986 to 2001. The cases occurred on farms across the Czech Republic. The pedigree of each case was examined for common maternal and paternal ancestors (inbreeding loops) and for ancestors shared by other cases of the defect. The average relatedness coefficient of each individual was computed based on the relationship matrix. The results of the analysis of pedigrees and of the relationship matrix support the hereditary aetiology. The 13 calves affected by aplasia genitalis had common ancestors in 12 cases. The results indicate hereditary causation with recessive inheritance. In atresia ani et recti, some of the pedigrees of 25 affected calves support hereditary causation, and repeating ancestors were found for 11 calves. Our analysis of 11 hernia cerebralis cases also hints at the genetic background, but not as unequivocally as in other congenital defects studied. A high number of descendants fathered by sires of affected calves constitutes a risk for future. The relationship matrix and pedigree analysis could help in managing genetic health, although the final goal in terms of inherited defects must be the description of causal genes and mutations. Measures to control sires and dams with affected calves should be appropriate under the current knowledge, which include culling or prudent use of breeding with the monitoring of descendants.

Effects of Selection on Breed Contribution in the Caballo de Deporte Español.

The equine breeding industry for sport's performance has evolved into a fairly profitable economic activity. In particular, the Caballo de Deporte Español (CDE) is bred for different disciplines with a special focus on Show Jumping. The main aim of this study was to determine the effects of 15 years of selection and to find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole pedigree of 19,045 horses registered as CDE was used, comprising 47,884 animals (18,799 males and 29,085 females). An analysis performed to check for the pedigree completeness level yielded a number of equivalent complete generations (t) equal to 1.95, an average generation interval (GI) of 10.87 years, mean inbreeding coefficient (F) of 0.32%, an average relatedness coefficient (AR) of 0.09% and an effective population size (Ne) of 204. For the analyses, animals were divided into fourteen breed groups. Additionally, in order to study the evolution of these breeds over time and their influence on CDE pedigree, five different periods were considered according to the year of birth of the animals. Performance data used in the analyses were the estimated breeding values (EBV) of the Show Jumping sport discipline of 12,197 horses in the CDE pedigree, available from the 2020 routine genetic evaluations of the CDE breeding program (starting in 2004). Dressage and Eventing EBV values were also assessed. Results showed values of F higher than expected under random mating; this pointed to some degree of inbred matings. With regard to the evolution of breeding values, we found that, in general, EBVs of offspring were higher than the EBVs of parents. Notwithstanding, there is still a need for improvement in population management and the coordination of the breeders to get higher responses but controlling the loss of genetic diversity in the CDE 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.

Process of Introduction of Australian Braford Cattle to South America: Configuration of Population Structure and Genetic Diversity Evolution.

Simple SummaryThe Braford breed originated in the USA and Australia from a cross between the Brahman and Hereford breeds to obtain animals suitable for the subtropical climate and resistant to hoof diseases, eye cancer, and ectoparasites, mainly ticks. This resistance to ticks was what attracted the attention of South American breeders, who acquired animals from Australia. The first breeder to do so was Uruguay around 1970. From then on, the breed was distributed across Argentina, Paraguay, and Brazil. Each country has its own association of breeders, and each one keeps the herdbook of the breed where the animals are registered. Selective breeding was conducted, thereby shaping genetic diversity over the years. The analysis of the pedigree database allowed us to evaluate these changes and the evolution of diversity over time. The objective of the present work was to analyze the population structure of the Braford breed in four countries, the repercussions of founders and ancestors, and the parameters of genetic diversity to suggest effective strategies for Braford breeders.This study analyzes the evolution of the population structure and genetic diversity of Braford cattle in South America from 1949 to 2019 to suggest effective strategies for breeding in the future. The percentage of bulls historically increased. The average generational interval decreased to 11.78 years for the current population. Average inbreeding (F) and coancestry (C) are low and show a historically increasing trend (0.001% to 0.002%, respectively). The degree of nonrandom mating (α) increased from −0.0001 to 0.0001 denoting a change in the trend to mate similar individuals. The average relatedness coefficient (ΔR) increased in the current period from 0.002% to 0.004%. A single ancestor explained 4.55% to 7.22% of the population’s gene pool. While the effective population size based on the individual inbreeding rate (NeFi) was 462.963, when based on the individual coancestry rate (NeCi), it was 420.168. Genetic diversity loss is small and mainly ascribed to bottlenecks (0.12%) and to unequal contributions of the founders (0.02%). Even if adequate levels of diversity can be found, practices that consider the overuse of individual bulls (conditioned by nature or not), could lead to a long-term reduction in diversity. The present results permit tailoring genetic management strategies that are perfectly adapted to the needs that the population demands internationally.

Population structure of Marwari sheep through pedigree analysis

Marwari sheep breed is the main constituent of the migratory sheep flocks in the Rajasthan, India. The purpose of this research was to use pedigree data to evaluate population structure and genetic variability in a closed flock of Marwari sheep in Rajasthan, India. Pedigree information of 11,659 sheep lambed from 1981–2020 (39 years) in the closed flock of Marwari sheep reared at ICAR-CSWRI-ARC, Beechwal, Bikaner, Rajasthan, India were included in the analysis. Lambs born during 2017–2020 were considered as reference population. The mean of maximum generation (MG), complete generation (CG) and equivalent complete generation (EqG) was 9.12, 2.75 and 5.35, respectively. The completeness of pedigree was 92.70 % (1st generation), 83.03 % (2nd generation) and 73.79 % (3rd generation). Average inbreeding coefficient for animals in the whole and reference populations was 1.49 and 2.40 %, respectively. The average relationship coefficient for whole and reference population was 2.51 and 3.34 %, respectively. Mean generation interval (GI) were 3.5 and 3.3 years for whole and reference population. The realized effective population size was 87.17 for whole population. Effective numbers of founders (fe), ancestors (fa) and founder genome (fg) was 80, 46 and 16.76, respectively for reference population. The fe/fa ratio in the reference population was 1.74, indicating that bottlenecks had occurred. The genetic contribution of the 16 most powerful ancestors represented half of the genetic variability in the reference population. The findings showed that there were proofs of bottleneck and genetic drift however, there was also considerable genetic diversity present in the population. The continuous flow of genes has contributed to the maintenance of genetic variability in the closed flock reflecting that management was in right direction in the Marwari sheep nucleus flock.

Population structure and inbreeding effects on growth traits of Morada Nova sheep

Genealogical records of 6,631 animals were used to describe the population structure, evaluate the genetic variability, and estimate the effect of inbreeding on the growth traits of Morada Nova sheep. The depth of the whole population was shallow (t = 1.25), that the way we used a reference population (t = 2.99), formed by animals with both parents known and born in the last four year, to make the inferences. For this population, birth weight (BW, n = 220), weaning weight (WW, n = 157), and pre-weaning weight gain (WG, n = 155) were available. The effective numbers of founders (fe) and ancestors (fa) were 43 and 34, respectively; 12 ancestors were responsible for 50% of the genetic variability in this reference population. The effective sizes for maximum, complete, and equivalent generations were 113.63, 41.67, and 60.97, respectively. The effective size, average inbreeding (2.88%), average relatedness coefficient (1.24%), the fe⁄fa (1.26), beyond other results, indicate attention with the future of the breed, which is not comfortable in relation to inbreeding and variability. Inbreeding depression was observed only for BW, where for each one percent increase in the average of individual increase inbreeding there is an average decrease of 0.0751kg in birth weight.

Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis.

Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs.Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0< Fi ≤ 6.25, 6.25< Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs.Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD.Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.

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 inbreeding depression load for morphological traits and defects in the Pura Raza Espa\xf1ola horse

BackgroundInbreeding is caused by mating between related individuals and is associated with reduced fitness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological traits and two morphology defects in the Pura Raza Española (PRE) horse breed.ResultsThe regression coefficients that were calculated between trait performances and inbreeding coefficients demonstrated the existence of inbreeding depression. In total, 58,772,533 partial inbreeding coefficients (Fij) were estimated for the whole PRE population (328,706 horses). We selected the descendants of horses with a Fij ≥ 6.25% that contributed to at least four offspring and for which morphological traits were measured for the subsequent analysis of inbreeding depression load (639 horses). A pedigree was generated with the last five generations (5026 animals) used as the reference population (average inbreeding coefficient of 8.39% and average relatedness coefficient of 10.76%). Heritability estimates ranged from 0.08 (cresty neck) to 0.80 (height at withers), whereas inbreeding depression load ratios ranged from 0.01 (knock knee) to 0.40 (length of shoulder), for an inbreeding coefficient of 10%. Most of the correlations between additive and inbreeding depression load genetic values and correlations between inbreeding depression load genetic values for the different traits were positive or near 0.ConclusionsAlthough the average inbreeding depression loads presented negative values, a certain percentage of the animals showed neutral or even positive values. Thus, high levels of inbreeding do not always lead to a decrease in mean phenotypic value or an increase in morphological defects. Hence, individual inbreeding depression loads could be used as a tool to select the most appropriate breeding animals. The possibility of selecting horses that have a high genetic value and are more resistant to the deleterious effects of inbreeding should help improve selection outcomes.

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.

Analysis of the population structure of buffaloes in Brazil

The aim of this study was to evaluate the population structure of Brazilian buffaloes using of pedigree information. The pedigree used in the analyses included records of 16,915 animals. The population parameters were obtained through the ENDOG software. The estimates of mean of inbreeding (F) and average relatedness (AR) coefficients were 3.22% and 5.99%, respectively. The average generation interval was 6.39years. The effective number of founders and ancestors was 28 and 22, respectively. In this study, we concluded that the selection of individuals with lower AR is necessary to avoid an increase in matings between inbreeding individuals in this population, in order to obtain greater genetic gain by selection.

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.

Pedigree analysis of Santa Inês sheep and inbreeding effects on performance traits

Population parameters such as effective population size and coefficients of inbreeding are important information of a population but have rarely been studied in Santa Ines sheep. Therefore, this study aimed to estimate population parameters in a Santa Ines sheep flock and the inbreeding effect on performance traits. A dataset with 11,564 animals, born from 2003 to 2011, was recorded for weights at birth (BW1), 60 (BW60), 180 (BW180) and 270 (BW270) days of age, daily weight gain from birth to 60 d (DWG1), 60 to 180 d (DWG2), and 60 to 270 d (DWG3). Percentages of animals with known pedigrees decreased over generations, from 70 % in the first generation to less than 5 % in the third. The effective population size decreased from 665 in 2004 to 45 in 2010. The effective number founders and ancestors were 285 and 273, respectively. Furthermore, the average relatedness coefficient was 0.47 %. The highest frequency of inbred animals was concentrated between 0 and 10 % of the inbreeding coefficient and only 263 animals showed F>10 %. The inbreeding coefficient had its lowest value in 2004 (0.19 %) and a highest value in 2008 (2.86 %). Significant inbreeding effect was found for BW1 (0.0054 ± 0.0015), DWG2 (-0.9837 ± 0.3025), and DWG3 (-0.5628 ± 0.2377), while the analysis of breeding values indicated significant inbreeding depression for all traits, except DWG1. Results suggested that inbreeding had a negative effect on growth traits. To avoid losses in these traits it is necessary to mate non-related sires and dams.

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.