Knowledge of the extent and range of linkage disequilibrium (LD), defined as non-random association of alleles at two or more loci, in animal populations is extremely valuable in localizing genes affecting quantitative traits, identifying chromosomal regions under selection, studying population history, and characterizing/managing genetic resources and diversity. Two commonly used LD measures, r 2 and D', and their permutation based adjustments, were evaluated using genotypes of more than 6,000 pigs from six commercial lines (two terminal sire lines and four maternal lines) at ~4,500 autosomal SNPs (single nucleotide polymorphisms). The results indicated that permutation only partially removed the dependency of D' on allele frequency and that r 2 is a considerably more robust LD measure. The maximum r 2 was derived as a function of allele frequency. Using the same genotype dataset, the extent of LD in these pig populations was estimated for all possible syntenic SNP pairs using r 2 and the ratio of r 2 over its theoretical maximum. As expected, the extent of LD highest for SNP pairs was found in tightest linkage and decreased as their map distance increased. The level of LD found in these pig populations appears to be lower than previously implied in several other studies using microsatellite genotype data. For all pairs of SNPs approximately 3 centiMorgan (cM) apart, the average r 2 was equal to 0.1. Based on the average population-wise LD found in these six commercial pig lines, we recommend a spacing of 0.1 to 1 cM for a whole genome association study in pig populations.

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. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled “Genome to Phenome: A USDA Blueprint for Improving Animal Production” in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories “Science to Practice,” “Discovery Science,” and “Infrastructure.” New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The updated blueprint that follows describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic. Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.

Three groups of beef cows that were similar in growth and mature size, but different in genetic potential for level of milk provided to their calves, were studied. A procedure for fitting grafted polynomials based on calf suckling data was used to estimate the total amount of milk produced by each cow during 205-d lactations. Estimated 205-d milk production of the high milk group exceeded that of the medium and low milk groups by 186 and 561 kg, respectively. Differences in milk production of the three groups tended to increase as dams got older. The pooled, within milk-group correlation between calf gain to 205 d and milk intake was .60. Calves suckling dams with low milk production relied earlier and to a greater extent on alternative food sources of lower nutritional value than milk. Calves suckling high milk-group dams had 16.9 kg greater 205-d weaning weight than those suckling low milk-group dams, solely because of differences in maternal environment. Calves from the high milk group maintained 63% of the advantage over those in the low milk group in 205-d weight through a fairly rapid postweaning growth period to slaughter.

Studies on a base population of mice were used to establish an index of components of litter size and a physiological model for measuring uterine capacity to be used subsequently in a selection experiment evaluating alternative methods for practicing selection to increase litter size. Heritability estimates of litter size, ovulation rate and ova success (fraction of ova resulting in fully formed pups) were .18, .33 and .15, respectively. No significant genetic or phenotypic correlation was found between overall ovulation rate and ova success. Phenotypic means and genetic variances were higher for characteristics measured on the right than on the left side of the reproductive tract. Linear and quadratic selection indexes, derived for a quadratic definition of breeding value, were compared. The linear index was predicted to be .99 as efficient as the quadratic one. Due to simplicity, the linear index (I = 1.21 x ovulation rate + 9.05 x ova success), scaled to have variance the same as litter size, was chosen for use. Ovulation rate in unilaterally ovariectomized females was .95 of that in females with both ovaries. No hypertrophy of the ipsilateral uterine horn in unilaterally ovariectomized females was found before implantation of embryos. Thus, unilateral ovariectomy appears to provide a physiological state to measure uterine capacity (as litter size) in the mouse.

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