GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach

Pedigree analysis of Korean native chickens: unraveling inbreeding and genetic diversity

This study assessed the trends in inbreeding, effective population size, and genetic diversity across six Korean native chicken lines using pedigree records from 54,383 chickens. Understanding these genetic parameters is significantly important for maintaining healthy and viable chicken populations. The primary objective was to analyze the pedigree data to assess the levels of inbreeding and genetic diversity and to evaluate the effective population size across the different lines. Pedigree analysis revealed that pedigree completeness peaked in the first generation and declined in subsequent generations for all lines. Line A exhibited a mean inbreeding coefficient of 0.0201, whereas the other lines displayed lower mean values ranging from 0.0009 to 0.0098, indicating that inbreeding levels were within an acceptable range and considered safe from extinction. Average relatedness consistently increased with time. Individual increases in inbreeding were the highest in Line A (0.62%), with smaller increases in the other lines ranging from 0.02 to 0.23%. Effective population sizes varied from 81 to 2500, with average coancestry within parental populations ranging from 0.0032 to 0.0290. The fe/fa ratio between 1.00 and 1.69 in the 6 lines suggested a moderate impact during bottleneck events, with subsequent populations recovering well. The genetic diversity loss due to genetic drift and unequal founder contributions ranged from 0.66-3.15%, indicating that considerable genetic variability remains within the populations. The results of this study have practical applications in the management and conservation of genetic resources in poultry breeding programs. By highlighting the importance of monitoring inbreeding and maintaining genetic diversity, the findings can help develop strategies to ensure the long-term sustainability of these chicken lines. This study provides valuable insights into the genetic management of Korean native chicken lines, emphasizing the need for strategic breeding practices to preserve genetic health and diversity.

Ballou's Ancestral Inbreeding Coefficient: Formulation and New Estimate with Higher Reliability

Inbreeding is unavoidable in small populations. However, the deleterious effects of inbreeding on fitness-related traits (inbreeding depression) may not be an inevitable phenomenon, since deleterious recessive alleles causing inbreeding depression might be purged from populations through inbreeding and selection. Inbreeding purging has been of great interest in conservation biology and animal breeding, because populations manifesting lower inbreeding depression could be created even with a small number of breeding animals, if inbreeding purging exists. To date, many studies intending to detect inbreeding purging in captive and domesticated animal populations have been carried out using pedigree analysis. Ballou's ancestral inbreeding coefficient (FBAL-ANC) is one of the most widely used measurements to detect inbreeding purging, but the theoretical basis for FBAL-ANC has not been fully established. In most of the published works, estimates from stochastic simulation (gene-dropping simulation) have been used. In this report, the author provides a mathematical basis for FBAL-ANC and proposes a new estimate by hybridizing stochastic and deterministic computation processes. A stochastic simulation suggests that the proposed method could considerably reduce the variance of estimates, compared to ordinary gene-dropping simulation, in which whole gene transmissions in a pedigree are stochastically determined. The favorable property of the proposed method results from the bypass of a part of the stochastic process in the ordinary gene-dropping simulation. Using the proposed method, the reliability of the estimates of FBAL-ANC could be remarkably enhanced. The relationship between FBAL-ANC and other pedigree-based parameters is also discussed.

Characterizing and Eliminating the Inbreeding Load

The authors evaluated the relevant literature related to purging, which is the interaction between selection and inbreeding in which the population may eliminate its inbreeding load at least partially. According to the relevant literature, the inbreeding load and the process of purging were evaluated via pedigree methods based on ancestral inbreeding, the inbreeding-purging model, and expressed opportunity of purging, along with genomic methods. Most ancestral inbreeding-related studies were performed in zoos, where only a small proportion of the studied populations show signs of purging. The inbreeding-purging model was developed with Drosophila, and it was used to evaluate different zoo ungulates and Pannon white rabbits. Purging was detected in both studies. The expressed opportunity of purging was applied in Jersey cattle and Pannon white rabbits. In the Jersey cattle, it had an effect of 12.6% for fitness, while in the Pannon white rabbits, the inbreeding load was between 40% and 80% of its original value. The genomic studies also signalled purging, but they also made it clear that, contrary to the detected purging, the evaluated populations still suffered from inbreeding depression. Therefore, especially for domesticated animals, it can be concluded that deliberate inbreeding with the purpose of generating purging is not advocated.

Inbreeding Depression and Purging for Meat Performance Traits in German Sheep Breeds

This study provides estimates on genetic parameters, inbreeding depression and purging for meat performance measures from 25 German sheep breeds. All German meat, merino sheep breeds and breeds of other breeding directions with a sufficient number of pedigree and performance data were included in this study. Phenotypic traits retrieved from the national database OviCap were evaluated: daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness. We employed animal models to estimate heritability, variance and covariance components for these meat performance traits as well as inbreeding depression and purging. The heritabilities, on average, reached estimates of 0.55, 0.34, 0.53 and 0.61 for daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness, respectively. We estimated the linear regression slopes for the individual rate of inbreeding, new and ancestral inbreeding, as well as the inbreeding coefficient and its interaction with the inbreeding coefficient of Ballou, employing animal models with non-genetic effects and the additive genetic effect of the animal. Across all breeds, inbreeding was only significant for daily weight gain, whereas for all other traits, estimates were not significant. Within sheep breeds, we found significant inbreeding depression for daily weight gain in German Mutton Merino and German Blackheaded Mutton as well as for the meatiness score in German Whiteheaded Mutton. Significant effects for purging, based on ancestral inbreeding and the interaction effect of the classical inbreeding coefficient with the inbreeding coefficient of Ballou, were not obvious either across or within any sheep breed. A 1% increase in inbreeding significantly decreased the phenotypic trait median of daily weight gain across all sheep breeds by 0.50% and 0.70% of phenotypic and genetic standard deviation, respectively. Purging effects due to ancestral inbreeding were not significant in any breed or across breeds. The results of this study may indicate that inbreeding depression may be more harmful in traits under stronger selection than in traits that exert low selection pressure. The results of this study demonstrate the different effects that result in meat performance traits due to inbreeding. With increasing rates of inbreeding and critical effective population sizes, selection intensity for breeding objectives has to be critically reviewed for each sheep breed. Inbreeding depression and purging should be evaluated in order to prevent a decrease in trait means due to inbreeding and to determine whether detrimental alleles are eliminated.

Inbreeding depression and its effect on sperm quality traits in Pietrain pigs

In most cases, inbreeding is expected to have unfavourable effects on traits in livestock. The consequences of inbreeding depression could be substantial, primarily in reproductive and sperm quality traits, and thus lead to decreased fertility. Therefore, the objectives of this study were (i) to compute inbreeding coefficients using pedigree (FPED ) and genomic data based on runs of homozygosity (ROH) in the genome (FROH ) of Austrian Pietrain pigs, and (ii) to assess inbreeding depression on four sperm quality traits. In total, 74,734 ejaculate records from 1034 Pietrain boars were used for inbreeding depression analyses. Traits were regressed on inbreeding coefficients using repeatability animal models. Pedigree-based inbreeding coefficients were lower than ROH-based inbreeding values. The correlations between pedigree and ROH-based inbreeding coefficients ranged from 0.186 to 0.357. Pedigree-based inbreeding affected only sperm motility while ROH-based inbreeding affected semen volume, number of spermatozoa, and motility. For example, a 1% increase in pedigree inbreeding considering 10 ancestor generations (FPED10 ) was significantly (p < 0.05) associated with a 0.231% decrease in sperm motility. Almost all estimated effects of inbreeding on the traits studied were unfavourable. It is advisable to properly manage the level of inbreeding to avoid high inbreeding depression in the future. Further, analysis of effects of inbreeding depression for other traits, including growth and litter size for the Austrian Pietrain population is strongly advised.

Impact of Inbreeding and Ancestral Inbreeding on Longevity Traits in German Brown Cows

A recent study on the population structure of the German Brown population found increasing levels of classical and ancestral inbreeding coefficients. Thus, the aim of this study was to determine the effects of inbreeding depression and purging on longevity traits using classical and ancestral inbreeding coefficients according to Kalinowski (2002) (Fa_Kal, FNew), Ballou (1997) (Fa_Bal), and Baumung (2015) (Ahc). For this purpose, uncensored data of 480,440 cows born between 1990 and 2001 were available. We analyzed 17 longevity traits, including herd life, length of productive life, number of calvings, lifetime and effective lifetime production for milk, fat, and protein yield, the survival to the 2nd, 4th, 6th, 8th, and 10th lactation number, and the culling frequencies due to infertility, or udder and foot and leg problems. Inbreeding depression was significant and negative for all traits but for culling due to udder and to foot and leg problems. When expressed in percentages of genetic standard deviations, inbreeding depression per 1% increase in inbreeding was -3.61 to -10.98%, -2.42 to -2.99%, -2.21 to -4.58%, and 5.13% for lifetime production traits, lifetime traits, survival rates, and culling due to infertility, respectively. Heterosis and recombination effects due to US Brown Swiss genes were positive and counteracted inbreeding depression. The effects of FNew were not significantly different from zero, while Fa_Kal had negative effects on lifetime and lifetime production traits. Similarly, the interaction of F with Fa_Bal was significantly negative. Thus, purging effects could not be shown for longevity traits in German Brown. A possible explanation may be seen in the breed history of the German Brown, that through the introgression of US Brown Swiss bulls ancestral inbreeding increased and longevity decreased. Our results show, that reducing a further increase in inbreeding in mating plans is advisable to prevent a further decline in longevity due to inbreeding depression, as purging effects were very unlikely in this population.

Genetic Diversity and Trends of Ancestral and New Inbreeding in German Sheep Breeds by Pedigree Data

In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of rams may risk losing genetic diversity and increasing rates of inbreeding. On the other hand, breeds with a low number of founder animals and only regional popularity may not leave their endangered status, as the number of breeders interested in the breed is limited. The objective of the present study was to determine demographic measures of genetic diversity and recent as well as ancestral trends of inbreeding in all autochthonous German sheep breeds and sheep of all breeding directions, including wool, meat, and milk. We used pedigree data from 1,435,562 sheep of 35 different breeds and a reference population of 981,093 sheep, born from 2010 to 2020. The mean number of equivalent generations, founders, effective founders, effective ancestors, and effective founder genomes were 5.77, 1669, 123.2, 63.5, and 33.0, respectively. Genetic drift accounted for 69% of the loss of genetic diversity, while loss due to unequal founder contributions was 31%. The mean inbreeding coefficient, individual rate of inbreeding (∆F_i), and realized effective population size across breeds were 0.031, 0.0074, and 91.4, respectively, with a significantly decreasing trend in ∆F_i in 11/35 breeds. New inbreeding, according to Kalinowski, contributed to 71.8% of individual inbreeding, but ancestral inbreeding coefficients showed an increasing trend in all breeds. In conclusion, in our study, all but one of the mountain-stone sheep breeds and the country sheep breed Wald were the most vulnerable populations, with N_e < 50. The next most endangered breeds are exotic, country, and heath breeds, with average N_e of 66, 83, and 89, respectively. The wool, meat, and milk breeds showed the highest genetic diversity, with average N_e of 158, 120, and 111, respectively. The results of our study should help strengthen conservation program efforts for the most endangered sheep breeds and maintain a high genetic diversity in all sheep breeds.

The effect of new and ancestral inbreeding on milk production traits in Iranian Holstein cattle

Inbreeding depression, the reduction of fitness and performance, is due to an increase in the mating of related individuals. Based on the purge hypothesis, inbreeding and breeding over generations reduce the effect of deleterious alleles responsible for inbreeding depression. Thus, recent inbreeding is assumed to be more harmful than ancestral inbreeding. This study aimed at evaluating the effects of new and ancestral inbreeding on milk, fat and protein production in Iranian Holstein cattle. The secondary objective was to examine the changes in predicted breeding values when the inbreeding effect was included in the model's analysis. To this end, inbreeding coefficients were calculated using the pedigree of 2,394,517 Holstein cattle to achieve these goals. In addition, 419,132 records of milk, fat and protein yields of first parity cows were collected to assess inbreeding depression and breeding values. The average inbreeding coefficients were 0.83% and 1.68% for the whole population and the inbred animals, respectively. A 1% increase in classical pedigree-based inbreeding coefficient was associated with a decrease of 11.99 kg in milk, 0.39 kg in fat and 0.29 kg in protein. The effect of ancestral inbreeding was more detrimental to performance traits than the effect of new inbreeding. This result contradicted the hypothesis of purging. By including the inbreeding coefficient in the model, the rank of animals remained unchanged, but the average predicted breeding values increased. In general, inbreeding depression was observed in Iranian Holstein cows; however, no evidence of purging was observed. The average of inbreeding coefficients was not high in this population, although accounting for inbreeding coefficients in the analytical model did significantly increase the predicted breeding values. It is recommended that the analytical model incorporate the inbreeding coefficient to improve the accuracy of genetic evaluation. In future studies, inbreeding depression should be assessed using genomic data for performance and reproduction traits.

Inbreeding depression on growth and prolificacy traits in two lines of rabbit

Inbreeding depression in closed populations impairs animal fitness, health, and productivity. However, not all inbreeding is expected to be equally damaging. Recent inbreeding is thought to be more harmful than ancient inbreeding because selection decreases the frequency of unfavourable alleles with time. Accordingly, selection efficiency is improved by inbreeding in a process called purging. This research aimed to quantify inbreeding depression on growth and prolificacy traits in two lines of rabbits selected for just one growth (Caldes line) or prolificacy (Prat line) trait, and also to find some evidence of purging of deleterious alleles by selection. Caldes line comprised 51 generations and 124,371 animals in the pedigree. Prat line comprised 34 generations and 161,039 animals in the pedigree. The effects of old, intermediate, and new inbreeding (Fold, Fint, and Fnew), as well as total cumulated classical inbreeding (F) and 3 measurements of ancestral inbreeding (AHC, Fa.K, and Fa.B) were estimated for average daily gain (ADG), slaughter weight (SW), weaning weight (WW), born alive (BA), the total number of kits (NT), and the number of weaned kits (NW). There was a clear inbreeding depression for all growth and prolificacy traits in the Caldes line (-7.19 g/d, -0.45 kg, -0.25 kg, -6 kits, -4 kits, and -4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively) and also in Prat line (-7.48 g/d, -0.31 kg, -0.11 kg, -4 kits, -5 kits, and -4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively). The inbreeding partition appears to be a reliable alternative for assessing inbreeding depression and purging. Thus, for example, in the Caldes line and for ADG the regression coefficients were -7.61, -5.41, and 7.76 g/d per unit of increase in Fnew, Fint, and Fold, respectively. In addition, AHC and Fa.B may provide more accurate evidence of purging than Fa.K. This study confirms the existence of inbreeding depression for growth and prolificacy traits in both lines of rabbits and shows evidence of purging of deleterious recessive alleles involved both in growth and prolificacy, independently of the selection criteria established in the line.

Genealogical analysis of European bison population revealed a growing up population despite very low genetic diversity

In 1919, the European bison population became extinct in the wild. The rescue of the lowland subspecies and the whole species was achieved mainly thanks to individuals from the Białowieża Forest (Polish-Belarusian border). There are currently two breeding lines—the lowland (purebred B. b. Bonasus) founded by 7 individuals and the lowland-Caucasian (hybrids of B. b. Bonasus and B. b. caucasicus) founded by 12 individuals. This genealogical study was conducted on 15,071 individuals recorded in the pedigree book between 1881 and 2020. Its objective was to determine the level of genetic variability and inbreeding almost 100 years after the rescue measures were initiated. The completeness of the pedigree of the reference population was 77% in the fifth generation backwards. A maximum of 23 generations can be traced back in the pedigree. The average inbreeding coefficient and the mean average relatedness of the reference population were very high, about 17% and 16% respectively. No significant amount of new inbreeding was discovered. The reference population has lost 9.11% of the total genetic diversity compared to the population of founders. A male of the Caucasian subspecies Kaukasus was discovered among the ancestors of the lowland lineage reference population. The effective population size calculated based on the increase in inbreeding was 23.93 individuals, based on complete generations equivalent it was 16.1 individuals. Wright’s F-statistics showed very small differences in genotypic frequencies between individuals within the two lineages in the reference population (FIS = 0.10), between individuals and the total population (FIT = 0.04) and low differentiation between lineages (FST = 0.06). The population of the European bison from the Białowieża Forest is generally very uniform but still shows good fitness.

Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse

BACKGROUND

Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -F_HOM-, the diagonal elements of the genomic -F_G-, and hybrid matrixes -F_H-) and ROH measures (F_RZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.

RESULTS

The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (F_RZ for three generations, F_H and F_HOM) to 0.11 (F_RZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with F_HOM) and 0.79 (F with F_RZ). In addition, the correlations between F_RZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated.

CONCLUSIONS

Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.

Inbreeding and pedigree analysis of the European red dairy cattle

BACKGROUND

Red dairy cattle breeds have an important role in the European dairy sector because of their functional characteristics and good health. Extensive pedigree information is available for these breeds and provides a unique opportunity to examine their population structure, such as effective population size, depth of the pedigree, and effective number of founders and ancestors, and inbreeding levels. Animals with the highest genetic contributions were identified. Pedigree data included 9,073,403 animals that were born between 1900 and 2019 from Denmark, Finland, Germany, Latvia, Lithuania, the Netherlands, Norway, Poland, and Sweden, and covered 32 breeds. The numerically largest breeds were Red Dairy Cattle and Meuse-Rhine-Yssel.

RESULTS

The deepest average complete generation equivalent (9.39) was found for Red Dairy Cattle in 2017. Mean pedigree completeness ranged from 0.6 for Finncattle to 7.51 for Red Dairy Cattle. An effective population size of 166 animals was estimated for the total pedigree and ranged from 35 (Rotes Höhenvieh) to 226 (Red Dairy Cattle). Average generation intervals were between 5 and 7 years. The mean inbreeding coefficient for animals born between 1960 and 2018 was 1.5%, with the highest inbreeding coefficients observed for Traditional Angler (4.2%) and Rotes Höhenvieh (4.1%). The most influential animal was a Dutch Meuse-Rhine-Yssel bull born in 1960. The mean inbreeding level for animals born between 2016 and 2018 was 2% and highest for the Meuse-Rhine-Yssel (4.64%) and Rotes Hohenvieh breeds (3.80%).

CONCLUSIONS

We provide the first detailed analysis of the genetic diversity and inbreeding levels of the European red dairy cattle breeds. Rotes Höhenvieh and Traditional Angler have high inbreeding levels and are either close to or below the minimal recommended effective population size, thus it is necessary to implement tools to monitor the selection process in order to control inbreeding in these breeds. Red Dairy Cattle, Vorderwälder, Swedish Polled and Hinterwälder hold more genetic diversity. Regarding the Meuse-Rhine-Yssel breed, given its decreased population size, increased inbreeding and low effective population size, we recommend implementation of a breeding program to prevent further loss in its genetic diversity.

Pedigree-Based Description of Three Traditional Hungarian Horse Breeds

Simple Summary

The most important purpose of animal conservation programs is to maintain genetic variability. The Furioso-North Star, the Gidran, and the Nonius are indigenous Hungarian horse breeds from the Mezőhegyes Stud. In the last century, the role of the horses was changed, the technical innovations and motorization replaced them, so the population size and the genetic variability of these breeds were reduced. Nowadays these breeds are endangered. The aims of this study were to give information about the current breeding population and support breeder associations during their gene conservation work. The pedigree quality, generation intervals, probability of gene origin, and inbreeding were evaluated. We found that breeds had a large bottleneck effect during breeding history. The level of inbreeding was measured with different methods, such as Ballou’s, Wright’s, and Kalinowski’s coefficient. Most of the current inbreeding coefficient was the result of previously fixed alleles for each breed. Effective population size was also estimated, and the status of the breeds was found to be not critical according to FAO criteria.

Abstract

The Mezőhegyes Stud was founded in 1784 where three different horse breeds were developed: the Furioso-North Star, the Gidran, and the Nonius. These breeds were based on the same mare population, but each breed had different utilization purposes. Our aim was to analyze the pedigree information of these three indigenous breeds. The genealogical information was traced back from the actual breeding population back to the founder animals, and the final database contained more than 47,000 horses. The reference populations were defined as the registered breeding animals in 2019. The complete generation equivalent was 16.45 for the Gidran breed, 15.18 for Furioso-North Star, and 12.64 for Nonius, respectively. Due to the utilization of English Thoroughbred during the breeding history, the average maximum generations were close to 36 generations for each breed. The average relatedness was approximately 4%. The average Wright’s inbreeding coefficient was the highest for the Nonius breed (5.59%). Kalinowski’s decomposition of inbreeding showed that inbreeding is originated mainly from the past; the current fixation of alleles was higher for the Nonius horse breed. There was a reasonable bottleneck effect for each breed. The estimated effective population sizes suggest that there is no problem with the maintaining of Mezőhegyes horse breeds.

Genetic Diversity and Trends of Ancestral and New Inbreeding in Deutsch Drahthaar Assessed by Pedigree Data

Simple Summary

Deutsch Drahthaar (DD) is the most popular hunting dog in Germany, fulfilling all aspects of hunting including searching for trails. This breed was newly created at the beginning of the 20th century from a large number existing versatile hunting dog breeds. The aim of the breed was, and still is, to achieve the best performance in all aspects of hunting. We analyzed pedigrees of DD using demographic measures to quantify genetic diversity such as probabilities of gene origin and degrees of ancestral and individual inbreeding. A large number of genetically diverse founder dogs should open up the opportunity of creating a breed with a high genetic diversity and a low increase of inbreeding per generation. On the other hand, intense use of top sires and dams from a limited number of breeding lines may accelerate breeding progress in hunting abilities but reduce genetic diversity. Monitoring genetic diversity should help to maintain a high diversity of breeding populations. Our analysis of pedigree data from 101,887 DD dogs revealed inbreeding measures (coefficient of inbreeding F = 0.042, individual rate of inbreeding ΔF_i = 0.00551) and effective population size (Ne = 92) in the mean range compared to a wide range of other dog breeds. Ancestral inbreeding had a strong increasing trend, whereas trends in individual inbreeding and rate of individual inbreeding were slightly negative.

Abstract

Loss of genetic diversity and high inbreeding rates confer an increased risk of congenital anomalies and diseases and thus impacting dog breeding. In this study, we analyzed recent and ancestral inbreeding as well as other measures of genetic variability in the Deutsch Drahthaar (DD) dog population. Analyses included pedigree data from 101,887 animals and a reference population with 65,927 dogs born between 2000 and 2020. The mean equivalent complete generations was 8.6 with 69% known ancestors in generation 8. The mean realized effective population size was 92 with an increasing trend from 83 to 108 over birth years. The numbers of founders, effective founders and effective ancestors, as well as founder genomes, were 814, 66, 38 and 16.15, respectively. Thirteen ancestors explained 50% of the genetic diversity. The mean coefficient of inbreeding and individual rate of inbreeding (ΔF_i) were 0.042 and 0.00551, respectively, with a slightly decreasing trend in ΔF_i. Exposure of ancestors to identical-by-descent alleles explored through ancestral coefficients of inbreeding showed a strong increasing trend. Comparisons between new and ancestral inbreeding coefficients according to Kalinowski et al. showed an average relative contribution of 62% of new inbreeding to individual inbreeding. Comparisons among average coancestry within the parental population and average inbreeding in the reference population were not indicative of genetic substructures. In conclusion, the creation of the DD dog breed about 120 years ago resulted in a popular breed with considerable genetic diversity without substructuring into lines or subpopulations. The trend of new inbreeding was declining, while ancestral inbreeding through ancestors who were autozygous at least once in previous generations was increasing.

Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region

Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (F_PED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.

purgeR: inbreeding and purging in pedigreed populations

SUMMARY

Inbreeding depression and genetic purging are important processes shaping the survivability and evolution of small populations. However, detecting purging is challenging in practice, in part because there are limited tools dedicated to it. I present a new R package to assist population analyses on detection and quantification of the inbreeding depression and genetic purging of biological fitness in pedigreed populations. It includes a collection of methods to estimate different measurements of inbreeding (Wright's, partial and ancestral inbreeding coefficients) as well as purging parameters (purged inbreeding, and opportunity of purging coefficients). Additional functions are also included to estimate population parameters, allowing to contextualize inbreeding and purging these results in terms of the population demographic history. purgeR is a valuable tool to gain insight into processes related to inbreeding and purging, and to better understand fitness and inbreeding load evolution in small populations.

AVAILABILITY AND IMPLEMENTATION

purgeR is an R package available at CRAN, and can be installed via install.packages("purgeR"). Source code is maintained at a GitLab repository (https://gitlab.com/elcortegano/purgeR).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse

Inbreeding depression is the reduction of performance caused by mating of close relatives. In livestock populations, inbreeding depression has been traditionally estimated by regression of phenotypes on pedigree inbreeding coefficients. This estimation can be improved by utilising genomic inbreeding coefficients. Here we estimate inbreeding depression for insect bite hypersensitivity (IBH) prevalence, the most common allergic horse disease worldwide, in Old Kladruber horse. In a deep pedigree with 3214 horses (187 genotyped), we used a generalised linear mixed model with IBH phenotype from 558 horses examined between 1996 and 2009 (1368 records). In addition to the classical pedigree information, we used the single-step approach that enabled joint use of pedigree and genomic information to estimate inbreeding depression overall genome and equine leucocyte antigen (ELA) class II region. Significant inbreeding depression was observed in all models fitting overall inbreeding coefficients (odds ratio between 1.018 and 1.074, P < 0.05) with the exception of Kalinowski's new inbreeding (P = 0.0516). The increase of ELA class II inbreeding was significantly associated with increased prevalence of IBH (odds ratio 1.018; P = 0.027). However, when fitted jointly with the overall inbreeding coefficient, the effect of ELA class II inbreeding was not significant (odds ratio 1.016; P = 0.062). Overall, the higher ELA class II and/or overall inbreeding (pedigree or genomic) was associated with increased prevalence of IBH in Old Kladruber horses. The single-step approach provides an efficient use of all the available pedigree, genomic, and phenotype information for estimation of overall and regional inbreeding effects.

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

Simple Summary

The main aim of modern breeding programs in dairy cows is to improve productivity, functional and health traits. The use of only a few top sires leads to more efficient milk production, but also it could lead to a decline in the gene pool, smaller effective population size and an increase of inbreeding. Deleterious effects of inbreeding in dairy cattle may reduce the benefits of the genetic gains. Due to this fact, it is important to monitor the genetic diversity in dairy cattle breeds. In this study, pedigree data were used to show the losses of genetic variability and its association with the heavy use of imported US Brown Swiss bulls and semen in the German Brown population. Strategies to decrease rate of inbreeding through sires with less relationships to the most important ancestors should be considered in future breeding strategies.

Abstract

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

Assessment of between-founder heterogeneity in inbreeding depression for reproductive traits in Baluchi sheep

Magnitude of inbreeding depression could be different among descendants of various founder animals, when recessive genetic composition of a population is unevenly distributed among founder animal genomes. Reproductive records of Baluchi sheep for the litter variables size at birth (LSB), size at weaning (LSW), mean weight/lamb born (LMWLB), mean weight/lamb weaned (LMWLW), total weight at birth/ewe lambing (TLWB) and total weight at weaning/ewe lambing (TLWW) were used to examine heterogeneity in inbreeding depression between founder animals. Pedigree-based inbreeding coefficients were proportioned into components coming from founder animals and Mendellian contribution from non-founder animals. Two approaches were used to assess effects of inbreeding: overall inbreeding coefficients or partial inbreeding of the four main founder animals as possible covariates included in statistical models. Among the traits evaluated, there were effects on LMWLB, LMWLW and TLWW of inbreeding with there being a -8, -48, and -95 g decrease per 1% increase in inbreeding, respectively. Linear regressions of traits on partial inbreeding coefficients due to founder animals were of different magnitudes and ranged between -0.12 and +0.128. Heterogeneous contribution of founder animals to inbreeding depression occurred for LSB, LMWLB, and TLWW. These results indicate there was uneven distribution of recessive genetic composition among genomes of founder animals or differences in selection pressures on unfavorable alleles between different founder lines. The observed variation in founder-specific inbreeding depression indicates a small number of alleles with major effects are contributing to inbreeding depression.

Effect of recent and ancient inbreeding on production and fertility traits in Canadian Holsteins

BACKGROUND

Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, but rather could be distinctly associated with more recent or more ancient inbreeding. Therefore, splitting inbreeding into different age classes could help in assessing detrimental effects of different ages of inbreeding. Hence, this study sought to investigate the effect of recent and ancient inbreeding on production and fertility traits in Canadian Holstein cattle with both pedigree and genomic records. Furthermore, inbreeding coefficients were estimated using traditional pedigree measure (F_PED) and genomic measures using segment based (F_ROH) and marker-by-marker (F_GRM) based approaches.

RESULTS

Inbreeding depression was found for all production and most fertility traits, for example, every 1% increase in F_PED, F_ROH and F_GRM was observed to cause a - 44.71, - 40.48 and - 48.72 kg reduction in 305-day milk yield (MY), respectively. Similarly, an extension in first service to conception (FSTC) of 0.29, 0.24 and 0.31 day in heifers was found for every 1% increase in F_PED, F_ROH and F_GRM, respectively. Fertility traits that did not show significant depression were observed to move in an unfavorable direction over time. Splitting both pedigree and genomic inbreeding into age classes resulted in recent age classes showing more detrimental inbreeding effects, while more distant age classes caused more favorable effects. For example, a - 1.56 kg loss in 305-day protein yield (PY) was observed for every 1% increase in the most recent pedigree age class, whereas a 1.33 kg gain was found per 1% increase in the most distant pedigree age class.

CONCLUSIONS

Inbreeding depression was observed for production and fertility traits. In general, recent inbreeding had unfavorable effects, while ancestral inbreeding had favorable effects. Given that more negative effects were estimated from recent inbreeding when compared to ancient inbreeding suggests that recent inbreeding should be the primary focus of selection programs. Also, further work to identify specific recent homozygous regions negatively associated with phenotypic traits could be investigated.

Networks of inbreeding coefficients in a selected population of rabbits

The correlation between pedigree and genomic-based inbreeding coefficients is usually discussed in the literature. However, some of these correlations could be spurious. Using partial correlations and information theory, it is possible to distinguish a significant association between two variables which is independent from associations with a third variable. The objective of this study is to implement partial correlations and information theory to assess the relationship between different inbreeding coefficients using a selected population of rabbits. Data from pedigree and genomic information from a 200K SNP chip were available. After applying filtering criteria, the data set comprised 437 animals genotyped for 114,604 autosomal SNP. Fifteen pedigree- and genome-based inbreeding coefficients were estimated and used to build a network. Recent inbreeding coefficient based on runs of homozygosity had 9 edges linking it with different inbreeding coefficients. Partial correlations and information theory approach allowed to infer meaningful associations between inbreeding coefficients and highlighted the importance of the recent inbreeding based on runs of homozygosity, but a good proxy of it could be those pedigree-based definitions reflecting recent inbreeding.

Historical Changes and Description of the Current Hungarian Hucul Horse Population

Simple Summary

Originally, the Hucul horse breed was bred in the northeastern parts of the forested Carpathians. Only a few animals survived the Second World War and the regeneration of the breed started in those times. The aim of the current work was to give an overview of this rescue work from gene conservation point of view with the evaluation of the population changes within this few decades-long time interval. The pedigree quality, gene origin, inbreeding and status of stallion lines and mare families were evaluated. The main finding of the study was that inbreeding in the recent years was successfully limited and current inbreeding levels are the reason of previous gene fixations. Due to the increased number of mare families, genetic variability also increased. However, the proper management of the stallion utilization is important to prevent the future increasing of the inbreeding level of the Hucul breed.

Abstract

Gene conservation and management of small populations requires proper knowledge of the background and history of the breed. The aim of the study was the evaluation of population structure and changes of the Hungarian Hucul horse population. Population changes were described for the actual breeding stock as well as for groups of 10-year epochs reflecting major periods of change in the breed. Pedigree data of the registered population were analyzed using Endog and GRain software. The average value of equivalent complete generations was above nine for the actual breeding population. The longest generation interval was the sire-to-daughter pathway. The f_e/f ratio had smaller changes than f_a/f_e ratio across the population history. Inbreeding and average relatedness as well as ancestral coefficients had increased during history. Kalinowski’s decomposition of inbreeding showed that present inbreeding is smaller than it was done earlier during the last 20 years. Due to the continuous imports from other breeder countries, the genetic variability increased during the evaluated time periods.

Inbreeding depression for kit survival at birth in a rabbit population under long-term selection

Background

Accumulation of detrimental mutations in small populations leads to inbreeding depression of fitness traits and a higher frequency of genetic defects, thus increasing risk of extinction. Our objective was to quantify the magnitude of inbreeding depression for survival at birth, in a closed rabbit population under long-term selection.

Methods

We used an information theory-based approach and multi-model inference to estimate inbreeding depression and its purging with respect to the trait ‘kit survival at birth’ over a 25-year period in a closed population of Pannon White rabbits, by analysing 22,718 kindling records. Generalised linear mixed models based on the logit link function were applied, which take polygenic random effects into account.

Results

Our results indicated that inbreeding depression occurred during the period 1992–1997, based on significant estimates of the z-standardised classical inbreeding coefficient z.F_L (CI_95% − 0.12 to − 0.03) and of the new inbreeding coefficient of the litter z.F_NEWL (CI_95% − 0.13 to − 0.04) as well as a 59.2% reduction in contributing founders. Inbreeding depression disappeared during the periods 1997–2007 and 2007–2017. For the period 1992–1997, the best model resulted in a significantly negative standardised estimate of the new inbreeding coefficient of the litter and a significantly positive standardised estimate of Kalinowski’s ancestral inbreeding coefficient of the litter (CI_95% 0.01 to 0.17), which indicated purging of detrimental load. Kindling season and parity had effects on survival at birth that differed across the three periods of 1992–1997, 1997–2007 and 2007–2017.

Conclusions

Our results support the existence of inbreeding depression and its purging with respect to kit survival at birth in this Pannon White rabbit population. However, we were unable to exclude possible confounding from the effects of parity and potentially other environmental factors during the study period, thus our results need to be extended and confirmed in other populations.

Revised Calculation of Kalinowski’s Ancestral and New Inbreeding Coefficients

To test for the presence of purging in populations, the classical pedigree-based inbreeding coefficient (F) can be decomposed into Kalinowski’s ancestral (FANC) and new (FNEW) inbreeding coefficients. The FANC and FNEW can be calculated by a stochastic approach known as gene dropping. However, the only publicly available algorithm for the calculation of FANC and FNEW, implemented in GRain v 2.1 (and also incorporated in the PEDIG software package), has produced biased estimates. The FANC was systematically underestimated and consequently, FNEW was overestimated. To illustrate this bias, we calculated FANC and FNEW by hand for simple example pedigrees. We revised the GRain program so that it now provides unbiased estimates. Correlations between the biased and unbiased estimates of FANC and FNEW, obtained for example data sets of Hungarian Pannon White rabbits (22,781 individuals) and Dutch Holstein Friesian cattle (37,061 individuals), were high, i.e., >0.96. Although the magnitude of bias appeared to be small, results from studies based on biased estimates should be interpreted with caution. The revised GRain program (v 2.2) is now available online and can be used to calculate unbiased estimates of FANC and FNEW.

Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle

Background

Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Recent inbreeding is expected to be more harmful than ancient inbreeding, because selection decreases the frequency of deleterious alleles over time. Selection efficiency is increased by inbreeding, a process called purging. Our objective was to investigate effects of recent and ancient inbreeding on yield, fertility and udder health traits in Dutch Holstein–Friesian cows.

Methods

In total, 38,792 first-parity cows were included. Pedigree inbreeding (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{PED}$$\end{document}FPED) was computed and 75 k genotype data were used to compute genomic inbreeding, among others based on regions of homozygosity (ROH) in the genome (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{ROH}$$\end{document}FROH).

Results

Inbreeding depression was observed, e.g. a 1% increase in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{ROH}$$\end{document}FROH was associated with a 36.3 kg (SE = 2.4) decrease in 305-day milk yield, a 0.48 day (SE = 0.15) increase in calving interval and a 0.86 unit (SE = 0.28) increase in somatic cell score for day 150 through to 400. These effects equalled − 0.45, 0.12 and 0.05% of the trait means, respectively. When \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{PED}$$\end{document}FPED was split into generation-based components, inbreeding on recent generations was more harmful than inbreeding on more distant generations for yield traits. When \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{PED}$$\end{document}FPED was split into new and ancestral components, based on whether alleles were identical-by-descent for the first time or not, new inbreeding was more harmful than ancestral inbreeding, especially for yield traits. For example, a 1% increase in new inbreeding was associated with a 2.42 kg (SE = 0.41) decrease in 305-day fat yield, compared to a 0.03 kg (SE = 0.71) increase for ancestral inbreeding. There were no clear differences between effects of long ROH (recent inbreeding) and short ROH (ancient inbreeding).

Conclusions

Inbreeding depression was observed for yield, fertility and udder health traits. For yield traits and based on pedigree, inbreeding on recent generations was more harmful than inbreeding on distant generations and there was evidence of purging. Across all traits, long and short ROH contributed to inbreeding depression. In future work, inbreeding depression and purging should be assessed in more detail at the genomic level, using higher density information and genomic time series.

Population Structure Analysis of the Border Collie Dog Breed in Hungary

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

Animal models with group-specific additive genetic variances: extending genetic group models

BACKGROUND

The animal model is a key tool in quantitative genetics and has been used extensively to estimate fundamental parameters, such as additive genetic variance or heritability. An implicit assumption of animal models is that all founder individuals derive from a single population. This assumption is commonly violated, for instance in crossbred livestock or when a meta-population is split into genetically differentiated subpopulations. Ignoring that base populations are genetically heterogeneous and thus split into different 'genetic groups' may lead to biased parameter estimates, especially for additive genetic variance. To avoid such biases, genetic group animal models, which account for the presence of more than one genetic group, have been proposed. Unfortunately, the method to date is only computationally feasible when the breeding values of the groups are allowed to differ in their means, but not in their variances.

RESULTS

We present an extension of the animal model that permits estimation of group-specific additive genetic variances. This is achieved by employing group-specific relatedness matrices for the breeding value components to different genetic groups. We derive these matrices by decomposing the full relatedness matrix via the generalized Cholesky decomposition, and by scaling the respective matrix components for each group. We propose a computationally convenient approximation for the matrix component that encodes for the Mendelian sampling variance, and show that this approximation is not critical. In addition, we explain why segregation variances are often negligible when analyzing the complex polygenic traits that are frequently the focus of evolutionary ecologists and animal breeders. Simulations and an example from an insular meta-population of house sparrows in Norway with three distinct genetic groups illustrate that the method is successful in estimating group-specific additive genetic variances, and that segregation variances are indeed negligible in the empirical example.

CONCLUSIONS

Quantifying differences in additive genetic variance within and among populations is of major biological interest in ecology, evolution, and animal and plant breeding. The proposed method allows to estimate such differences for subpopulations that form a connected set of populations, and may thus also be useful to study temporal or spatial variation of additive genetic variances.

Founder-specific inbreeding depression affects racing performance in Thoroughbred horses

The Thoroughbred horse has played an important role in both sporting and economic aspects of society since the establishment of the breed in the 1700s. The extensive pedigree and phenotypic information available for the Thoroughbred horse population provides a unique opportunity to examine the effects of 300 years of selective breeding on genetic load. By analysing the relationship between inbreeding and racing performance of 135,572 individuals, we found that selective breeding has not efficiently alleviated the Australian Thoroughbred population of its genetic load. However, we found evidence for purging in the population that might have improved racing performance over time. Over 80% of inbreeding in the contemporary population is accounted for by a small number of ancestors from the foundation of the breed. Inbreeding to these ancestors has variable effects on fitness, demonstrating that an understanding of the distribution of genetic load is important in improving the phenotypic value of a population in the future. Our findings hold value not only for Thoroughbred and other domestic breeds, but also for small and endangered populations where such comprehensive information is not available.