A short critical history of the application of genomics to animal breeding

Two scientific schools have been in coexistence from the beginning of genetics, one of them searching for factors of inheritance and the other one applying biometrical models to study the relationships between relatives. With the development of molecular genetics, the possibilities of detecting genes having a noticeable effect in traits augmented. Some genes with large or medium effects were localized in animals, although the most common result was to detect markers linked to these genes, allowing the possibility of assisting selection programs with markers. When a large amount of simple and inexpensive markers were available, the SNPs, new possibilities were opened since they did not need the presence of genes of large or medium effect controlling a trait, because the whole genome was scanned. Using a large amount of SNPs permits having a prediction of the breeding value at birth accurate enough to be used in some cases, like dairy cattle, to halve its generation interval. In other animal breeding programs, the implementation of genomic selection is less clear and the way in which it can be useful should be carefully studied. The need for large populations for associating phenotypic data and markers, plus the need for repeating the process continuously, complicates its application in some cases. The implementation of the information provided by the SNPs in current genetic programs has led to the development of complex statistical tools, joining the efforts of the two schools, factorial and biometrical, that nowadays work closely related.

Genome-Wiide estimates of coancestry, in breeding 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.