Impact of genomic prediction on inbreeding in the Danish jersey breed

3 INTRODUCTION . 4 INBREEDING . 4 GENOMIC PREDICTION . 5 AIM AND HYPOTHESIS . 7 ADDITIONAL TERMS AND THEORY OF THE STUDY . 7 BREEDERS EQUATION . 7 NORDIC TOTAL MERIT. 7 PEDIGREE COMPLETENESS INDEX . 7 OPTIMAL CONTRIBUTION SELECTION . 7 EVA . 8 MATERIALS AND METHODS . 8 RESULTS . 9 DISCUSSION . 10 FURTHER STUDIES . 12 CONCLUSION . 12 ACKNOWLEDGMENT . 12 REFERENCES . 13 APPENDIX A: EVA . 14 APPENDIX B: THE INTERNSHIP . 15 MY INTRODUCTION TO VIKINGGENETICS, ASSENTOFT . 15 UNDERSTANDING BREEDING FROM THE INSIDE . 15 WHAT I LEARNED . 16 THANKS TO THE STAFF OF VIKINGGENETICS, ASSENTOFT . 17 Impact of genomic prediction on inbreeding in the Danish jersey breed Line Dinesen Jensen, (201206167) Aarhus University 3 Abstract Since the introduction of genomic prediction in VikingGenetics, all bulls are selected based on genomic estimated breeding values. This change of selection method affects the rate of inbreeding in the population. A study population consisting of males born in 2014 and high-index females born in 2012-2014 in the Danish Jersey breed was studied. The software EVA was used to estimate the predicted change in average relationship and genetic merit from the study population to the next generation based on genomic and parental estimated breeding values. Results show that breeding with genomic prediction can be used to increase genetic gain without raising the rate of increase in average relationship and thus long term inbreeding compared to conventional selection methods. Alternatively it can be used to reduce the average inbreeding with the same amount of genetic gain. Whether it is one or the other, depends on choices of the breeder. Impact of genomic prediction on inbreeding in the Danish jersey breed Line Dinesen Jensen, (201206167) Aarhus University 4 Introduction Each year VikingGenetics purchases around 60 Danish Jersey (DJ) bulls of which approximately 40 are entered into the herd book. The bulls that are included into the herd book are bulls used in production and the ones that contribute to the next generation. The bulls purchased are selected by breed manager Peter Larson, VikingGenetics based on genomic prediction (GP) and relationship to the other bulls selected (pers. comm. Peter Larson). DJ is a small breed with an effective population size estimated to 53 (Stachowicz et al., 2011). In small populations genetic variation is lost due to genetic drift. In farm animals genetic variation is also lost due to selection. Animals with high breeding values (BV) are on average more related than animals picked at random from the population. This is in fact the idea of artificial breeding and what makes it possible to improve domesticated animals through breeding. Years of selection and insensitive breeding have increased coancestry of the animals in DJ, and by that also increased inbreeding among the animals. Inbreeding Inbreeding is the phenomenon that individuals become autozygous at some or all of their loci. Autozygosity occurs when the two alleles at a locus are identical by descent (IBD). The inbreeding coefficient, F, is the probability that the individual has inherited two identical alleles on any locus, which are copies of the same allele in an ancestor. Such alleles are identical by descent. The inbreeding coefficient of an individual is equal to the coancestry of the two parents. The coefficient of coancestry is the probability that a randomly selected allele at a random locus in one individual is IBD with a randomly selected allele at the same locus in another individual. As the coancestry of parents increases, so does the inbreeding coefficient of their offspring. Thus inbreeding is a natural consequence of a high coefficient of coancestry within the parent population. (In this study it is important to know that coancestry also can be defined by 0.5x the coefficient of relationship. The software used mainly utilizes coefficient of relationship). Build-up of coancestry in the population is undesirable due to several negative effects of inbreeding: One negative effect is accumulation of recessive deleterious alleles and inbreeding depression which are two aspects of the same problem. As mentioned the inbreeding coefficient is the probability for to alleles at one locus to be IDB, the probability of being homozygous due to identity by descent (autozygous) at a locus. While most alleles are harmless as homozygotes, some are referred to as recessive deleterious alleles. These alleles are (mostly) harmless when the individual only carries one, due to dominance effects of the non-deleterious allele. But homozygosity for a recessive deleterious allele will cause negative effects on the phenotype or even death of the individual. Genetic drift measured by FST can explain both accumulation of recessive deleterious alleles and loss of genetic variation. FST is a measure of the proportion of total genetic variance in an earlier population lost in the current subpopulation. Due to the relatively large effect of genetic drift in small populations, this causes an accumulation of some recessive deleterious alleles. The negative effect of this accumulation is revealed as inbreeding depression. FIS measures the deviation from Hardy-Weinberg equilibrium within population caused by non-random mating. A positive value of FIS indicates a deficit of heterozygotes compared to a situation with random mating in the population. A positive value of FIS leads to an increased expression of recessive deleterious alleles segregating in the population. Impact of genomic prediction on inbreeding in the Danish jersey breed Line Dinesen Jensen, (201206167) Aarhus University 5 Another negative effect of inbreeding is that a build-up coancestry is harmful due to the loss of genetic variation. Genetic variation is one of the main components for breeding progress, with the loss of the genetic variation the progress in breeding value will be reduced. Third, increased coancestry makes the outcome of breeding programs less predictable. These consequences of inbreeding are obviously harmful to farm production and breeding. An animal lost before either dairy production or slaughter value is an unnecessary economic expense for the farmer. A breeding program going toward more inbred animals, will either decrease the gain of BV, or decrease the BV in total. To estimate the true value of inbreeding coefficient of the individuals in a population you need to trace back the pedigree to a base population. A base population is the start point of the population. At this point back in time no animals are considered related, hence all the alleles of the individuals in the population are considered to be independent and not IBD. Thus the base population has an inbreeding coefficient of F = 0. This is an importa