GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows

Genetic variants associated with traits such as age at puberty and litter size could provide insight into the underlying genetic sources of variation impacting sow reproductive longevity and productivity. Genomewide characterization and gene expression profiling were used using gilts from the University of Nebraska–Lincoln swine resource population (n = 1,644) to identify genetic variants associated with age at puberty and litter size traits. From all reproductive traits studied, the largest fraction of phenotypic variation explained by the Porcine SNP60 BeadArray was for age at puberty (27.3%). In an evaluation data set, the predictive ability of all SNP from highranked 1-Mb windows (1 to 50%), based on genetic variance explained in training, was greater (12.3 to 36.8%) compared with the most informative SNP from these windows (6.5 to 23.7%). In the integrated data set (n = 1,644), the top 1% of the 1-Mb windows explained 6.7% of the genetic variation of age at puberty. One of the high-ranked windows detected (SSC2, 12–12.9 Mb) showed pleiotropic features, affecting both age at puberty and litter size traits. The RNA sequencing of the hypothalami arcuate nucleus uncovered 17 differentially expressed genes (adjusted P \u3c 0.05) between gilts that became pubertal early (180 d of age). Twelve of the differentially expressed genes are upregulated in the late pubertal gilts. One of these genes is involved in energy homeostasis (FFAR2), a function in which the arcuate nucleus plays an important contribution, linking nutrition with reproductive development. Energy restriction during the gilt development period delayed age at puberty by 7 d but increased the probability of a sow to produce up to 3 parities (P \u3c 0.05). Identification of pleotropic functional polymorphisms may improve accuracy of genomic prediction while facilitating a reduction in sow replacement rates and addressing welfare concerns

The roles of age at puberty and energy restriction |in sow reproductive longevity: a genomic perspective

Approximately 50% of sows are culled annually with more than one-third due to poor fertility. Our research demonstrated that age at puberty is an early pre-breeding indicator of reproductive longevity. Age at puberty can be measured early in life, has a moderate heritability, and is negatively correlated with lifetime number of parities. Detection of age at puberty is tedious and time consuming and is therefore not collected by the industry, which limits genetic progress. Genomic prediction is a viable approach to preselect gilts that will express puberty early and have superior reproductive longevity. The hypothesis that genetic variants explaining differences in age at puberty also explain differences in sow reproductive longevity was tested. Phenotypes, genotypes, and tissues from the UNL resource population (n \u3e 1700) were used in genome-wide association analyses, genome, and RNA sequencing to uncover functional polymorphisms that could explain variation in puberty and reproductive longevity. A BeadArray including 56,424 SNP explained 25.2% of the phenotypic variation in age at puberty in a training set (n = 820). Evaluation of major windows and SNPs of subsequent batches of similar genetics (n = 412) showed that if all SNPs located in the major 1-Mb windows were tested, they explained a substantial amount of phenotypic variation (12.3 to 36.8%). Due to differences in linkage disequilibrium status, the most informative SNP from these windows explained a lower proportion of the variation (6.5 to 23.7%). To improve genomic predictive ability, the limited capability of BeadArray was enhanced by potential functional variants uncovered by genome sequencing of selected sires (n = 20; \u3e20X). There were 11.2 mil. SNPs and 2.9 mil. indels discovered across sires and reference genomes. The role of gene expression differences in explaining phenotypic variation in age at puberty was investigated by RNA sequencing of the hypothalamic arcuate nucleus (ARC) in gilts (n = 37) with different pubertal statuses. Seventy genes, including genes involved in reproductive processes, were differentially expressed between gilts with early and late puberty status (Padj \u3c 0.1). Dietary restriction of energy 3 mo before breeding delayed puberty by 7 d but improved the potential of a sow producing up to three parities (P \u3c 0.05). Energy restriction was associated with differential expression in 42 genes in the ARC, including genes involved in energy metabolism. This integrated genomic information will be evaluated in commercial populations to improve the reproductive potential of sows through genomic selection. This project is supported by AFRI Competitive grant no. 2013-68004-20370 from the USDA-NIFA. USDA is an equal opportunity provider and employer

QUANTIFICATION AND REPEATED MEASUREMENTS OF CONFORMATION TRAITS IN REPLACEMENT FEMALES TO OPTIMIZE SOW LONGEVITY

The objectives were to 1) assess the reliability of objective conformation trait measurements between evaluators, 2) evaluate effects of dietary energy and lysine during development and housing system during first gestation on longevity, reproductive performance, and conformation, 3) characterize conformation changes throughout life, 4) identify phenotypic associations between conformation and longevity, 5) estimate heritability of conformation traits, and 6) assess genetic relationships between conformation traits measured throughout life in sows. Sows (n = 622) were fed a standard, energy restricted, or standard energy with increased lysine diet during gilt development and housed in either a group pen or stall during first gestation. Conformation traits, including five body size traits, knee, hock, and pastern angles, rump slope, and foot directional position, were objectively measured at 16 time points between 112 days of age and parity 4 weaning. Three types of foot lesions were evaluated at the latter 14 time points. Intra-class correlations demonstrated objectively measured conformation traits are reliable between evaluators; they also improve consistency, encompass the full range of trait phenotypic values, and allow identification of small conformational differences. Energy restriction during development had favorable effects on performance, including increased feed intake and decreased body condition loss during lactation. Pen housing had detrimental effects on conformation, including steeper rumps and pasterns, more “toed out” rear feet, and increased foot lesion severity. Changes over time were observed for all conformation traits. Body size increased while knee and pastern angles decreased. A pattern of change following the gestation cycle was observed for several traits. Associations were identified between sow longevity and conformation traits, including body depth, height, knee angle, rear foot directional position, heel-sole cracks, and total rear foot lesions. Objectively measured conformation traits and foot lesions were heritable (median h2 = 0.11 to 0.37). Genetic correlations between body size traits, knee, hock, and pastern angles, and rump slope evaluated throughout life suggest these traits have the same genetic determinism from first to fourth gestation. Advisor: Benny E. Mot

Quantification and Repeated Measurements of Conformation Traits in Replacement Females to Optimize Sow Longevity

The objectives were to 1) assess the reliability of objective conformation trait measurements between evaluators, 2) evaluate effects of dietary energy and lysine during development and housing system during first gestation on longevity, reproductive performance, and conformation, 3) characterize conformation changes throughout life, 4) identify phenotypic associations between conformation and longevity, 5) estimate heritability of conformation traits, and 6) assess genetic relationships between conformation traits measured throughout life in sows. Sows (n = 622) were fed a standard, energy restricted, or standard energy with increased lysine diet during gilt development and housed in either a group pen or stall during first gestation. Conformation traits, including five body size traits, knee, hock, and pastern angles, rump slope, and foot directional position, were objectively measured at 16 time points between 112 days of age and parity 4 weaning. Three types of foot lesions were evaluated at the latter 14 time points. Intra-class correlations demonstrated objectively measured conformation traits are reliable between evaluators; they also improve consistency, encompass the full range of trait phenotypic values, and allow identification of small conformational differences. Energy restriction during development had favorable effects on performance, including increased feed intake and decreased body condition loss during lactation. Pen housing had detrimental effects on conformation, including steeper rumps and pasterns, more “toed out” rear feet, and increased foot lesion severity. Changes over time were observed for all conformation traits. Body size increased while knee and pastern angles decreased. A pattern of change following the gestation cycle was observed for several traits. Associations were identified between sow longevity and conformation traits, including body depth, height, knee angle, rear foot directional position, heel-sole cracks, and total rear foot lesions. Objectively measured conformation traits and foot lesions were heritable (median h2 = 0.11 to 0.37). Genetic correlations between body size traits, knee, hock, and pastern angles, and rump slope evaluated throughout life suggest these traits have the same genetic determinism from first to fourth gestation

GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows

Genetic variants associated with traits such as age at puberty and litter size could provide insight into the underlying genetic sources of variation impacting sow reproductive longevity and productivity. Genomewide characterization and gene expression profiling were used using gilts from the University of Nebraska–Lincoln swine resource population (n = 1,644) to identify genetic variants associated with age at puberty and litter size traits. From all reproductive traits studied, the largest fraction of phenotypic variation explained by the Porcine SNP60 BeadArray was for age at puberty (27.3%). In an evaluation data set, the predictive ability of all SNP from highranked 1-Mb windows (1 to 50%), based on genetic variance explained in training, was greater (12.3 to 36.8%) compared with the most informative SNP from these windows (6.5 to 23.7%). In the integrated data set (n = 1,644), the top 1% of the 1-Mb windows explained 6.7% of the genetic variation of age at puberty. One of the high-ranked windows detected (SSC2, 12–12.9 Mb) showed pleiotropic features, affecting both age at puberty and litter size traits. The RNA sequencing of the hypothalami arcuate nucleus uncovered 17 differentially expressed genes (adjusted P \u3c 0.05) between gilts that became pubertal early (180 d of age). Twelve of the differentially expressed genes are upregulated in the late pubertal gilts. One of these genes is involved in energy homeostasis (FFAR2), a function in which the arcuate nucleus plays an important contribution, linking nutrition with reproductive development. Energy restriction during the gilt development period delayed age at puberty by 7 d but increased the probability of a sow to produce up to 3 parities (P \u3c 0.05). Identification of pleotropic functional polymorphisms may improve accuracy of genomic prediction while facilitating a reduction in sow replacement rates and addressing welfare concerns

Effects of energy restriction during gilt development on milk nutrient profile, milk oligosaccharides, and progeny biomarkers.

An ongoing study at the University of Nebraska-Lincoln (which included 14 batches of gilts; n = 90 gilts/batch) demonstrated that energy restriction during the developmental period of a gilt increases longevity and may also have beneficial effects on progeny health and growth, particularly, parity 1 progeny. Therefore, we hypothesized that energy restriction during gilt development may affect milk nutrient profile, milk oligosaccharides (OS), and postnatal progeny biomarkers. During the development period, batch 14 gilts (n = 128, 8 gilts/pen) were fed 3 dietary treatments including the following: 1) Control diet formulated to NRC (2012) specifications (CTL); 2) Restricted (20% energy restriction via addition of 40% soy hulls; RESTR); and 3) CTL diet plus addition of crystalline amino acids equivalent to the SID Lys:ME of the RESTR diet (CTL+). All diets were fed ad libitum and applied in a 3-phase feeding regimen during gilt development (days 123 to 230 of age). Average daily feed intake was used to estimate daily metabolizable energy intake (Mcal/d) during each phase (Phase 1: 10.13, 6.97, 9.95; Phase 2: 11.25, 8.05, 10.94; and Phase 3: 9.47, 7.95,11.07) for CTL, RESTR, and CTL+, respectively. After 230 d of age, gilts were bred and fed a common diet. Milk samples were collected from batch 14 gilts (n = 7 per treatment) on days 0 and 14 postfarrowing for compositional analysis of N, CP, dry matter (DM), GE, insulin, and OS. Piglet blood samples (n = 6 piglets/gilt) were obtained on days 1 and 15 postfarrowing for quantification of glucagon-like peptide-2 (GLP-2) and insulin. No effects of developmental diet were observed for milk N, CP, DM, or GE; however, N, CP, DM, and insulin were increased (P < 0.05) on day 1 compared with day 14. A total of 61 different milk OS were identified. Milk OS profile was significantly different for neutral and acidic OS (P < 0.05) on day 0, but there were no significant differences on day 14. For piglet GLP-2, a treatment by day interaction was observed (P < 0.009); specifically, on day 1 GLP concentrations were greater (P < 0.001) in CTL+ compared with RESTR (6.73 vs. 1.21 ng/mL). For serum insulin, a treatment by day interaction was observed (P < 0.01); specifically, insulin in RESTR progeny was greater (P < 0.03) than CTL on day 1. In conclusion, nutritional management of the developing gilt may affect milk nutrient composition, milk OS profile, and piglet serum biomarkers