Use of Computerized Mate Selection Programs to Control Inbreeding of Holstein and Jersey Cattle in the Next Generation - K. A. Weigel* and S. W. Lin† *Department of Dairy Science, University of Wisconsin, Madison 53706 †Department of Industrial Engineering, University of Wisconsin, Madison 53706 2000 J Dairy Sci 83:822–828

The expected role of computerized mate selection programs with regard to inbreeding and lifetime profitability of Holstein and Jersey cattle was examined using data from 25 large registered herds of each breed. Sire selection and mate allocation were carried out using linear programming with the following objectives: 1) minimum inbreeding, 2) maximum net merit subject to a fixed inbreeding threshold, and 3) maximum expected lifetime profit after adjustment for inbreeding depression. Inbreeding of actual matings was similar to inbreeding from random matings, indicating that current inbreeding avoidance programs in these herds are ineffective. Inbreeding was reduced by 1.6 and 1.9% in Holsteins and Jerseys, respectively, when a mate allocation program was applied with service sires and usage levels fixed at the actual values. Benefits of mate selection programs increased when both sire selection and mate pair allocation were considered. Maximization of mean net merit with inbreeding restricted to a fixed level (5% in Holsteins and 8% in Jerseys) led to decreases in inbreeding of 0.9 and 1.4% and increases in lifetime profit of $16.66 and $26.86 in Holsteins and Jerseys, respectively, relative to programs that ignored inbreeding. Maximization of mean expected lifetime profit after adjustment for inbreeding depression decreased inbreeding by 1.8 and 2.8% and increased lifetime profit by $37.37 and $59.77 in Holsteins and Jerseys, respectively. Inbreeding coefficients estimated with pedigree traced to 1985 were inadequate predictors of inbreeding coefficients estimated with pedigrees traced to 1960. Mate selection programs cannot function optimally unless extensive historical pedigree data are available, particularly for service sires. Computerized mate selection programs can reduce inbreeding in the next generation, which will lead to an increase in farm profitability. However, if genetic diversity is to be maintained in the long term, procedures for selecting parents of AI sires must also be considered.
http://jds.fass.org/cgi/reprint/83/4/822.pdf



Effects of Inbreeding on Production and Survival in Holsteins - J. R. Thompson,* R. W. Everett,* and N. L. Hammerschmidt† *Department of Animal Science, Cornell University, Ithaca, NY 14853-4801 †Holstein Association, USA, Brattleboro, VT 05302 2000 J Dairy Sci 83:1856–1864

Responses of registered Holstein cows to various levels of inbreeding were examined with pedigree data supplied by the Holstein Association USA and test-day production data from 1970 through 1998 obtained from the Animal Breeding Center at Cornell University. Rate of increase in level of inbreeding has been accelerating over time, making it more difficult for producers to make matings that avoid the potentially deleterious effects of inbreeding. Milk production losses per lactation caused by inbreeding were generally 35 kg per percentage inbreeding level 0.01 but increased to 55 kg per percentage inbreeding level from 0.07 to 0.10. Somatic cell score was not affected by level of inbreeding. Inbreeding had the greatest effect on production at ages 22 mo and early in lactation. Early onset of the deleterious effects of inbreeding resulted in larger net present value losses than when effects of inbreeding occurred later. Losses were likely enhanced due to the need to freshen animals as early as possible to maximize net present value returns. Survival decreased as level of inbreeding increased and was likely to have a greater negative impact on the financial health of the dairy enterprise than production losses.
http://jds.fass.org/cgi/reprint/83/8/1856.pdf



Analysis of Levels of Inbreeding and Inbreeding Depression in Jersey Cattle - FILIPPO MIGLIOR, BILL SZKOTNICK1,2 and EDWARD B. BURNSIDE* Centre for Genetic Improvement of Livestock Deparbnent of Animal and Poultry Science
University of Guelph Guelph, ON, Canada NIG 2Wi 1992 J Dairy Sci 75:1112-1118

A pedigree file of 157,015 male and female Jersey cattle (born after 1955) from the Canadian herdbooks was investigated for the occurrence of inbreeding. A large proportion of Jersey bulls and cows were inbred (32.4 and 36.3% for bulls and cows, respectively). However, average inbreeding coefficients of these inbred cows and of all cows were low. First lactation milk, fat, and fat percent- age records for 53,592 Jersey cows were analyzed. Inbreeding was included in the animal model as a linear covariate. The regression coefficients of milk, fat, and fat percentage on inbreeding were -9.8 kg, -.55 kg, and -.0011% 1% increase of inbreeding. Inbreeding depression was not enough to cause large reductions of milk and fat yield of a cow with average inbreeding. However, when the inbreeding coefficient was greater than 12.5%, the inbreeding depression was significantly higher than expected and such that intentional inbreeding is not justified unless the mating is to an animal with exceptionally high breeding value.
(Key words: inbreeding coefficient, in-
http://jds.fass.org/cgi/reprint/75/4/1112.pdf



Selection and mating considering expected inbreeding of future progeny - P. M. VanRaden and L. A. Smith Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350, USA. Journal of Dairy Science, Vol 82, Issue 12 2771-2778

Animals most related or least related to current members of their breed were revealed by calculating the expected inbreeding of their future progeny. A sample of potential mates was chosen by randomly selecting 600 females from a recent birth year (1995). Relationships among the sample were computed by the tabular method. Relationships of other animals to the sample population were computed quickly from the relationships of their parents or ancestors. To-Mar Blackstar-ET and Round Oak Rag Apple Elevation were most related to the Holstein breed with expected inbreeding of 7.9 and 7.7%, respectively. Corresponding Jersey bulls were Highland Magic Duncan and Soldierboy Boomer Sooner of CJF with expected inbreeding of 10.9 and 9.5%, respectively. The highest expected inbreeding was 11.1% for Selwood Bettys Commander, 8.6% for Forest Lawn Simon Jetway, 10.1% for Dutch Mill Telestars Fayette, and 7.4% for Korncrest Pacesetter for Ayrshire, Brown Swiss, Guernsey, and Milking Shorthorn breeds, respectively. Regression on inbreeding in the genetic evaluation model removed effects of past inbreeding. Future inbreeding effects could be included for each potential mating or by adjusting breeding values for average inbreeding expected with random mating. The correlation between Holstein breeding values unadjusted and adjusted for inbreeding was 0.9976. The estimated genetic trend was 6% lower with future inbreeding included.
http://jds.fass.org/cgi/reprint/82/12/2771.pdf



The Effects of Inbreeding on the Lifetime Performance of Dairy Cattle - L. A. SMITH,1 B. G. CASSELL,2 and R. E. PEARSON Department of Dairy Science, Virginia Polytechnic Institute and State University, Blacksburg 24061-0315 1998 J Dairy Sci 81:2729–2737

The effects of inbreeding on the lifetime performance of dairy cattle were examined using data for production, somatic cell score, and linear type for all Holstein cows that were scored between 1983 and 1993. The results of fixed and mixed animal models differed. Relative net income adjusted for opportunity cost for the 2,610,123 cows with an 84-mo opportunity for herdlife was depressed by $14.79 for fluid market pricing and by $12.40 for manufacturing pricing per 1% increase in inbreeding. Mixed model estimates of depression per 1% of increase in inbreeding were +0.55 d for age at first calving, –6 d for days of productive life, and –4.8 for days in milk. Inbreeding decreased the mature equivalent production of milk, fat, and protein during first lactation by 27, 0.9, and 0.8 kg and the lifetime production of milk, fat, and protein by 177, 6.0, and 5.5 kg, respectively, per 1% increase in inbreeding. Inbreeding had little effect on conformation traits. The effects of inbreeding were cumulative, and effects on lifetime profit functions were relatively larger than the effects on lactation traits. Registered cows had higher levels of inbreeding and larger standard deviations than did grade cows. Inbreeding in registered cows depressed relative net income adjusted for opportunity cost for fluid and manufacturing prices by $24.43 and $21.78, respectively; income was depressed $9.43 and $9.02, respectively, for grade cows. The difference between registered and grade cattle is likely due to the incomplete pedigree information in grade animals. Inbreeding among cows in this study was not high on average, but economic losses represented a significant cost to the producer.
http://jds.fass.org/cgi/reprint/81/10/2729.pdf



Calculation and Use of Inbreeding Coefficients for Genetic Evaluation of United States Dairy Cattle - 0. R. WlGGANS and P. M. VanRADEN Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350
J. ZUURBIER1 Department of Animal Sciences University of Maryland College Park 20742 1995 J Dauy Sci 78:1584-1590

Inbreeding coefficients are calculated routinely for all animals included in national genetic evaluations for yield traits. The base population for inbreeding is defined as animals born during 1960. Animals with unknown parents are assumed to have inbreeding coefficients that are equal to the mean of coefficients for animals with known parents born during the same year. Mean inbreeding coefficients reached .03 to .04 for recent years, and coefficients for some animals exceeded SO. The annual increase in level of inbreeding was highest for Milking Shorthorns, but the rate of change of that increase was greatest for Holsteins. Accounting for inbreeding in calculation of the inverse of the relationship matrix had only a small effect on evaluations. For Jerseys, the maximum change in breeding value was 73 kg of milk for COWS and 40 kg of milk for bulls with 210 daughters. Estimates of inbreeding depression were similar across breeds for production traits and were -29.6 kg of milk, -1.08 kg of fat, and -.97 kg of protein per 1% of inbreeding for Holsteins. In January 1994, the USDA began considering the percentage of inbreeding when calculating inverses of relationship matrices, the largest matrix representing over 20 million Holsteins; this inbreeding percentage was released to the dairy industry for bulls.
http://jds.fass.org/cgi/reprint/78/7/1584.pdf



Effects of Inbreeding on Production and Survival in Jerseys - J. R. Thompson,* R. W. Everett,* and C. W. Wolfe† *Department of Animal Science, Cornell University, Ithaca, NY 14853-4801 †American Jersey Cattle Association, Reynoldsburg, OH 43068-2362 2000 J Dairy Sci 83:2131–2138

Responses of registered Jersey cows to various levels of inbreeding were examined with pedigree data supplied by the American Jersey Cattle Association and test-day production data from 1970 through 1998 obtained from the Animal Breeding Center at Cornell University. Rate of increase in level of inbreeding is accelerating with time, making it more difficult for producers to make matings that avoid the potentially deleterious effects of inbreeding. Production losses caused by inbreeding were significant and curvilinear for all traits studied except somatic cell linear score, with the greatest losses at higher levels of inbreeding. Inbreeding was found to have the greatest effect on production at early ages and early in lactation. Early onset of the deleterious effects of inbreeding resulted in larger net present value losses than if effects of inbreeding occurred later in the life of an animal. Losses were probably enhanced because of the need to freshen animals as early as possible to maximize net present value returns. Survival decreased as level of inbreeding increased and was likely to have a greater negative impact on the financial health of the dairy enterprise than production losses.
http://jds.fass.org/cgi/reprint/83/9/2131.pdf




Inbreeding in Swiss Braunvieh and Its Influence on Breeding Values Predicted from a Repeatability Animal Model - L. CASANOVA,’ C. HAGGER, and N. KUENZI Institute of Animal Science Swiss Federal Institute of Technology cKBo92 Zudch, Switretland M. SCHNEEBERGER Animal Genetics and Breeding University of New England Arddale, New South Wales 2351, Australla 1992 J Dairy Sci 75:111 – 1126

Inbreeding coefficients were computed for 910,444 animals of the Swiss Braunvieh population. Of the animals born in 1984, 71.5% were inbred with 67.9, 3.4, and 2% having inbreeding Coefficients between >0 and 5%, >5 to 10%, and >lo%, respectively. The average inbreeding coefficient was 1.14% but, for animals with both parents and at least one grandparent known, it was 1.67%. Breeding values for total milk, fat, and protein yields and for fat and protein pemtages were predicted using a repeatability animal model including a regression on the inbreeding coefficient. Phenotypic performance was sizeably depressed for milk yield only (-26 kgJ% of inbreeding or 2.4% of the phenotypic standard deviation). Adjusting for in- breedjng increased the estimated genetic trend slightly. Inbreeding is only partially accounted for when it is ignored in the construction of the inverse of the numerator relationship matrix. This effect was investigated by comparing predicted breeding values from a model including the complete matrix with predicted breeding values from a model including a matrix constructed with in breeding ignored. Only 3% of all predicted breeding values were affected by more than f5.5 kg. The maximum difference observed was 55.3 kg. The observed average absolute differences between the breeding values of offspring predicted with the two models increased with inbreeding of parents.
http://jds.fass.org/cgi/reprint/75/4/1119.pdf



Use of Computerized Mate Selection Programs to Control Inbreeding of Holstein and Jersey Cattle in the Next Generation - K. A. Weigel* and S. W. Lin† *Department of Dairy Science, University of Wisconsin, Madison 53706 †Department of Industrial Engineering, University of Wisconsin, Madison 53706 2000 J Dairy Sci 83:822–828

The expected role of computerized mate selection programs with regard to inbreeding and lifetime profitability of Holstein and Jersey cattle was examined using data from 25 large registered herds of each breed. Sire selection and mate allocation were carried out using linear programming with the following objectives: 1) minimum inbreeding, 2) maximum net merit subject to a fixed inbreeding threshold, and 3) maximum expected lifetime profit after adjustment for inbreeding depression. Inbreeding of actual matings was similar to inbreeding from random matings, indicating that current inbreeding avoidance programs in these herds are ineffective. Inbreeding was reduced by 1.6 and 1.9% in Holsteins and Jerseys, respectively, when a mate allocation program was applied with service sires and usage levels fixed at the actual values. Benefits of mate selection programs increased when both sire selection and mate pair allocation were considered. Maximization of mean net merit with inbreeding restricted to a fixed level (5% in Holsteins and 8% in Jerseys) led to decreases in inbreeding of 0.9 and 1.4% and increases
in lifetime profit of $16.66 and $26.86 in Holsteins and
Jerseys, respectively, relative to programs that ignored inbreeding. Maximization of mean expected lifetime profit after adjustment for inbreeding depression decreased inbreeding by 1.8 and 2.8% and increased lifetime profit by $37.37 and $59.77 in Holsteins and Jerseys, respectively. Inbreeding coefficients estimated with pedigree traced to 1985 were inadequate predictors of inbreeding coefficients estimated with pedigrees traced to 1960. Mate selection programs cannot function optimally unless extensive historical pedigree data are available, particularly for service sires. Computerized mate selection programs can reduce inbreeding in the next generation, which will lead to an increase in farm profitability. However, if genetic diversity is to be maintained in the long term, procedures for selecting parents of AI sires must also be considered.
http://jds.fass.org/cgi/reprint/83/4/822.pdf


Applications:


Should we be concerned about inbreeding in dairy cattle? - Gary W. Rogers
Dairy cattle selection programs have favored specific families and produced populations of dairy cattle that are related more than they were several decades ago. Geneticists have know for a long time that intense breeding programs would tend to favor certain families and create populations made up of closely related individuals. This increase in familial relationships is one of the trade-offs to intense selection for improved performance.
So, how far have we gone in creating populations of dairy cattle that are closely related?
Is this currently a problem or will it be a problem soon? What happens to the offspring when we mate closely related individuals? Is this something that only breeding companies should consider or does it affect producer herds directly?
http://animalscience.ag.utk.edu/dairy/pdf/pubs/ShouldWeBeConcernedAboutInBreedingInDairyCattle_DairyMail_1_03.pdf


Inbreeding Levels in Canadian Dairy Cattle - Larry R. Schaeffer, Centre for Genetic Improvement of Livestock, Animal & Poultry Science, University of Guelph
Inbreeding is generated by the mating of related individuals. The objective of inbreeding is to concentrate the desirable genes of a family such that they are consistently transmitted to offspring. Unfortunately, inbreeding will concentrate some of the undesirable genes as well. This may result in the occurrence of lethal genetic traits. In general, the net result of inbreeding is known as "inbreeding depression". Research has shown that each percentage increase in inbreeding in dairy cattle results in a 22 kilogram decrease in milk production, and may have greater impact on reproduction and calf viability.
Not all inbreeding is bad. Inbreeding has been a useful tool in plant breeding and in the poultry industry where the occurrence of undesirable genes is quickly overcome by short generation intervals and vast numbers of offspring from single matings. Dairy cattle do not have these advantages, and therefore inbreeding could have more long lasting effects. Mild forms of inbreeding have been used in dairy cattle. For example, some of the Roybrook sires in the Holsteins breed have been inbred. When these sires were bred widely to unrelated cows in the population, the offspring performed fairly well. In general, inbreeding should be done with caution.
http://cgil.uoguelph.ca/pub/articles/inbreedlevel.html


Inbreeding - Bennet G. Cassell, Extension Dairy Scientist, Genetics and Management, Virginia Tech
The mating of related individuals is called inbreeding. New dairy animals created by AI or natural service inherit a random sampling of the genetic makeup of each parent. If the parents are related, some of the genes transmitted to offspring by each parent will be copies of the same genes found in the common ancestor(s) which caused the parents to be related. As the genetic relationship between parents increases, the likelihood that pairs of genes in offspring are copies of a single gene in an ancestor generations back increases. Such genes are said to be "identical by descent."
The most extreme form of inbreeding is selfing, that is the mating of an individual to itself. This process is possible in many plant species because each individual produces both male and female germ cells. Suppose a plant has genotype Bb for some part of its chromosome structure. Since germ cells contain a sample half of the plant’s genetic material, half of all germ cells would carry B and half would carry b for both male and female cells. If the plant were "selfed," offspring would be BB, Bb, or bb in ratios of 1:2:1. BB individuals are called "homozygous" for the B allele, while bb individuals are homozygous for the b allele. Bb individuals are called "heterozygous" as they carry both B and b in their genetic material. If offspring of the selfed plant were also selfed, only BB offspring would result from the BB individuals and bb offspring from the bb individuals. The Bb individuals would again produce BB, Bb, and bb offspring in ratios of 1:2:1. The process, continued over several generations, would continue to increase the frequency of BB and bb (homozygous) individuals and reduce by half in each generation the number of Bb individuals. Selfing is not possible in mammals such as dairy cattle, but the same process of increased homozygosity and decreased heterozygosity occurs with inbreeding in all species.
Inbreeding does not change gene frequency, that is the total number of B or b genes in a population. It only changes the arrangement of those genes in pairs of BB, Bb, or bb. If some of those combinations are non-fertile, a selection process will occur which will change gene frequency.
http://www.ext.vt.edu/pubs/dairy/404-080/404-080.html


Investigations on Inbreeding in Jerseys – JC Wilk, BT McDaniel, C H Brown, P L Williams, and C W Wolfe
In recent years, the Jersey breed has placed concentrated attention on selection for increased yield by placing heavy emphasis on sire selection. A side effect of the extensive use of an elite group of sires has been that relatively few sires have had a major impact on the breed. Most of these sires are related. More over, most young bulls being sampled obtained the bulk of their genes from this same group of elite sires.
The success of the emphasis on selection is leading to a subtle but steady increase in inbreeding. This may be a prelude to problems that accompany increased inbreeding such as reduced reproductive efficiency, increased calf mortality, various health problems, and eventually decreased yield. Thus, inbreeding is becoming an increasing concern to the Jersey breed. Ways in which genetic diversity can be maintained while continuing to effectively emphasize intense selection for yield is becoming a priority. Other dairy breeds face a similar situation.
http://www.cals.ncsu.edu/an_sci/ann_rep94/jcwil76.html


Inbreeding Calculator – Canadian Dairy Network
To calculate the level of inbreeding for potential matings, complete the form below by selecting one cow and one or more potential sires.
http://www.cdn.ca/inbreed.htm


Effect of Inbreeding On Cow Performance & Mate Selection in Dairy Cows - Bennet G. Cassell, Extension Dairy Scientist, Genetics and Management, Virginia Polytechnic Institute and State University
As a group, dairy producers agree fairly well about what they want to change in dairy cows through genetic selection. There is disagreement about which bull is the ‘best’ bull, but general agreement about which bulls are in the top group. Consequently, cows and A.I. bulls have become more related over time because a few individual animals appear frequently in pedigrees. For instance, Pawnee Farm Arlinda Chief and Round Oak Rag Apple Elevation are each responsible for about 12% of the genes segregating in the U.S. Holstein population.
We need to recognize that this isn't a situation where mismanagement has set the woods on fire. Selection efforts to improve dairy cattle have been effective. Other dairy populations around the world have turned to U.S. genetics to improve their own cows. Globalization of semen marketing efforts has increased ties between previously unrelated dairy populations. Inbreeding has emerged as a factor in assigning mates to produce replacement females. Simply put, more of our cows are fairly closely related to the bulls that we want to use as service sires than was the case several years ago.
http://www.oznet.ksu.edu/dp_ansi/dairycon/EffectOfInbreeding.pdf