Genotyping more cows increases genetic gain and reduces rateof true inbreeding in a dairy cattle breeding scheme using female reproductive technologies

摘要

Both small dairy cattle populations and dairy cattlepopulations with a low level of linkage disequilibrium(LD) suffer from low reliability of genomic prediction.In this study, we investigated whether adding moregenotyped cows to the reference population influencesthe rate of genetic gain and rate of inbreeding by affectingthe reliability. A standard breeding program witha large reference population and high LD, which mimickeda breeding program for Danish Holstein population,was simulated as a reference. A Danish Jerseypopulation with a small reference population and highLD and a Red Dairy Cattle population with a largereference population and low LD were also simulated.Two additional breeding programs were simulated forDanish Jersey and Red Dairy Cattle populations, where2,000 additional genotyped cows were included in thepopulation for genomic selection. All 5 simulated breedingprograms were initiated by a founder population togenerate LD resembling the real LD pattern, followedby a 20-yr conventional progeny-testing scheme with1,000 or 10,000 genotyped progeny-tested bulls and a10-yr genomic selection scheme with or without 2,000additional genotyped cows. Evaluation criteria were annualmonetary genetic gain and rate of true inbreeding.Our results showed that adding more genotyped cowsto the reference in dairy cattle populations has the potentialto increase genetic gain and reduce the rate ofinbreeding, regardless of reference population size andlevel of LD. However, it is still not possible to reach thesame genetic gain as in the simulated Danish Holsteinpopulation with either a small reference population orlow LD. Our results also showed that in a small referencepopulation with high LD, it is difficult to manageinbreeding because of lower accuracy compared withthe simulated Danish Holstein population and a smallernumber of relevant families to select from. Therefore,breeding strategies need to be chosen to match populationsize and structure. The rate of true inbreedingis always underestimated by pedigree inbreeding andeven more in genomic breeding programs, indicatingthat some forms of genome-wide inbreeding, instead ofpedigree-based inbreeding, should be used to monitorinbreeding when genomic selection is implemented.