Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027.

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research.

Genetic selection for lifetime reproductive performance.

Genetic improvement of sow lifetime reproductive performance has value from both the economic perspectives of pork producers and the pork industry, but also from the perspective of ethical and animal welfare concerns by the general public. Genetic potential for piglets produced from individual litters is a primary determinant of lifetime prolificacy, but females must be able to sustain productivity without injury or death beyond the achievement of positive net present value. Evidence exists for between- and within-line genetic variation in sow lifetime performance, suggesting that improvements may be made by both line choices and genetic selection within lines.

Association of HOXA10, ZFPM2, and MMP2 genes with scrotal hernias evaluated via biological candidate gene analyses in pigs.

Objective: To evaluate the associations between 14 biological candidate genes and scrotal hernias in pigs.

Animals: 1,534 Pietrain-based pigs, including 692 individuals from 298 pig families and 842 male pigs without family information.

Procedures: Pigs were classified as affected or unaffected for scrotal hernias.

Association and haplotype analyses of positional candidate genes in five genomic regions linked to scrotal hernia in commercial pig lines.

Scrotal hernia in pigs is a complex trait likely affected by genetic and environmental factors. A large-scale association analysis of positional and functional candidate genes was conducted in four previously identified genomic regions linked to hernia susceptibility on Sus scrofa chromosomes 2 and 12, as well as the fifth region around 67 cM on chromosome 2, respectively. In total, 151 out of 416 SNPs discovered were genotyped successfully.

Embryonic loss in sows with repeated propensity for small litter size.

Information is lacking as to the timing and cause of sows that repeatedly have low litter size over several parities. Sows evaluated for the present study had at least two parities either small or=12 (NL) litter size. Following breeding of sows with contemporary boars, reproductive tracts were obtained on day 30 of gestation.