Genomics in the U.S. Dairy Industry: current and future challenges

Abstract

The first U.S. dairy cattle genomic evaluation was released in April 2008. Since then, the number of animals genotyped per year has rapidly increased. The over 2 million genotypes currently stored, have increased by nearly 500,000 (90/10% ratio for female and male animals, respectively) added annually since 2016. Most animals are genotyped with chips that have between 18,000 and 30,000 single-nucleotide polymorphism (SNP) markers. In order to ensure the highest quality of SNP genotypes in the US system, only CDCB approved genotyping laboratories or other national genetic evaluation centers representing international exchange partners are allowed to submit genotypes to the U.S. cooperators’ database. The SNP genotypes in each submission are evaluated for call rate, portion heterozygous, and parent-progeny consistency. Each animal genotype is checked against its parents and a grandparent if the parent has not been genotyped. Considering only animals with genotypes that are usable for genomic evaluation, 97% had sires and 38% had dams that were already genotyped. Each genotype is compared with all others to discover identical genotypes and parent-progeny relationships not in the pedigree and possible grandsires if they are unknown or unlikely. These checks will soon be revised due to the growth of the genomic database. Since October 2017, animals with an unlikely grandsire detected are excluded from evaluation. Currently, 60,671 SNPs are used in U.S. genomic evaluation of dairy cattle, and research is ongoing to increase that number to ~77,000. Various genetic abnormalities are also tested for, and these test results are included in the imputation to provide an imputed indication of carrier status for animals that are not tested. Haplotypes that affect fertility also are used to detect reproductive defects. To date, 12 such haplotypes have been detected, with the latest introduced in December 2017 (AH2, Ayrshire second haplotype affecting fertility). Genomic evaluations for production, conformation and fertility/calving traits are released on a weekly basis for new animals. In 2017, 2 new traits (cow livability and gestation length) were introduced. The CDCB will start publishing 6 new health traits on Holsteins in April 2018. Reliance on genomic evaluations to select bulls has increased rapidly in the US. In 2016, 67% of breedings through AI were to bulls with no milking progeny. The age of parents at bull birth has dropped to just over 2 years, nearly the biological minimum. This reduction in generation interval has led to almost doubling the annual genetic improvement (over $80/year for lifetime net merit, a genetic-economic index). Other improvements planned for 2018 are to provide more standardized and documented feedback to customers and to perform a revision of the genotype process system and accommodate the increasing number of genotypes received.