Increase In Coancestry Research Articles

Turopolje Pig: Between Conservation and Sustainability

The Turopolje pig is a fatty-type pig breed created during the Middle Ages in the Turopolje region in Central Croatia. Although the population of the Turopolje pig is stable today, this breed is still one of the endangered breeds that are severely threatened by inbreeding. The aim of this work was to evaluate the genetic diversity parameters of the recent Turopolje pig population in Croatia and to consider mating strategies to limit the increase in inbreeding in the population using algorithms within an optimal contribution selection frame. The pedigree of 1155 individuals was analysed. In addition to the basic pedigree structure, the following population parameters were analysed: average coefficient of inbreeding; mean rate of increase in coancestry; increase in coancestry between any individuals; effective population size. Based on obtained parameters, mating optimization using estimated kinship between candidates in several scenarios was carried out, restricting maximal kinship between candidates on a minimal possible value 0.07, as the least possible level of kinship, candidates on a value of 0.10, and candidates on a value of 0.25. The average inbreeding coefficient (F) in the population was 0.03, while the average F of inbred animals was 0.10. The effective population size obtained from pedigrees based on the increase in coancestry (0.17) was 29.14. Mating plans were created from 5 active boars and 120 sows in different scenarios with constraint on the level of kinship between candidates. The least possible level of kinship was 0.07, and no available solutions were under this level. With the increase in the allowed kinship between candidates, the level of inbreeding increased from 0.01 to 0.06 in the next generation. Under practical conditions, mating between ideal individuals in local pig populations is not always possible, and the use of optimisation algorithms allows alternative mating within existing populations to be considered. Finally, this approach opens up the possibility of potentially improving sustainable breeding through selection by considering breeding values for economically important traits. This approach can help to differentiate the Turopolje pig breed from other commercial and local breeds, e.g., for meat quality traits.

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population.

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

Estimation of Population-Specific Genetic Parameters Important for Long-Term Optimum Contribution Selection—Case Study on a Dairy Istrian Sheep Breed

The Istrian sheep breed has been subjected to selection for dairy traits for more than two decades. However, a detailed study of some important population-specific parameters such as effective population size (Ne) and connectedness between flocks has never been carried out. The aim of the study was to examine the above parameters in dairy Istrian sheep subjected to a national selection program. The Ne was estimated as the mean rate of increase in coancestry, and connectedness was determined using four different statistics. The Ne was estimated at 73 animals with pedigree constraints imposed on 4 equivalent generations and 3 full generations. Analysis of ΔNe (“sliding window approach”) revealed a negative ΔNe indicating a progressive loss of genetic variability (ΔNeNEG≥4 = −6.6, p < 0.01; ΔNeNFG≥3 = −4.9, p > 0.05). The overall connectedness (r¯ ~ 0.0001) was below the acceptable level for unbiased ranking of the animals belonging to different flocks (ri,j = 0.05). OCS appears to be the best option for the long-term survival (self-sufficiency) of the breed, but genetic links between flocks need to be strengthened to allow unbiased ranking of the animals based on the estimated breeding values.

SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

Accurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

Genetic variability and population structure based on pedigree information for Muzaffarnagari sheep in India

Abstract The objective of this study was to use pedigree analysis to evaluate the population structure and retention of genetic diversity in a flock of Muzaffarnagari sheep in India. Pedigrees of 5955 animals born between 1974 and 2003 was used to estimate the generation interval, pedigree completeness, and rate and level of inbreeding. Effective population size and parameters characterizing probabilities of gene origin were computed for lambs born between 2001 and 2003. The average numbers of equivalent complete generations were 3.41 and 5.00 for the whole and reference populations, respectively. The mean generation interval was 3.42 years. Average inbreeding coefficients for animals in the whole and reference populations were 1.79 and 1.23 %, respectively, and the rate of inbreeding was 0.68 % per generation. The average additive relationships for all animals and those in the reference population were 3.93 and 6.43 %, respectively. The realized effective population size, estimated from either the increase in coancestry between pairs of individuals or by regression of the average inbreeding coefficient on number of equivalent complete generations was approximately 76. Probabilities of gene origin were estimated by calculating effective numbers of founders (fe), ancestors (fa), founder genomes (fg), and non-founder genomes (fng) (33, 30, 15.4, and 28.9, respectively). The 10 most influential ancestors accounted for 50 % of the genetic variability, with a maximum individual contribution 6.53 %. The fe/fa ratio in the reference population was 1.10, indicating that occasional bottlenecks had occurred. Approximately 3.2 % of the initial heterozygosity had disappeared from the population. The results revealed that although there was some evidences of bottlenecks and genetic drift, considerable genetic variability remained in the population.

Demographic structure and genetic diversity of the endangered Bísaro pig: Evolution and current status

Bísaro pig, a local endangered swine breed, has gained popularity in the recent years. A complete pedigree was used to evaluate the population structure and investigate the current breed’s genetic variability in two reference populations (AlivePop and AliveBpop). Since the breed’s foundation, the number of registered animals, producers, and farrowing records has increased. The mean progeny size for sires was 116.17 ± 210.81, and 3.24% of the breeding boars originated 26.54% of all registered births showing a marked unbalanced use of certain sires. The mean calculated equivalent generations was 4.54, and 98.1% of all the animals had known parents, indicating a good degree of pedigree completion and depth. Approximately half of the individuals were inbred, with average inbreeding values of 10.41, 9.02, and 8.58% for the whole and reference populations, respectively. Considering both reference populations, a low effective founder/ancestor ratio was obtained (1.12), showing a well-balanced founder/ancestor contribution, and subsequent genetic transfer. However, the effective founder/founder ratio was particularly low (0.06 and 0.12) compared with other native breeds. The founder genome/effective founder ratios were 0.37 and 0.41 for AlivePop and AliveBpop. Contrarily to the whole population, the random genetic drift weighted significantly more than the drift due to unequal founder contribution in the reference populations. The effective population size based on the increase in coancestry ranged from 62.39 and 54.66, and 16.74 and 24.84 based on the increase of individual inbreeding, for the whole and reference populations. The genetic conservation index steadily grew over the years with a mean value of 6.53 for the whole pedigree. Genetic variability losses and diffuse structuring might have occurred in the Bísaro population. Notwithstanding, the recent genetic variability indicators seem positive, yet supported by an open herdbook policy. These characteristics must be taken into account to define future mating policies and selection programs.

Genetic variability of a small captive population of the cobia (Rachycentron canadum) through pedigree analyses

The genealogical information of a small captive population of the cobia fish was evaluated to assess the genetic variability and the status of inbreeding through pedigree analyses. Pedigree data (n = 238) for 6 years (2010–2016) were analyzed and offspring born from 2015 to 2016 were considered as reference population to compute the population genetic parameters based on the gene origin probabilities using the program ENDOG (version 4.8). Molecular marker based FAP (Family Assignment Program, version 3.6) was used for parentage assignment. The pedigree completeness was 68% for the parent, 29% for the grandparents and 7% for the great-grandparents generations with a mean equivalent to complete generations of 2.66. Mean generation interval, computed from four pathways, was 2.38 years. Considering the reference population into account the coefficients of average inbreeding and average relatedness were computed as 9.6% and 9.9%, respectively. The mean values of individual increase in inbreeding (rate of inbreeding) were 6.5% and 2.5% for the reference population and for the whole pedigree, respectively. Realized effective population size was computed from the individual increase in inbreeding and from the individual increase in coancestry as 7.7 and 10.6, respectively. The effective numbers of founders (fe), ancestors (fa), founder genomes (fg) and non-founder genomes (nfe) for the reference population were computed as 6, 6, 3.8 and 11.1, respectively. About 85% of total genetic variation was explained by 7 most influential ancestors, with a maximum individual contribution of 33.5%. Though the genetic bottleneck, as expressed by the fe/fa ratio as 1.0, was not evident, the loss of genetic variability caused by genetic drift was evident by fg/fe ratio which was 0.64 for the reference population. The analysis revealed the evidences on loss of genetic diversity with a very critical effective population size. Recommendations were made to improve the genetic variability in the herd. The present study signifies the importance of maintaining the pedigree and can help in carrying out similar studies on captive-bred fish species where small populations are inevitable.

Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (Ne), the effective number of founders (fe), the effective number of ancestors (fa) and the number of founder genome equivalents (fg) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the meanFand AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and thefe,faandfgwere 342, 223, 40, 22 and 9.6 for the RP. The large differences observed betweenfe, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability.Neestimated via an individual increase in inbreeding per generation (N¯e), and paired increase in coancestry(​N¯eC), were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.

Estimation of effective population size by different methods for Czech endangered horse breeds based on genealogical information

There are four Czech horse breeds: Silesian Noriker, Czech-Moravian Belgian, Old Kladruber (grey and black colour variety) and Hutsul included among the endangered breeds (Genetic Resources). These populations are currently closed to outside breeding. Effective population size is an important parameter used to assess genetic diversity for conservation program in these endangered breeds. Pedigree records for reference population, which included animals born in a 14-year period (from 1996 to 2010) were used for calculation. Realized effective population size was estimated from the individual rate in coancestry, from the individual increase in inbreeding and as effective population size based on population sex ratio. The values of effective population sizes were found low for all four analysed breeds. The results shown, that calculation based on population sex ratio gives overestimated values of effective population size. The approaches using either individual increase in inbreeding or individual increase in coancestry are more accurate and useful.

Genetic diversity of Iranian Lori-Bakhtiari sheep assessed by pedigree analysis

In this study a pedigree analysis was conducted to characterize the genetic structure and diversity of the closed nucleus of Iranian Lori-Bakhtiari sheep. Herdbook information collected between 1992 and 2014, was used to estimate generation interval, pedigree completeness level, inbreeding and its evolution during the studied years. Animals born between 2011 and 2014 were selected as a reference population for estimating parameters derived from probability of gene origins. The mean generation interval was 3.42 year in the studied period. Average inbreeding coefficient of the animals in the reference population was 1.02%. The rate of inbreeding was 0.17% per generation (P<0.01) in the studied period. Realized effective population size estimated from individual increase in coancestry was 101. The effective number of founders, effective number of ancestors and founder genome equivalent of the reference population were 77, 43 and 21 respectively. The results indicated that population under study has fairly good genetic diversity. However, population has lost a part of its genetic diversity due to unbalanced contribution of founders, bottlenecks and genetic drift. For continued genetic gain, enlarging the selection basis and implementation of methods that maximize the selection response at an acceptable level of inbreeding are recommended.

GENEALOGICAL DECOMPOSITION OF THE EFFECTIVE POPULATION SIZE: A CASE STUDY ON CROATIAN AUTOCHTHONOUS CATTLE BREEDS

Effective population size (Ne) is one of the most important tools used to assess genetic diversity for conservation purposes. Using pedigree data of three Croatian autochthonous cattle breeds (Busa, Istrian and Slavonian Syrmian Podolian) the effective maternal (NeF), paternal (NeM) and combined maternal-paternal (NeFM) population size was estimated. Additionally, we estimated the effective population size based on the census population sex ratio (Nes), the effective population size from the individual increase in inbreeding (NeFi) and the effective population size from individual increase in coancestry (NeCi). We compared these sizes with the values obtained for 20 additional cattle populations, as well as with the newly calculated NeFM. The effective population sizes calculated for three autochthonous breeds were consistently the lowest in amongst all considered cattle breeds. Utilisation of extremely small numbers of breeding males is the main reason for the observed reduction in the effective population size. The decomposition of effective population size into maternal and paternal components is shown to be an informative parameter in detecting the reduction of the effective population size as a consequence of unequal sex contribution. Still, the impact of the pedigree depth and completeness on the NeF, NeM and NeFM estimation remain to be analysed. We observed a large deviation between Nes and all other methods of Ne estimation and it is our recommendation that breeders and stakeholders should consider using alternative methods of Ne estimation when planning breeding programmes as well as in the determination of the endangered status of animal populations.

History, structure, and genetic diversity of Brazilian Gir cattle

The Gir cattle breed (Bos indicus) is an important genetic resource for milk production throughout the tropics. The small number of Gir animals introduced in Brazil, rapid dissemination of this breed recently, and the intensification of selection practices could contribute to increase of inbreeding level and reduce genetic diversity in this population. The population was analyzed in terms of pedigree completeness level, inbreeding coefficient, coancestry, generation interval, effective population size, effective number of founders and ancestors, among others. Despite the low mean inbreeding (around 2%), minor problems were identified in the population structure of the Brazilian Gir cattle, e.g., trend of narrower bottlenecks in the pedigree in recent years. The effective population sizes based on inbreeding (94) or coancestry (165.9) as well as the effective number of ancestors (76) and founders (143) were relativity high. The major subdivision of the Gir breed was observed between 1993 and 2002 (dairy and dual-purpose herds, wide use of within-herd matings). In this period the level of inbreeding remained at a higher level, there was a small increase in coancestry and the number of equivalent subpopulations was approximately 6. After 2002, there was genetic exchange between subpopulations, reduction in the average inbreeding, pronounced increase in the average coancestry, and the number of equivalent subpopulations was about 2. Furthermore, it was found that the mean generation interval of the population tended to increase in recent years (around 9 years). About 2.3% of genetic diversity has been lost since the first generation of founders. Based on the effective population size, number of equivalent subpopulations, inbreeding, coancestry, and loss of genetic diversity, the Gir population is still highly structured, but there is ample room for artificial selection. The results regarding the effective number of founders and ancestors in the present population demonstrate the existence of bottlenecks in the pedigree and indicate the need for population structure monitoring. Nevertheless, the Brazilian Gir breed can perfectly face a breeding program with high selection intensity.

Brazilian Sport Horse: Pedigree Analysis of the Brasileiro de Hipismo Breed

Brasileiro de Hipismo (BH) represents an open population that permits genetic input from breeds recognised by the World Breeding Federation for Sport Horses. The aim of this study was the genetic characterisation of the population as the first of a series aiming at the consolidating the current selection programme. The Brazilian Association of the Brazilian Sport Horse Breeders provided genealogical data from 1977 to 2011. A data bank containing 34,393 horses was analysed for population genetic parameters including: individual inbreeding (F), effective population size (Ne), effective number of founders (fe), effective number of ancestors (fa), and number of founder genome equivalents (fg). Analysis were run twice: for animals born until 1995 (PREVIOUS) and for those born in the last 15 years (15YEARS). Ne estimated via paired increase in coancestry consisted of 188.59 (±3.24) animals. fe was 466 and 222 for PREVIOUS and 15YEARS, respectively. Ancestors were represented by fa of 274 and 129. Mean F for 15YEARS was 0.6%; 1444 animals were inbred, with mean inbreeding of 3.33%. The difference found in fa and fe parameters, between PREVIOUS and 15YEARS, indicated the loss of original alleles. The increase in contribution from some founders represents the breeder’s preference for a few horses, without the negative effect of high inbreeding levels. Brasileiro de Hipismo genetic variability agrees with its large based formation history, and should allow for genetic gain of heritable traits through selection.

Pedigree analysis in White Shorthaired goat: First results

Abstract. Pedigree records of 1 682 animals of the White Shorthaired goat in Slovakia were investigated. The reference population was defined as the animals born from 2008 to 2011 with at least one ancestor known in the second ancestral generation (670 animals kept in eight flocks). The numbers of founders (286), ancestors (256), effective founders (73), effective ancestors (45) and founder genome equivalents (32) were assessed. Fifteen ancestors were needed to explain 50 % of genetic variability. Marginal contributions of the ten most influential ancestors varied between 5.45 % and 2.47 % and accounted for 39.8 % of genetic variability. The mean values of inbreeding and co-ancestry were 0.69 % and 1.55 %, respectively. The effective population size was assessed to consist of 182 and 142 individuals, depending whether it was calculated from the individual increase in inbreeding or the individual increase in co-ancestry. The number of maximum generations traced, fully traced generations and equivalent complete generations traced were 5.62, 1.97 and 3.04, respectively. The first, second and third ancestral generation were 100 %, 83 % and 71 % complete, respectively. The completeness decreased to as low as 35 % and 11 % in the fourth and fifth generation. To be able to keep genetic links across generations in touch, the amount of pedigree information needs to be increased. This is a serious requirement for appropriate monitoring and management of genetic relations within the population.

Pedigree analysis and inbreeding depression on growth traits in Brazilian Marchigiana and Bonsmara breeds1

The study of population structure by pedigree analysis is useful to identify important circumstances that affect the genetic history of populations. The intensive use of a small number of superior individuals may reduce the genetic diversity of populations. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchigiana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F(i)) or individual increases in inbreeding coefficient (ΔF(i)) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchigiana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreeding effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scrotal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchigiana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explaining 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bonsmara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depression was observed for most of the growth traits. The model including ΔF(i) can be considered more adequate to quantify inbreeding depression. The inclusion of F(i) or ΔF(i) in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with simultaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, providing additional information to producers and breeders.

Computing effective population size from molecular data: The case of three rare Spanish ruminant populations

The aim of this study was to compare different methodologies to compute the effective size when the genealogies are not available (or are shallow) in three rare Spanish ruminant populations. For this purpose the authors used molecular information from three Spanish local ruminant populations (the Pajuna cattle, Payoya goat and Merino de Grazalema sheep populations). Several methods based on molecular or pedigree data were applied to estimate the effective population size in the three studied populations. Estimates based on increase in molecular coancestry (N efm) in Pajuna (8.5) and Payoya (16.7) populations were 2- and 3-fold lower than those obtained using the linkage disequilibrium method. However, N efm in Merino de Grazalema population reached a higher value (110.5 vs 86.2). Regarding the effective size using temporal methods (F statistics and coalescence theory), the results for Pajuna were very similar across methodologies with values ranging from 6.0 to 7.8. In the Payoya goat, the results obtained ranged from 15.0 to 33.4. For Merino de Grazalema was not possible to estimate the N e using temporal methods. Regarding the genealogical methods, pedigrees highly compatible with molecular information were generated from the genotypes of the individuals, the correlations between the molecular and the genealogical coancestry matrix were high from 0.82 to 0.94. The effective population sizes based on individual increase in inbreeding were similar for Pajuna (17.0) and Payoya (18.1) and for Merino de Grazalema was 24.2. The N e based on an increase in coancestry (N ec) was higher in all cases ranging from 20.2 for Pajuna to 38.3 for Merino de Grazalema. The N ec for Payoya was 27.1. We can conclude that there is no single value of molecular-based N e for each population, because high ranges for effective size where found across methodologies. However, the assessed ranking was steady: the Pajuna is the most endangered population, followed by Payoya and Merino de Grazalema. When the priority for conservation is of concern, all methods seem to be useful, but it is not possible to combine them. It is recommendable to use the same method across populations to define the risk status of the list of populations. Moreover, if a precise value of N e is needed, for example, to define the size of sampled animals to be genotyped under a genomic selection scenario, different methodologies would lead to different conclusions. Further research seems to be needed on this issue.

Estimation of effective population size from the rate of coancestry in pedigreed populations

We introduce a simple method to estimate effective population size from increase in coancestry (Δc(jk)) for all pairs of individuals j and k in a reference subpopulation. An increase in pairwise coancestry for any pair of individuals j and k can be defined assuming that a hypothetical mating between them would give an individual with an inbreeding coefficient equal to c(jk), where c(jk) is the coancestry coefficient between the individuals j and k. The equivalent measure to discrete generations value (g(jk)) corresponding to the individual jk can be computed by averaging discrete equivalents generations of its parents (g(j) and g(k)). The mean increase in coancestry for all pairs of individuals in a reference subpopulation can be used to estimate a realized effective population size based on coancestries that would provide information on the effective size of a population under random mating. Performance of the new parameter was tested on simulated and empirical (horse) populations with different mating strategies and population structures. The routines needed to compute the introduced parameters have been included in a new version of the program ENDOG.

Inbreeding trend and inbreeding depression in the Danish populations of Texel, Shropshire, and Oxford Down1

The objective of this study was to analyze the development of inbreeding and estimate inbreeding depression in the Danish populations of 3 major meat type sheep breeds. The pedigrees contained 29,336 Texel, 22,838 Shropshire, and 11,487 Oxford Down. The rate of inbreeding was approximately 1% per generation for all breeds, but the rate of increase in co-ancestry was somewhat lower (0.45 to 0.71), indicating that more inbreeding has been accumulating than would be expected if mating was at random. Inbreeding depression for birth weight, ADG from birth until 2 mo, and litter size was estimated for all 3 breeds using a minimum of 15,000 records per trait and breed. All traits showed depression due to inbreeding of the animal itself. For most combinations of trait and breed, there was also a significant reduction of the phenotype due to inbreeding in the dam. The size of inbreeding depression was 1.2 to 2.6% of the mean, resulting in an increase in the inbreeding coefficient of the individual of 0.10, and estimates were similar for similar increases in maternal inbreeding. The rate of inbreeding in these breeds needs to be reduced in the future to avoid a further decline in birth weight, ADG, and litter size.

Minimization of rate of inbreeding for small populations with overlapping generations.

We propose a method that minimizes the rate of inbreeding (delta F) for small unselected populations with overlapping generations and several reproductive age classes. It minimizes the increase in coancestry of parents and optimizes the contribution of each selection candidate. The carrying capacity of the population is limited to a fixed number of animals per year. When survival rate equalled 100%, only animals from the oldest age class were selected, which maximized the number of parents per generation, slowed down the turnover of generations and minimized the increase of coancestry across sublines. However, the population became split into sublines separated by age classes, which substantially increased inbreeding within sublines. Sublines were prevented by a restriction of selecting at least one sire and one dam from the second-oldest age class, which resulted in an L times lower delta F, where L equals the average generation interval of sires and dams. Minimum coancestry mating resulted in lower levels of inbreeding than random mating, but delta F was approximately the same. For schemes where the oldest animals were selected, delta F increased by 18-52% compared with the proposed method.