Relationship between the magnitude of the inbreeding coefficient and milk traits in Holstein and Jersey dairy bull semen used in Brazil

Artificial insemination has been used to improve production in Brazilian dairy cattle; however, this can lead to problems due to increased inbreeding. To evaluate the effect of the magnitude of inbreeding coefficients on predicted transmitting abilities (PTAs) for milk traits of Holstein and Jersey breeds, data on 392 Holstein and 92 Jersey sires used in Brazil were tabulated. The second-degree polynomial equations and points of maximum or minimal response were estimated to establish the regression equation of the variables as a function of the inbreeding coefficients. The mean inbreeding coefficient of the Holstein bulls was 5.10%; this did not significantly affect the PTA for percent milk fat, protein percentage and protein (P = 0.479, 0.058 and 0.087, respectively). However, the PTAs for milk yield and fat decreased significantly after reaching inbreeding coefficients of 6.43 (P = 0.034) and 5.75 (P = 0.007), respectively. The mean inbreeding coefficient of Jersey bulls was 6.45%; the PTAs for milk yield, fat and protein, in pounds, decreased significantly after reaching inbreeding coefficients of 15.04, 9.83 and 12.82% (P < 0.001, P = 0.002, and P = 0.001, respectively). The linear regression was only significant for fat and protein percentages in the Jersey breed (P = 0.002 and P = 0.005, respectively). The PTAs of Holstein sires were more affected by smaller magnitudes of inbreeding coefficients than those of Jersey sires. It is necessary to monitor the inbreeding coefficients of sires used for artificial insemination in breeding schemes in Brazil, since the low genetic variability of the available sires may lead to reduced production.     

Pedigree and marker information requirements to monitor genetic variability

There are several measures available to describe the genetic variability of populations. The average inbreeding coefficient of a population based on pedigree information is a frequently chosen option. Due to the developments in molecular genetics it is also possible to calculate inbreeding coefficients based on genetic marker information. A simulation study was carried out involving ten sires and 50 dams. The animals were mated over a period of 20 discrete generations. The population size was kept constant. Different situations with regard to the level of polymorphism and initial allele frequencies and mating scheme (random mating, avoidance of full sib mating, avoidance of full sib and half sib mating) were considered. Pedigree inbreeding coefficients of the last generation using full pedigree or 10, 5 and 2 generations of the pedigree were calculated. Marker inbreeding coefficients based on different sets of microsatellite loci were also investigated. Under random mating, pedigree-inbreeding coefficients are clearly more closely related to true autozygosity (i.e., the actual proportion of loci with alleles identical by descent) than marker-inbreeding coefficients. If mating is not random, the demands on the quality and quantity of pedigree records increase. Greater attention must be paid to the correct parentage of the animals.     

Possible negative effects of inbreeding on semen quality in Shetland pony stallions

Inbreeding is widely believed to negatively affect reproductive performance. Indeed, in some species, high levels of inbreeding are thought to be the major cause of poor semen quality. It is, however, not clear whether inbreeding affects fertility in horses. In this study, the relationship between inbreeding and semen quality was examined in 285 immature Shetland pony stallions submitted for breeding soundness examination in March-April of the years 1992-1997. The majority of stallions examined were 3 years old (85%) and their coefficients of inbreeding ranged from 0 to 25% (mean+/-S.D.: 3+/-4.6%). For the purpose of analysis, stallions were divided into six inbreeding classes (0-1, 1-2, 2-5, 5-8, 8-12 and >12%) containing 132, 40, 42, 27, 25 and 19 animals, respectively. The degree of inbreeding significantly affected many aspects of sperm production and quality, based on a standard examination of two ejaculates collected at a 1.5-3h interval. In particular, coefficients of inbreeding above 2% were associated with lower percentages of motile (p<0.01) and morphologically normal sperm (p<0.001). When the data set was used to estimate heritability of semen characteristics, the high values calculated for sperm progressive motility (0.46) and concentration (0.24) suggested that these traits could be improved by phenotypic selection. These findings support the hypothesis that inbreeding has a detrimental effect on semen quality in Shetland ponies, although examination of multiple ejaculates after repeated semen collection to bring the animals to daily sperm output is needed to confirm this conclusion. Nevertheless, the results support previous suggestions that inbreeding is an important cause of reduced semen quality.     

Sustainable long-term conservation of rare cattle breeds using rotational AI sires

The development of inbreeding in rotation breeding schemes, sequentially using artificial insemination (AI) sires over generations, was investigated for a full AI scheme. Asymptotic prediction formulae of inbreeding coefficients were established when the first rotation list of AI sires (possibly related) was in use. Simulated annealing provided the optimal rotation order of sires within this list, when the sires were related. These methods were also used for subsequent rotation lists, needed by the exhaustion of semen stores for the first bulls. Simulation was carried out starting with groups of independent sires, with different sizes. To generate a yearly inbreeding rate substantially lower than 0.05% (considered to be within reach by conventional conservation schemes using frequent replacements), the results obtained showed that the number of sires should be at least 10–15 and that the same sires should be used during at least 50 years. The ultimate objective was to examine the relevance of implementing rotation in breeding schemes on the actual rare French cattle breeds under conservation. The best candidate for such a test was the Villard-de-Lans breed (27 bulls and 73 000 doses for only 340 females) and it turned out to be the best performer with an inbreeding coefficient of only 7.4% after 500 years and five different sire lists. Due to the strong requirements on semen stores and on the stability of population size, actual implementation of this kind of conservation scheme was recommended only in special (''niche'') cattle populations.     

The use of frozen semen to minimize inbreeding in small populations

In this study, we compared the average coancestry and inbreeding levels for two genetic conservation schemes in which frozen semen from a gene bank is used to reduce the inbreeding in a live population. For a simple scheme in which only semen of generation-0 (G0) sires is used, the level of inbreeding asymptotes to 1/(2N), where N is the number of newborn sires in the base generation and rate of inbreeding goes to zero. However, when only sires of G0 are selected, all genes will eventually descend from the founder sires and all genes from the founder dams are lost. We propose an alternative scheme in which N sires from generation 1 (G1), as well as the N sires from G0, have semen conserved, and the semen of G0 and G1 sires is used for dams of odd and even generation numbers, respectively. With this scheme, the level of inbreeding asymptotes to 1/(3N) and the genes of founder dams are also conserved, because 50% of the genes of sires of G1 are derived from the founder dams. A computer simulation study shows that this is the optimum design to minimize inbreeding, even if semen from later generations is available.     

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.     

Population structure of the Trakehner Horse breed

The objective of this study was to examine the population structure of the Trakehner Horse breed. A total of 13 793 pedigree records were used for analysing the active breeding population and their ancestors dating back to 1950. Ancestors that were born before 1950 were called as base animals. The average generation interval was calculated as 10.2 years. The effective population size (Ne) was estimated by the increase in average year-wise inbreeding coefficient and average coancestry, respectively. Two methods were applied to estimate the effective population size: 1. Numerator-relationship-matrix (NRM), which did not consider missing ancestries. 2. Uncertain-parentage-matrix (UPM), which considered a probabilistic correction for unknown ancestors. There were no major differences between these two methods with respect to the rate of increase in inbreeding although the global levels using the UPM method were observed to be higher. Estimates for the inbreeding coefficients and the average coancestries varied little between both methods. The estimates of the effective population size per generation based on the rate of inbreeding ranged from 169 (NRM) to 150 (UPM) and 158 (NRM) to 144 (UPM) calculated by the average coancestry. From the early 1990s onwards, a strong increase in the rate of inbreeding was observed. This may be due to an increasing variance of the family size of sires and may be interpreted as a consequence of the growing use of artificial insemination. Analysing coancestries within and between the centrally managed regional breeding societies in Germany further revealed the Trakehner horse breed to be a genetically fragmented population with a main partition corresponding to formerly divided East and West Germany. The average rate of gene contributions (Thoroughbred (xx), Arab Horse breed (ox)) to the defined actual breeding population was calculated to be 22.3% xx-genes and 11.7% ox-genes.     

Minimising inbreeding in small populations by rotational mating with frozen semen

Mating plans are investigated in order to minimize inbreeding in small populations when frozen semen is available. For a single dam line it was found that specific sire rotations minimized the asymptotic level of inbreeding when semen is used repeatedly from certain generations. When semen of N foundation (G0) sires is used rotationally over generations it is shown that the inbreeding level asymptotes to 1/(2(N+1) - 2). However, if only G0 sires are used then all genes will eventually descend from the founder sires. Inbreeding can be reduced further by using sires from generation one (G1) and later as this retains genes from the founder dams in the long-term gene pool. If semen from NG0 sires and N unrelated G1 sons is used rotationally then inbreeding asymptotes to (2(N-1) + 1)/(2(2N+1) - 2). When there are more founder dams than sires, the asymptotic inbreeding can be reduced even further by using the semen of half-sib G1 sires in rotation. Optimal rotations using full-sib G1 sires or generation 2 (or later) sires will lower the asymptotic inbreeding also, but generally not by much. It was found that when unlimited frozen semen from a specified group of sires was available, the optimal mating plan was achieved by selecting each generation the sire with the least co-ancestry with the current female of the dam line.     

Variance of prediction error with mixed model equations when relationships are ignored

Summary Formulas are presented to illustrate the calculation of correct variances of prediction error (PEV) and the correlation between true and predicted values (r_TI) when the incorrect variance-covariance matrix for the random effects is used in mixed-model equations (MME). The example with progeny records of highly related and inbred sires showed that PEV were underestimated from the diagonals of the inverse of the coefficient matrix of the MME when sires were assumed unrelated and not inbred and were overestimated when relationships among sires were calculated with Henderson's simple rules for the inverse of the numerator relationship matrix, A^-1, which do not consider inbreeding. When Quaas' rules for A^-1, which do consider inbreeding, are used, the correct PEV are obtained. In the example, calculations of r_TI from the diagonals of the inverse of the coefficient matrix were too large when relationships and inbreeding were ignored and were obviously wrong when the approximation to the numerator relationship matrix, A, was based on the simple rules for calculating A^-1. If the correct A is used in the MME, the calculation of r_TI may be incorrect if inbreeding of the evaluated individual is not considered. If inbreeding is known, adjustment for inbreeding is easy for calculation of r_TI.Published as paper no. 9947, Journal Ser, Nebraska Agric Res Div, University of Nebraska, Lincoln, Neb.     

Inbreeding and reproduction in mice divergently selected for response to a dietary toxin

This study was conducted to determine whether inbreeding coefficients of selected parents or of progeny differed between lines of mice selected for increased or decreased responsiveness to a nutritional toxicosis. A second objective was to determine whether the influence of inbreeding of parents and/or progeny on reproductive traits differed between those lines. Mice were selected divergently for 8 generations for the effect on post-weaning growth of endophyte-infected fescue seed in their diet. Forty pairs (or in Generation 7, 20 pairs) were selected and mated per generation in each line. Inbreeding increased 0.5 to 0.6% per generation in both lines, a rate close to that predicted from genetic theory. Inbreeding coefficients of selected parents were not higher in the susceptible than in the resistant line. A difference would have been expected if the inbreeding coefficient had been correlated with susceptibility to toxicosis. The magnitudes of inbreeding depression for reproductive traits did not differ significantly between lines. The average inbreeding coefficient of the potential litter tended to be higher in nonfertile than fertile matings (P = 0.10), but inbreeding coefficients of sires and dams did not differ between successful and unsuccessful matings. Inbred litters tended to be born earlier than noninbred litters (P = 0.10). Inbred dams produced smaller litters than noninbred dams (main effect P < 0.05) but only when the litter also was inbred (interaction P < 0.01). Sex ratio was not influenced by inbreeding of sire, dam or litter, but there was a higher proportion of male progeny in the susceptible than in the resistant line (P = 0.01). To avoid reduced reproductive fitness, laboratory animal populations should be managed to minimize inbreeding of progeny and dam.     

Prion octapeptide-repeat polymorphism in Polish Black-and-White cattle

The study was carried out in a Polish Black-and-White cattle population, represented by 167 AI sires, 200 young tested bulls, 190 bull-dams, and 606 randomly chosen cows from commercial herds. The fragment of the bovine prion protein gene (PRNP) coding the octapeptide-repeat sequence, was identified by PCR analysis. Two different gene variants of 349 bp and 373 bp in size, produced three genotypes: PRNP 6/6, PRNP 6/5 and PRNP 5/5, respectively. Allele frequency in all examined populations, on average 0.894 for PRNP 6 and 0.106 for PRNP 5, shows a significant difference between the group of cows from commercial herds, characterised by high frequency of PRNP 5 (q = 0.137) in comparison to AI sires (q = 0.077), young tested bulls (q = 0.052) and bull-dams (q = 0.084). Moreover, both analysed female groups of bull-dams and cows from commercial herds are distinguished by the presence of PRNP 5/5 homozygous animals, which were not recorded in the AI sires and young tested bulls, and had never been recognised in earlier examined Holstein-Friesian populations. Analysis of the genetic equilibrium indicates a very high conformity between observed and expected number of animals in the separate PRNP genotype groups. However, some tendency of difference is observed in highly selected cows, qualified as bull-dams on the basis of very high level of milk performance traits.     

Computing numerator relationships between any pair of animals

We describe a simple method to compute the numerator relationship between any or all pairs of animals in the numerator relationship matrix. The method depends on output of the MTDFNRM program from the MTDFREML set of programs. An option of the MTDFNRM program creates a file that includes the inbreeding coefficient for each animal. The method also makes use of how the inbreeding coefficient is traditionally calculated: one-half of the relationship between the animal's parents. To obtain the numerator relationship between any pair of animals, the original pedigree file is augmented with a dummy animal with an identification number (ID) greater than for any animal in the original pedigree file. The ID of the pair of animals for which the relationship is wanted is included as parents. MTDFNRM is then run with the option to create a file of ordered and original IDs for animals and their parents along with the inbreeding coefficients. We then multiply the inbreeding coefficient for a dummy animal by two to obtain the numerator relationship between the two animals designated as parents.     

Pedigree analysis of the closed nucleus of Iranian Baluchi sheep

A study was conducted to characterise genetic diversity in the closed nucleus of Baluchi sheep using pedigree analysis. Herdbook information collected between 1979 and 2008, including pedigree records on 21,721 animals, was used to compute inbreeding and average generation intervals. Effective population size and parameters derived from probability of gene origin were computed for ewes born between 2005 and 2008 with both parents known (female reference population). The average complete generation equivalent of the female reference population was 5.47. The mean generation interval was 3.33 years in the studied period. From 1983 to 1994, the rate of increase in inbreeding was approximately 0.2% per year, but, after 1994, inbreeding did not increase as in the preceding years and had an approximately flat trend over time. The mean relationship coefficients among rams, among ewes and between rams and ewes in active animals were calculated to predict the future level of inbreeding. The effective number of founders, effective number of ancestors and founder genome equivalent of the reference population were 80, 47 and 19.5, respectively. The realised effective population size was 134 animals. The results of this study indicated that the population under study has fairly good genetic variability.     

Silent point mutation polymorphism of the bovine CD18 encoding gene

We report on a PCR-RFLP procedure for recognising of a silent point mutation of ITGB2 CD18 subunit gene in cattle. Polymorphism screening was performed in a Polish Black-and-White cattle population (n=210). The genotype and allele frequencies were established in the sires and cows. Further research is needed to explain the possible applications of the CD18 silent point mutation as a potential molecular marker for high milk productivity.     

Genome-Wide Estimates of Coancestry,Inbreeding and Effective Population Size in the Spanish Holstein Population

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.     

Analysis of inbreeding depression in the first litter size of mice in a long-term selection experiment with respect to the age of the inbreeding

An understanding of inbreeding and inbreeding depression are important in evolutionary biology, conservation genetics, and animal breeding. A new method was developed to detect departures from the classical model of inbreeding; in particular, it investigated differences between the effects of inbreeding in recent generations from that in the more distant past. The method was applied in a long-term selection experiment on first-litter size in mice. The total pedigree included 74,630 animals with approximately 30,000 phenotypic records. The experiment comprised several different lines. The highest inbreeding coefficients (F) within a line ranged from 0.22 to 0.64, and the average effective population size (N(e)) was 58.1. The analysis divided F into two parts, corresponding to the inbreeding occurring in recent generations ('new') and that which preceded it ('old'). The analysis was repeated for different definitions of 'old' and 'new', depending on length of the 'new' period. In 15 of these tests, 'new' inbreeding was estimated to cause greater depression than 'old'. The estimated depression ranged from -11.53 to -0.79 for the 'new' inbreeding and from -5.22 to 15.51 for 'old'. The difference was significant, the 'new' period included at least 25 generations of inbreeding. Since there were only small differences in N(e) between lines, and near constant N(e) within lines, the effect of 'new' and 'old' cannot be attributed to the effects of 'fast' versus 'slow' inbreeding. It was concluded that this departure from the classical model, which predicts no distinction between this 'old and 'new' inbreeding, must implicate natural selection and purging in influencing the magnitude of depression.     

A mating method accounting for inbreeding and multi-trait selection in dairy cattle populations

Selection in dairy cattle populations usually takes into account both the breed profiles for many traits and their overall estimated breeding values (EBV). This can result in effective contributions of breeding animals departing substantially from contributions optimised for saving future genetic variability. In this work, we propose a mating method that considers not only inbreeding but also the detailed EBV of progeny or the EBV of sires in reference to acceptance thresholds. Penalties were defined for inbreeding and for inadequate EBV profiles. Relative reductions of penalties yielded by any mating design were expressed on a scale ranging from 0 to 1. A value of 0 represented the average performance of random matings and a value of 1 represented the maximal reduction allowed by a specialized, single-penalty, mating design. The core of the method was an adaptative simulated annealing, where the maximized function was the average of both ratios, under the constraints that both relative penalty reductions should be equal and that the within-herd concentration criterion should be equal to a predefined reasonable value. The method was tested on two French dairy cattle populations originating from the same AI organization. The optimised mating design allowed substantial reductions of penalty: 70% and 64% for the Holstein and the Normandy populations, respectively. Thus, this mating method decreased inbreeding and met various demands from breeders.     

Incorporation of new founders into captive populations

This report describes preliminary studies intended to develop generalizations for the optimal incorporation of newcomers into breeding pools. Small populations, which grow from four to a stable size of 16 animals per generation, were simulated on a computer. New founders were introduced and various breeding schemes tried and evaluated for their effect on inbreeding coefficients and founder representation. Two variables were examined for their effects on inbreeding and founder representation: number of progeny produced by crossing new founders with the established population, and number of mates the new founder had from the established population. Increasing the value of these variables to the point at which new-founder representation was equal to the original founders' representations decreased inbreeding. Beyond this point, inbreeding increased.     

Evaluation of genetic variation in the international Brown Swiss population

The international Brown Swiss cattle population pedigree was studied to measure genetic variations and to identify the most influential animals. Twenty-two countries provided pedigree information on 71 497 Brown Swiss bulls used for artificial insemination (AI). The total number of animals with the pedigree is 181 094. The mean inbreeding coefficient for the pedigree population was 0.77%. There was, in most cases, an increase in the mean inbreeding coefficient, with the highest value at 2.89% during the last 5-year period (2000 to 2004). The mean average relatedness for the pedigree population was 1.1%. The effective population size in 2004 was 204. There was notable variation between average generation intervals for the four parental pathways. The longest average generation interval, at 8.73 years, was observed in the sire–son pathway. The average generation interval for the whole population was 6.53 years. Most genetically influential individuals were sires. The highest contributing founder was a sire with a 3.22% contribution, and the highest contributing founder dam made a contribution of 1.75%. The effective number of founders and the effective number of ancestors were 141 and 88, respectively. The study showed that genetic variation within the pedigree population has been decreasing over recent years. Increasing the number of AI bulls with a low individual coefficient of inbreeding could help to maintain a good level of genetic variation in the Brown Swiss population.     

Prediction of rates of inbreeding in populations selected on best linear unbiased prediction of breeding value

Predictions for the rate of inbreeding (DeltaF) in populations with discrete generations undergoing selection on best linear unbiased prediction (BLUP) of breeding value were developed. Predictions were based on the concept of long-term genetic contributions using a recently established relationship between expected contributions and rates of inbreeding and a known procedure for predicting expected contributions. Expected contributions of individuals were predicted using a linear model, u(i)(()(x)()) = alpha + betas(i), where s(i) denotes the selective advantage as a deviation from the contemporaries, which was the sum of the breeding values of the individual and the breeding values of its mates. The accuracy of predictions was evaluated for a wide range of population and genetic parameters. Accurate predictions were obtained for populations of 5-20 sires. For 20-80 sires, systematic underprediction of on average 11% was found, which was shown to be related to the goodness of fit of the linear model. Using simulation, it was shown that a quadratic model would give accurate predictions for those schemes. Furthermore, it was shown that, contrary to random selection, DeltaF less than halved when the number of parents was doubled and that in specific cases DeltaF may increase with the number of dams.