Impact of inbreeding Managing a declining Holstein gene pool Dr. Filippo Miglior R&D Coordinator, CDN, Guelph, Canada

Transcription

1 Impact of inbreeding Managing a declining Holstein gene pool Dr. Filippo Miglior R&D Coordinator, CDN, Guelph, Canada In dairy cattle populations, genetic gains through selection have occurred, largely as a result of widespread use of genetically superior proven AI sires, resulting in many thousands of daughters per sire and extensive sampling of their sons by AI organizations. Although this extreme selection has been responsible for rapid genetic progress over the short term, there is an increasing concern that the extensive use of a few outstanding sires might narrow the genetic base and result in detrimental effects from inbreeding over the long term. The aim of this paper is to give a general overview of the impact of inbreeding in dairy cattle, and to identify possible solutions to address the problem of a declining gene pool in Holsteins worldwide. Defining inbreeding Two animals are related when they have at least one ascendant in common. Two individuals having a common ancestor may both carry a copy of the same gene possessed by the ancestor; if they mate they may pass the same gene to the progeny. Mating of related individuals produces an inbred offspring, and its degree of inbreeding is described by the inbreeding coefficient, which is one-half the additive relationship between its parents (Wright, 1922). Inbred individuals may carry two genes at a locus that are replicates of one and the same gene in previous generations, and the two genes are called identical by descent (Falconer, 1989). The coefficient of inbreeding is the probability that the two genes at any locus in an individual are identical by descent (Malécot, 1948). Effects of inbreeding Falconer (1989) outlined the effects of inbreeding as: increased homozygosity (animals with a copy of the same allele at one locus); redistribution of genetic variances (decrease of within family genetic variance and increase of between family genetic variance); higher chance of appearance of lethal recessive genes in the homozygous state (BLAD), decrease of homeostasis (inbred animal less adaptive to environmental changes); and, reduction of the animal's performance, particularly in terms of reproduction, fertility and health (inbreeding depression). On average the inbreeding depression per each 1% increase in the inbreeding coefficient is -25 kg, -.9 kg, -.8 kg, for milk, fat and protein yield, respectively. Nelson and Lush (1950) investigated, in US Holsteins, the effects of inbreeding on body measurements at different ages of the animal. The traits considered were weight, heart girth, wither height, body length, chest depth and paunch girth. Overall, effects of inbreeding were small. Hodges et al. (1979) reported, in the Canadian Holsteins, an increase of.2 days of calving interval per 1% increase in inbreeding. For the same trait Hudson and VanVleck (1984) found an increase of.1 day in the US Holsteins. Hoeschele (1991) studied the effect of inbreeding on days open, and found an increase of.13 days for 1% increase in inbreeding. For example, a cow with an inbreeding coefficient equal to 6.25% (paternal grand sire = maternal great grand sire) on average will have the following changes in performance, when compared to a non inbred animal: -156 kg of milk, -5.6 of fat, -5 kg of protein, SCC, +1 day of calving interval. How does inbreeding accumulate In animal breeding we can distinguish active inbreeding, where animals are mated according to family relatedness (inbreeding coefficient? 6.25%), from passive inbreeding, that is the result of small effective population size (inbreeding coefficient < 6.25%). In the first case, inbreeding accumulates at a faster rate and severe inbreeding depression is possible. In the second case, inbreeding accumulates slower, and natural and/or artificial selection eliminates most deleterious genes. In dairy cattle populations inbreeding is expected to increase as a result of several changing breeding practices: high intensity of selection, use of reproductive techniques (artificial insemination, multiple ovulation and embryo transfer, in vitro fertilization and embryo production, ovum pick up, cloning), use of 1

2 genetic markers, animal model evaluations (higher probability of co-selection of close relatives). A further increase in levels of inbreeding is expected over the long term, due to global sire rankings and use of a few top sires worldwide to breed the elite cows. When breeding is at a global scale, every country uses the much larger, but the same, gene pool. Figure 1 shows the trend of usage of bull sires worldwide by year of birth of the bulls. From 1970 to 1990 there is an increasing percentage of bulls born sired by the 5 bulls with most sons for the three groups of countries. In 1990 North America (Canada and US) has the highest percentage (61%) of bulls, sons of the 5 sires with most sons, followed by Oceania (Australia and New Zealand) with 55% and Europe (France, Germany, Italy and The Netherlands) with 47%. By 1995 all countries appear to have diversified their breeding scheme and balanced the number of bulls per sires, with North America showing the largest change (from 61% in 1990 to 30% in 1995). Figure 2 shows that diversification is also occurring in terms of using more bloodlines for the same three groups of countries. In 1990 Europe used 95% of bull sires from North America, and North America used 100% local bull sires. Five years later, Europe used 50% of bull sires from North America and 50% from European countries. Trends in inbreeding (Europe and North America) Inbreeding trends over the past 30 years are shown in Figure 3 for five countries. Overall, two different phases can be distinguished: before and after the end of the eighties. Initially there was a slow increase in inbreeding levels up to 1989 with annual increases in inbreeding coefficient varying from.02 to.09%. Birth years 1990 to 1999 show the most dramatic increase in inbreeding rates, with annual increases in inbreeding coefficient varying from.14 to.29%. In the 1990s yearly rates were greater than expected values calculated through a simulation. Goddard and Smith (1990) reported an expected increase in inbreeding rates of.125% per year with 20 bull sires per generation and.25% with 10 bull sires per generation. Furthermore, they estimated the annual rate of inbreeding at.19% from the increase in the degree of relationship among registered North-American Holsteins, values estimated from Young et al. (1988). European countries seem in a better position than North American countries. Their average rate in inbreeding in the last 10 years is equal to.17%, while US and Canada average.26%. This means that, if rates follow the same speed, in ten years North American countries will have accumulated 1% of inbreeding more than European countries. However, up to now North American countries have carried out a selection mainly restricted to North American animals, while Europeans have experienced a more diversified selection scheme, exchanging animals and semen among each other, and of course importing from North America. This trend is changing with some European bulls having been marketed in Canada and US. Also, North American Holstein associations have recently changed their policies, opening their Herd Books to registration of non-north American germplasm. Is inbreeding always negative? Generally a common slope is usually fitted to account for decreased performance due to the level of inbreeding. However, inbreeding is a sampling process, and founders of a family may differ in the number and effect of deleterious recessive genes, thus affecting the magnitude of inbreeding depression in the descendants: strong negative effect in some, average in some and negligent or even positive in some other families. Miglior et al. (1994) found in the Canadian Holsteins that responses to inbreeding were highly variable, thus suggesting that common ancestors did differ substantially in response of their descendants to inbreeding. Magnitudes and directions of inbreeding depression among the common ancestors were consistent across the yield traits, thus, following the same pattern of the correlations among milk, fat and protein yield. Inbreeding depression in forty-eight families ranged from 79 to +14kg of milk per 1% of inbreeding (Figure 4). Further research is needed in order to exploit the heterogeneity of inbreeding depression. Solutions to address inbreeding Considering the various steps of a within breed selection scheme, for the Holsteins, inbreeding becomes relevant in: design of the selection scheme, genetic evaluations and mating both of elite and non-elite animals. 2

3 AI Centers are generally responsible for selection schemes. Specific formulae to predict future inbreeding in population should be applied based on the adopted selection scheme (number of bull sires and bull dams). Different selection schemes could then be compared, considering the maximum level of expected inbreeding. Finally, the selection scheme, which maximizes genetic gain at a predetermined fixed level of inbreeding, should be chosen. The selection scheme should be optimized, avoiding use of few bull sires and balancing the number of sons per each sire. Also, AI Centers could plan for the medium and long term, sampling few bulls, which are least related to the common and popular blood lines. Identifying outcross bulls, that have exceptional genetic merit for production and conformation, should become a goal of sire analysts worldwide. Use of such bulls to sire young bulls will slow down accumulation of inbreeding, providing new options for the future market with animals of high genetic value and lower relationship to the population. Animal model genetic evaluations are also responsible for faster accumulation of inbreeding. Two options are available to counteract this problem: accounting for inbreeding in the evaluations, and placing less emphasis on animal relationships in the animal model. Inbreeding coefficient of each animal should be included in the relationship matrix used in genetic evaluations to account for effect on additive genetic variance. Also, VanRaden and Smith (1999) of the AIPL-USDA have proposed to account for past inbreeding depression, adjusting estimated breeding values for average inbreeding expected with random mating. They concluded that a published value for each bull of expected inbreeding of future progeny would help breeders to find outcross bulls and reduce inbreeding. In the 1990s, several researchers studied methods of reducing rates of inbreeding within the context of selection on estimated breeding values (Toro and Perez-Enciso, 1990; Toro and Silio, 1992; Verrier et al., 1992; Grundy and Hill, 1993; Brisbane, 1994, Meuwissen, 1998). All authors agreed that reducing the weighting, given to family information in genetic evaluation and selection, seems to be the most powerful method to reduce rate of inbreeding. This can be achieved in different ways, e.g. using a heritability value greater than true heritability for genetic evaluation (Grundy and Hill, 1993), or selecting on estimated breeding value discounted for the average relationship of the evaluated animal to the other animals in the selected populations (Brisbane, 1994, Meuwissen, 1998). In terms of mating, AI centers should avoid mating of elite animals, which yield inbreeding coefficient greater or equal to 6.25%. At the herd level, the farmer should be provided with a series of information, like inbreeding coefficient of each bovine, trend in inbreeding for the herd in the last 5-10 years, a comparison with trends from farms in the same area or with national averages. Finally the farmer should use a mating program with the following options: a) full pedigree information on all females in the herd, b) identification of the best bulls available on the market, accounting for the expected inbreeding of the future progeny, c) avoidance of any mating, which yields an inbreeding coefficient greater or equal to 6.25%. Conclusion The average inbreeding level of Holstein populations is low, but the annual change in inbreeding has rapidly increased in the last decade, particularly in North America. Due to previously explained causes, inbreeding, both in terms of annual change and accumulated inbreeding, is expected to increase further, both in the short and long term. There are, however, a number of solutions to address this problem. AI organizations should optimize their breeding program to achieve the maximum genetic gain at a fixed level of inbreeding. Genetic Evaluation Centers should include inbreeding in their evaluations to account for the effect on additive genetic variance and past inbreeding depression. Also, a constraint or cost factor should be placed on the average relationship of selected animals. Finally, breed Associations and/or AI Organizations should provide computerized mating programs to farmers, thus helping them monitor inbreeding at the farm level, and avoiding any matings that yield an inbreeding coefficient greater or equal to 6.25%. Inbreeding can be monitored and delayed but not avoided. Avoiding active inbreeding (F? 6.25) is very important, as this would eliminate the main deleterious effects. Selection can in fact reduce most problems 3

4 caused by passive inbreeding (0% < F < 6.25%). Applying the right combination of solutions can diminish the negative consequences of inbreeding. Acknowledgments The author acknowledges ANAFI, INRA, USDA and NRS for providing inbreeding trends. References Brisbane, J. R Control and prediction of inbreeding in genetic improvement schemes for livestock. Ph.D. Dissertation, University of Guelph, Guelph, Ontario, Canada. Falconer, D. S Introduction to Quantitative Genetics. John Wiley & Sons, Inc., New York, NY. Goddard, M. G., and C. Smith Optimum number of bull sires in dairy cattle breeding. J. Dairy Sci. 73: Grundy, B., and W. G. Hill A method for reducing inbreeding with best linear unbiased prediction. Anim. Prod. 56:427 (Abstr.). Hodges, J., L. Tannen, B. J. McGillivray, P. G. Hiley, and S. Ellis Inbreeding levels and their effect on milk, fat and calving interval in Holstein-Friesian cows. Can. J. Anim. Sci. 59: Hoeschele, I Additive and nonadditive genetic variance in female fertility of Holsteins. J. Dairy Sci. 74: Hudson, G. F. S., and L. D. VanVleck Inbreeding of artificially bred dairy cattle in the Northeastern United States. J. Dairy Sci. 67: Malécot, G Les mathématiques de l'hérédité. Masson et Cie, Paris. Meuwissen, T. H. E Risk management and the definition of breeding objectives. Proc. 6th World Congr. Genet. Appl. Livest. Prod., Armidale, Australia 25:347. Miglior, F., E. B. Burnside, and W. D. Hohenboken. 1994c. Heterogeneity of inbreeding depression in Holstein cattle. Proc. 5th World Congr. Genet. Appl. Livest. Prod., Guelph, Ontario, Canada 18:93. Nelson, R. H., and J. L. Lush The effects of mild inbreeding on a herd of Holstein-Friesian cattle. J. Dairy Sci Toro, M. A., and M. Perez-Enciso Optimization of selection response under restricted inbreeding. Genet. Sel. Evol. 22: Toro, M. A., and L. Silio Consequences of mixed model methods for population structure and inbreeding. Proc. 43rd Ann. Meet. Europ. Assoc. Anim. Prod., Madrid, Sept , 1992 (Mimeo). VanRaden, P. M. and L. A. Smith Selection and mating considering expected inbreeding of future progeny. J. Dairy Sci. 82(12): Verrier, E., J. J. Colleau, and J. L. Foulley An investigation of long term consequences of using animal model BLUP in small selected lines. Proc. 43rd Ann. Meet. Europ. Assoc. Anim. Prod., Madrid, Sept , 1992 (Mimeo). Wright, S Coefficients of inbreeding and relationship. Am. Nat. 56: Young, C. W., W. J. Tyler, A. E. Freeman, H. H. Voelker, L. D. McGilliard, and T. M. Ludwick Inbreeding investigations with dairy cattle in the North Central region of the United States. North Central Reg. Res. Publ. 191, Minnesota Agric. Exp. Stn. Tech. Bull Univ. Minnesota, St. Paul. 4

5 70 60 Percentage of bulls EU NA OC Year of birth Figure 1. Percentage of bulls by the five sires with most sons for Europe (France, Germany, Italy and The Netherlands), North America (Canada and US) and Oceania (Australia and New Zealand) European sires North American sires Oceania sires Percentage of bulls 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% EU NA OC EU NA OC Year of birth Figure 2. Use of bull sires in three groups of countries (EU: France, Germany, Italy and The Netherlands; NA: Canada and US; and OC: Australia and New Zealand) in 1990 and

6 Inbreeding average (%) Canada France Italy The Netherlands United States Year of birth Figure 3. Trends of inbreeding by year of birth in five countries. Milk kg Family (N = 48) Figure 4. Inbreeding depression on milk kg for 1% increase in inbreeding in 48 families 6