256 GENOMIC EVALUATION OF FERTILITY TRAITS AND DISCOVERY OF HAPLOTYPES THAT AFFECT FERTILITY OF US DAIRY CATTLE
G. R. Wiggans A , D. J. Null A , J. B. Cole A and H. D. Norman BA Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, USA;
B Council on Dairy Cattle Breeding, Bowie, MD, USA
Reproduction, Fertility and Development 28(2) 260-260 https://doi.org/10.1071/RDv28n2Ab256
Published: 3 December 2015
Abstract
Genomic evaluations of dairy cattle became official in the United States in January 2009 for Holsteins and Jerseys, and later for Brown Swiss, Ayrshires, and Guernseys. Up to 33 yield, fitness, calving, and conformation traits are evaluated, and the fertility traits included daughter pregnancy rate and heifer and cow conception rates. Additional fertility traits, such as age at first calving and days from calving to first insemination, also are being studied. Male fertility (sire conception rate) is evaluated phenotypically rather than through genomics. Over 1 million animals have genotypes in the national database, which reflects collaboration with Canada and Europe. Most of the genotypes are from females and are from genotyping chips with <30 000 single nucleotide polymorphisms (SNP). To combine data across chips, genotypes are imputed to a set of >77 000 SNP. The imputation process involves dividing the chromosome into segments of approximately equal length and determining the paternal or maternal origin of the alleles. Because some segments were never homozygous, they were assumed to contain an abnormality that resulted in early embryonic death. If a decrease in sire conception rate could be associated with a bull that was a carrier of such a chromosomal segment, the haplotype was designated as affecting fertility. Once the region was identified, bioinformatic analysis was used to discover the causative variant for many of those haplotypes. Accuracy of genomic evaluations is determined by size of the reference population and heritability of the trait. The reference population for Holsteins includes >180 000 bulls and cows. Because fertility traits have low heritabilities, genomic information is particularly useful in improving evaluation accuracy. Accuracy of fertility evaluations is expected to increase further by discovering causative variants for various aspects of conception and gestation through investigation of sequence data.
