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.

Characterizing linkage disequilibrium in pig populations.

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.

Detection of kallikrein gene expression and enzymatic activity in porcine endometrium during the estrous cycle and early pregnancy.

Porcine conceptuses rapidly elongate within the uterine horns prior to the period of placental attachment. During the time of elongation, secretion of estrogen by the developing conceptuses occurs for the establishment of pregnancy through maintenance of corpora lutea and facilitation of placental attachment. Factors associated with the uterine luminal epithelium accentuate embryo attachment by allowing close contact between the conceptus and the uterine epithelium.

Plasma cholecystokinin-8 in pigs with divergent genetic potential for feed intake and growth.

Plasma cholecystokinin-8 (CCK-8) was studied in pigs with divergent genetic potential for feed intake. Differences in feed intake resulted from selection for either fast (line F) or slow (line S) postweaning gain. The hypothesis was that the relatively lesser feed intake in S versus F may be attributable, in part, to greater circulating concentrations of the putative satiety hormone CCK-8.

Mapping genomic regions associated with growth rate in pigs.

The objective of this study was to identify genomic regions associated with postweaning average daily gain (ADG) in swine. Two families were produced using sires obtained from the cross of lines divergently selected for high and low growth rate. Sires were mated to 29 unrelated dams that produced 124 and 115 offspring.

Relationship of growth hormone and insulin-like growth factor-1 genotypes with growth and carcass traits in swine.

The contribution of chromosomal regions linked to growth hormone (GH) and insulin-like growth factor-1 (IGF-1) loci to variation in preweaning average daily gain, postweaning average daily gain (ADG), 10th rib backfat, loin-eye area and muscle pH were evaluated. Offspring of four purebred sires (A-D; n = 150, 195, 148 and 136, respectively) and two cross-bred sires (E and F; n = 157 and 145, respectively) were genotyped initially with GH and IGF-1 markers. When results of single marker analysis suggested possible linkage with a quantitative trait locus (QTL), additional flanking markers were typed for the family and interval mapping was performed.

Polymerase chain reaction-based polymorphisms in the porcine cholecystokinin (CCK) gene and assignment to chromosome 13.

Polymorphisms were identified in the porcine cholecystokinin (CCK) gene by digestion of products from polymerase chain reaction (PCR) with the restriction enzyme DpnII. Individuals from the European pig gene mapping project (PiGMaP) consortium reference families (eight full-sib families, 91 total progeny) were genotype to determine linkage relationships between the CCK gene and previously mapped loci. Linkage analysis revealed that the CCK gene is located on porcine chromosome 13.

Quantitative genetics of transgenic mice: components of phenotypic variation in body weights and weight gains.

Transgenic mice possessing an ovine growth hormone gene were used to study the effects of elevated growth hormone on quantitative genetic variation. Males hemizygous for the transgene were mated to wild-type females to produce half- and full-sib families in which approximately half the progeny were transgenic and half were wild type. Analyses of body weights at 3-10 weeks, and weight gains from 3 to 6, and 6 to 10 weeks produced estimates of the proportion of total variance due to additive genetic effects (h2) and common litter effects (c2), and the genetic correlation between transgenic and wild-type expression of each trait.

Estimates of heritabilities and genetic and environmental correlations for left- and right-side uterine capacity and ovulation rate in mice.

Heritabilities for and genetic and environmental correlations between uterine capacity, ovulation rate, and body mass (BM) were estimated in mice. Uterine capacity was defined as the number of fetuses (LUC or RUC for left or right side) in one uterine horn for unilaterally ovariectomized females. Ovulation rate (corpora lutea, LCL or RCL for left or right ovary) was measured on the remaining single ovary in these same females.

Effect of divergent selection for postweaning average daily gain on front-end soundness of market-weight pigs.

A total of 975 barrows and gilts from lines divergently selected for postweaning ADG were evaluated for front-end structural soundness (scored on a scale from 1, extreme leg weakness, to 8, superior leg structure) at approximately 100 kg, as well as growth performance and backfat thickness. Selection was for either fast (line F) or slow (line S) ADG from 9 wk of age to 100 kg and was replicated in spring- and fall-farrowing groups. The cumulative divergent selection differential corresponding to the animals evaluated was .

Plasma growth hormone, insulin-like growth factor I, and insulin-like growth factor binding proteins in pigs with divergent genetic merit for postweaning average daily gain.

Characteristics of growth hormone (GH), IGF-I, and IGF-binding proteins (IGFBP) were studied in gilts sampled from lines of pigs selected for either fast (line F, n = 14) or slow (line S, n = 14) postweaning ADG. Repeated blood samples were obtained from gilts (approximately 55 kg BW) during a period of feed deprivation and again during refeeding. Averaged across time, the difference in mean plasma GH concentrations of F and S gilts was not significant (7.

Uterine capacity and ovulation rate in mice selected 21 generations on alternative criteria to increase litter size.

After 21 generations of selection for alternative criteria to change litter size in mice, responses in uterine capacity and ovulation rate were evaluated. Females from Generations 22 and 23 were sampled from 12 lines, representing three replicates of four selection criteria: LS = direct selection on litter size; IX = selection on an index of ovulation rate and the proportion of ova shed that resulted in fully formed offspring; UT = selection on uterine capacity measured as litter size from females unilaterally ovariectomized at 4 wk of age; and LC = unselected control. All females in the present evaluation (a total of 1,932) were unilaterally ovariectomized (either left or right ovary excised) at 4 wk, mated at 9 wk, and killed at d 17 of gestation.

Effects of three methods of selection for litter size in mice on pre-implantation embryonic development.

Characteristics of preimplantation embryonic development to Day 3.5 of gestation were evaluated in lines of mice after 21 generations of selection for litter size or components of litter size. Selection criteria were direct selection for number born (LS), selection on an index of ovulation rate and the proportion of ova shed that resulted in fully formed pups (IX), selection for number born in unilaterally ovariectomized females as an indication of uterine capacity (UT), and an unselected control (LC).

Growth and carcass characteristics of pigs selected for fast or slow gain in relation to feed intake and efficiency.

Selection in pigs for either fast (line F) or slow (line S) postweaning gain was replicated in spring (SREP) and fall (FREP) farrowing groups. Littermate barrows were sampled from F and S during Generations 2, 3, and 4 of the SREP and Generation 3 of the FREP. Beginning at approximately 35 kg (OTWT), barrows were either allowed ad libitum access to feed (AL) or limited to a standard total feed intake (LIM).

Alternative methods of selection for litter size in mice: II. Response to thirteen generations of selection.

Selection was conducted on an index of components of litter size (I = 1.21 x ovulation rate + 9.05 x ova success; ovulation rate measured by number of corpora lutea and ova success measured as number of pups born + number of corpora lutea), on uterine capacity (measured as number of pups born to unilaterally ovariectomized dams) and on litter size concurrent with an unselected control for 13 generations.

Alternative methods of selection for litter size in mice: I. Characterization of base population and development of methods.

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, .