Ruminations On Lessons To Be Hatched From Genomics Research In Cattle and Goats

High-throughput genomics has dramatically impacted livestock. Dairy cattle have been central in many of these innovations. This industry was positioned to leverage the first sequenced genome for a livestock species. A century of data recording culminated in  national genetic evaluations and dramatic selection progress. One hallmark of this genetic improvement, was the use of artificial insemination (AI). Extensive use of elite AI bulls resulted in large half-sib bull families. In 1999, we initiated the CDDR, a comprehensive collection of DNA samples of bulls tested by the largest AI companies. These bulls sired enough daughters to ensure accurate predictions of genetic merit. These factors "sowed the storm" being reaped in many unimagined ways. The first harvest was a doubling of genetic gain through application of genome-enhanced breeding values that reduced generation intervals and increased selection intensities. One consequence of this success has been tremendous growth in genotypic data; nearly 300,000 animals have been genotyped for calculation of genetic merit. These data represent incredibly deep and wide samplings of global dairy populations, spawning unanticipated whirlwinds into biological discovery. Coupled with strategic resequencing, these data have revealed causative SNP underlying two lethal haplotypes affecting fertility - phenotypes never observed directly! We hope that using genomics in other populations  holds promise. For species and populations lacking structured breeding programs and phenotypic records, alternative approaches must be developed that leverage population adaptation and differentiation. Breeding designs, numbers of offspring, and effective population size will all influence strategies used to enhance genetic progress in these populations.