L. A. Rempel

Genome-wide association study of swine farrowing traits. Part II: Bayesian analysis of marker data,

Reproductive efficiency has a great impact on the economic success of pork (sus scrofa) production. Number born alive (NBA) and average piglet birth weight (ABW) contribute greatly to reproductive efficiency. To better understand the underlying genetics of birth traits, a genome-wide association study (GWAS) was undertaken. Samples of DNA were collected and tested using the Illumina PorcineSNP60 BeadChip from 1,152 first parity gilts. Traits included total number born (TNB), NBA, number born dead (NBD), number stillborn (NSB), number of mummies (MUM), total litter birth weight (LBW), and ABW. A total of 41,151 SNP were tested using a Bayesian approach. Beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on the SSCX, SNP were assigned to groups of 5 consecutive SNP by chromosome-position order and analyzed again using a Bayesian approach. From that analysis, 5-SNP groups were selected having no overlap with another 5-SNP groups and no overlap across chromosomes. These selected 5-SNP non-overlapping groups were defined as QTL. Of the available 8,814 QTL, 124 were found to be statistically significant (P < 0.01). Multiple testing was considered using the probability of false positives. Eleven QTL were found for TNB, 3 on SSC1, 3 on SSC4, 1 on SSC13, 1 on SSC14, 2 on SSC15, and 1 on SSC17. Statistical testing for NBA identified 14 QTL, 4 on SSC1, 1 on SSC4, 1 on SSC6, 1 on SSC10, 1on SSC13, 3 on SSC15, and 3 on SSC17. A single NBD QTL was found on SSC11. No QTL were identified for NSB or MUM. Thirty-three QTL were found for LBW, 3 on SSC1, 1 on SSC2, 1 on SSC3, 5 on SSC4, 2 on SSC5, 5 on SSC6, 3 on SSC7, 2 on SSC9, 1 on SSC10, 2 on SSC14, 6 on SSC15, and 2 on SSC17. A total of 65 QTL were found for ABW, 9 on SSC1, 3 on SSC2, 9 on SSC5, 5 on SSC6, 1 on SSC7, 2 on SSC8, 2 on SSC9, 3 on SSC10, 1 on SSC11, 3 on SSC12, 2 on SSC13, 8 on SSC14, 8 on SSC15, 1 on SSC17, and 8 on SSC18. Several candidate genes have been identified that overlap QTL locations among TNB, NBA, NBD, and ABW. These QTL when combined with information on genes found in the same regions should provide useful information that could be used for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.

Association analyses of candidate single nucleotide polymorphisms on reproductive traits in swine.

The ability to identify young females with superior reproduction would have a large economic impact on commercial swine production. Previous studies have discovered SNP associated with economically important traits such as litter size, growth rate, and feed intake. The objective of this study was to test for association of candidate SNP with sow prolificacy reproductive traits in gilts of a Landrace-Duroc-Yorkshire composite population. Association analyses regressed additive (A), dominant (D), and imprinting (I) SNP effects on each trait with an animal model. A carnitine palmitoyltransferase 1A SNP and a glycogen synthase 1 SNP were associated with age at puberty (AP; D = 10 d; P = 0. 0037 and A = 3.8 d; P = 0.0078, respectively). Four IGF2 SNP were associated with AP as well, having additive or dominant effects (3.2 to 5.8 d; P < or = 0.0052). Two mannosidase 2B2 SNP and 2 prolactin receptor (PRLR) SNP were also associated with AP. Solute carrier 22, subfamily member 5 SNP was weakly associated with AP (D = 3.9 d; P < 0.10). Polymorphisms within glycogen synthase 1 and protein kinase AMP-activated, gamma 3 noncatalytic subunit had associations with ovulation rate. Estrogen receptor (ESR) 1, ESR2, PPAR gamma coactivator 1, and IGFBP3 SNP were significantly associated with weaning-to-estrus interval. Two PRLR SNP were associated with total number of piglets born (A = 0.57 piglets; P = 0.0095 and D = 0.61 piglets; P = 0.0016, respectively). A SNP within PRLR was also associated with number of piglets born alive (D = 0.61; P = 0.0016). The PPAR gamma coactivator 1 SNP was associated with total number of piglets born (D = 0.38 piglets; P = 0.0391) and number of piglets born alive (D = 0.53 piglets; P = 0.0032). The SNP within ESR1 (A = 0.65 piglets; P = 0.0950), ESR2 (A = -0.33 piglets; P = 0.0176), IGF2 SNP (A = -0.26 piglets; P = 0.0032), and IGFBP3 SNP (D = 0.35 piglets; P = 0.0683) were associated with number of piglets born dead. A leptin SNP was associated with mummified fetuses (D = 0.09 piglets; P = 0.0978). Many of the SNP analyzed in this study are from genes involved in regulation of metabolism, suggesting that there is an important link between physiological events associated with reproduction and energy utilization. Furthermore, these production and growth trait SNP may serve to assist in selection of young females for superior reproductive performance.

Genome-wide association study of swine farrowing traits. Part I: genetic and genomic parameter estimates.

The primary objective of this study was to determine genetic and genomic parameters among swine (Sus scrofa) farrowing traits. Genetic parameters were obtained using MTDFREML. Genomic parameters were obtained using GENSEL. Genetic and residual variances obtained from MTDFREML were used as priors for the Bayes C analysis of GENSEL. Farrowing traits included total number born (TNB), number born alive (NBA), number born dead (NBD), number stillborn (NSB), number of mummies (MUM), litter birth weight (LBW), and average piglet birth weight (ABW). Statistically significant heritabilities included TNB (0.09, P = 0.048), NBA (0.09, P = 0.041), LBW (0.20, P = 0.002), and ABW (0.26, P < 0.0001). Statistically significant genetic correlations included TNB-NBA (0.97, P < 0.0001), TNB-LBW (0.74, P < 0.0001), NBA-LBW (0.56, P < 0.0017), NSB-LBW (0.87, P < 0.0395), and LBW-ABW (0.63, P < 0.0002). Genetic parameters are similar to others found in the literature. The proportion of phenotypic variance explained by genomic markers (GP) generated by GENSEL was TNB (0.04), NBA (0.06), NBD (0.00), NSB (0.01), MUM (0.00), LBW (0.11), and ABW (0.31). Limited information is available in the literature about genomic parameters. Only the GP estimate for NSB is significantly lower than what has been published. The GP estimate for ABW is greater than the estimate for heritability found in this study. Other traits with significant heritability had GP estimates half the value of heritability. This research indicates that significant genetic markers will be found for TNB, NBA, LBW, and ABW that will have either immediate use in industry or provide a roadmap to further research with fine mapping or sequencing of areas of significance. Furthermore, these results indicate that genomic selection implemented at an early age would have similar annual progress as traditional selection, and could be incorporated along with traditional selection procedures to improve genetic progress of litter traits.

Relationships between day one piglet serum immunoglobulin immunocrit and subsequent growth, puberty attainment, litter size, and lactation performance

Colostrum affects gut and uterine gland development in the neonatal piglet, suggesting that subsequent growth and reproductive performance may be affected. Measuring immunoglobulin in piglet serum using the immunoglobulin immunocrit on Day 1 of age provides a simple, inexpensive indication of the amount of colostrum acquired by the piglet in the first day of life. Relationships between serum immunoglobulin immunocrit measures and subsequent growth rates, age at puberty, incidence of puberty failure, litter size, and lactation performance were examined in pigs born and subsequently farrowing between 2009 and 2013. Immunoglobulin immunocrit measures were collected on 16,762 piglets on Day 1 of age. Of these piglets, BW measurements were available from 15,324 (7,684 males and 7,640 females) piglets at a range of ages from weaning to 200 d of age, allowing an assessment of growth rates. Age at puberty was recorded from a subset of 2,857 of the females after observing them for estrous behavior from approximately 170 to 250 d of age. To examine relationships between d 1 immunocrit and puberty failure, gilts with immunocrit measures that failed to reach puberty (n = 119) were matched with littermate gilts with immunocrit measures that achieved puberty (n = 167). Similarly, number born alive was collected on a subset (n = 799) of females from first to fourth parities for which d 1 immunocrits were measured on them as neonates. Finally, d 1 immunocrit effect on adult lactational competence was assessed by measuring litter average (offspring of 440 females) and litter average piglet preweaning growth rate (offspring of 774 females) in females where d 1 immunocrits were available from them as neonates. Results indicated that low d 1 immunocrits were subsequently associated with reduced growth (P < 0.01), increased age at puberty (P < 0.01), reduced number born alive (P < 0.05), reduced litter average immunocrit (P < 0.05), and reduced litter average preweaning growth rate during lactation (P < 0.05). This suggests that management efforts to improve the amount of colostrum ingested by neonatal piglets would result in beneficial changes in production efficiency, particularly for gilts destined for the breeding herd. It also suggests that the immunoglobulin immunocrit can be useful in monitoring colostrum ingestion to maximize the beneficial effects of colostrum on subsequent performance.

Identification of an ionotropic glutamate receptor AMPA1/GRIA1 polymorphism in crossbred beef cows differing in fertility

A proposed functional polymorphism in the ionotropic glutamate receptor AMPA1 (GRIA1) has been reported to influence antral follicle numbers and fertility in cows. Repeat breeder cows that fail to produce a calf in multiple seasons have been reported to have reduced numbers of small (1 to 3 mm) antral follicles in their ovaries. Therefore, we tested the hypothesis that this GRIA1 polymorphism was affecting antral follicle numbers in repeat breeder cows. Repeat breeder cows (n = 64) and control cows (n = 72) that had always produced a calf were housed in a dry lot and observed twice daily for behavioral estrus. Blood samples were collected, and cows were genotyped for this GRIA1 polymorphism and for a polymorphism in the GnRH receptor (GnRHR) that was proposed to influence age at puberty. On d 3 to 8 after estrus cows were slaughtered, and reproductive organs were collected to determine antral follicle count, ovary size, and uterine horn diameter. Repeat breeder cows were older at first calving than control cows (P = 0.006). The length (P = 0.03) and height (P = 0.02) of the ovary contralateral to the corpus luteum (CL) were greater in control cows than repeat breeder cows. The endometrial diameter in the horn ipsilateral to the CL was greater in the control cows than the repeat breeder cows. Repeat breeder cows had fewer small (1 to 5 mm) antral follicles than control cows (P = 0.003); however, there was no association between GRIA1 genotype and antral follicle number. The GnRHR polymorphism was associated with age at first calving because cows that were homozygous for the C allele had a greater age at first calving than heterozygous cows or cows that were homozygous for the T allele (P = 0.01). In the granulosa cells from small (1 to 5 mm) antral follicles, mRNA abundances of 2 markers of oocyte quality, anti-Müllerian hormone and pentraxin 3, did not differ between fertility groups (P ≥ 0.12). We conclude that this GRIA1 polymorphism exists in beef cows but that it does not influence antral follicle numbers. The association between GnRHR genotype and age at first calving is likely not causal as this polymorphism is not functional. The utility of this polymorphism as a genetic marker for early conception in heifers will require further validation. Screening postpartum cows by ultrasonography to determine antral follicle numbers may aid in making culling decisions.

Uterine and placenta characteristics during early vascular development in the pig from day 22 to 42 of gestation

Insufficient placenta development is one of the primary causes of fetal death and reduced fetal growth after 35 days of gestation. Between day 22 and 42 the placenta consists of a central highly vascular placenta (HVP), adjacent to the fetus, a less vascular placenta (LVP), on either side of the fetus, and necrotic tips (NT). The objective of this study was to comprehensively evaluate uterine-placenta characteristics during early gestation in the gilt and determine time points and physiological changes. Gilts (n=25) were artificially inseminated at first detection of estrus (day 0) and 24h later, and harvested at 22, 27, 32, 37 or 42 days of gestation. Litter size, 12.1±3.4, was similar for all days of gestation. Fetal and placenta weight increased with day of gestation. The greatest increase in placenta weight occurred between 37 and 42 days of gestation. The LVP zones had no measurable fold formation until day 27. Necrotic tips became apparent after 27 days of gestation. Unoccupied areas of the uterus developed folds with changes in endometrial cell size and morphology from day 32 to 42 of gestation. Limited changes occurred in either fetal growth or placenta weight from day 27 through 32 of gestation; however, significant morphological changes occur at the maternal-fetal interface, demonstrating the dynamic architecture of the developing porcine placenta during early gestation. This work establishes fundamental time points in placenta development corresponding to fetal growth and microfold formation that may influence fetal growth and impact fetal survival.

Genetic parameter estimates among scale activity score and farrowing disposition with reproductive traits in swine.

The primary objective of this study was to determine if certain behavior traits were genetically correlated with reproduction. If 1 or both of the behavior traits were found to be correlated, a secondary objective was to determine if the behavior traits could be useful in selecting for more productive females. A scale activity score taken at 5 mo of age and a farrowing disposition score taken at farrowing were selected as the behavioral traits. Scale activity score ranged from 1 to 5 and farrowing disposition ranged from 1 to 3. Reproductive traits included age at puberty, number born alive, number born dead, litter birth weight, average piglet birth weight, number weaned, litter weaning weight, average weaning weight, wean-to-estrus interval, ovulation rate including gilts, and postweaning ovulation rate. Genetic correlations between scale activity score and reproduction ranged from -0.79 to 0.61. Three of the correlations, number born alive (P < 0.01), average piglet birth weight (P < 0.001), and wean-to-estrus interval (P = 0.014), were statistically significant but included both favorable and antagonistic correlations. In contrast, all but 1 of the farrowing disposition correlations was favorable and ranged from -0.66 to 0.67. Although only the correlation with litter birth weight was significant (P = 0.018), the consistent favorable direction of all farrowing disposition correlations, except average weaning weight, shows a potential for inclusion of farrowing disposition into a selection program.

Litter-of-origin trait effects on gilt development

The preweaning litter environment of gilts can affect subsequent development. In a recent experiment designed to test the effects of diet on gilt development, litter-of-origin traits including individual birth weights, immunocrits (a measure of colostrum intake), sow parity, number weaned, and individual weaning weights were collected for approximately 1,200 gilts that were progeny of approximately 300 sows. Subsequently, BW, LM area, and backfat were measured at 100 d of age and at 28-d intervals until slaughter (260 d of age). From 160 d of age to slaughter, gilts were observed daily for estrus. At slaughter, the reproductive tract and 1 mammary gland were recovered. The reproductive tract was classified as cyclic or prepubertal; the number of corpora lutea was counted. Uterine horn lengths and ovarian dimensions were measured. Uterus and ovary samples from every 10th gilt were prepared for histological evaluation of uterine gland development and follicle counts, respectively. Mammary gland tissue protein and fat were assayed. Day of the estrous cycle at slaughter was calculated using the first day of the most recent standing estrus (d 0) recorded previous to slaughter. Each gilt development trait was analyzed for association with each litter-of-origin trait, after adjusting for dietary treatment effects. Uterine length, ovarian dimensions, mammary gland protein and fat, and uterine gland development were also adjusted for day of the estrous cycle at slaughter. All litter-of-origin traits were associated ( < 0.05) with growth traits. Top-down (backward elimination) multiple regression analysis indicated that BW and LM accretion in gilts was positively associated with immunocrit ( < 0.01), birth weight ( < 0.01), preweaning growth rate ( < 0.01), and parity ( < 0.01). Backfat accretion was positively associated with preweaning growth rate ( < 0.01), number weaned ( < 0.05), and parity ( < 0.05). Age at puberty was associated with birth weight (positive; < 0.01) and preweaning growth rate (negative; < 0.01). Total uterine length was positively associated with only birth weights ( < 0.05). Mammary gland protein was negatively associated with preweaning growth ( < 0.01). Mammary gland fat was positively associated with birth weight and number of piglets weaned ( > 0.05). These results indicate that colostrum consumption, birth weights, preweaning growth rate, number weaned, and parity are associated with gilt development traits during later life.

Effect of creatine supplementation during the last week of gestation on birth intervals, stillbirth, and preweaning mortality in pigs1

We hypothesized that creatine supplementation would reduce birth intervals, stillbirth rate, and preweaning survival in pigs because of its reported improvement of athletic performance in humans. In Exp. 1, gilts (n = 42) and first parity sows (n = 75) were mated at estrus. Beginning on d 110 of gestation, dams received either no treatment or 20 g creatine daily until farrowing. At farrowing in November 2008, pigs were monitored by video camera to determine individual piglet birth intervals. On d 1, piglets were weighed, euthanized, and the cerebellum, brain stem, and spinal cord were collected from the largest and smallest piglets in each litter to measure myelin basic proteins, myelin cholesterol, glucocerebrosides, phosphatidylethanolamine, phosphatidylcholine, and sphingomyelin. Preweaning mortality of the remaining piglets was recorded, including whether a piglet had been overlayed by the dam. A second experiment was performed using gilts (n = 90), farrowing in July 2010, to test differential effects of creatine supplementation during hot, humid weather when dams typically have more difficulty farrowing. Once again, gilts were provided either no supplementation or 20 g creatine daily from d 110 to the day of farrowing. Gilts were video recorded during farrowing, piglets were weighed on d 1, and preweaning mortality (including overlays) was recorded. In Exp. 1, creatine supplementation had no effect on birth intervals or stillbirth rate. Creatine supplementation improved the amount of myelin lipids in brain regions of piglets, particularly the brain stem. Creatine supplementation also reduced overlays of low birth weight piglets from gilts but not second parity sows. Data from Exp. 2 were combined with gilt data from Exp. 1 to examine the effect of creatine, season, and their interaction. There were no effects of treatment or season on birth intervals, stillbirth rates, or overall preweaning mortality. Creatine treatment reduced the incidence of overlays in low birth weight piglets in the combined data set. These results suggest that creatine supplementation improved myelination and may reduce the incidence of low birth weight piglets being crushed by the dam.

Effect of essential fatty acid and zinc supplementation during pregnancy on birth intervals, neonatal piglet brain myelination, stillbirth, and preweaning mortality,

Omega fatty acids and zinc contribute to physiological pathways that could affect the farrowing process, stillbirth, preweaning mortality, and postweaning return to estrus. To determine effects of omega fatty acids and zinc on these reproductive traits, gilts were mated and fed either a control diet, a diet supplemented with 1.09% Gromega, a diet supplemented with 0.07% zinc sulfate, or a diet supplemented with both Gromega and zinc sulfate from d 80 of gestation until farrowing. Farrowings were video recorded to obtain birth intervals for each piglet, and the number of live and stillborn piglets was recorded. On d 1 after farrowing, piglets were weighed, and the smallest piglet in each litter was sacrificed. A blood sample was collected to measure the immunoglobulin immunocrit ratio, and brain, cerebellum, brain stem, full and empty stomach (to calculate stomach content weight), and heart weights were recorded. Because myelination of specific brain regions may affect preweaning mortality, brain stem, cerebellum, and spinal cord tissues were measured for content of myelin basic proteins and myelin lipids. For remaining piglets, survival to weaning and weaning weights were recorded. Results indicated a weak positive correlation (r = 0.23, P < 0.05) between immunocrit values and brain stem high molecular weight myelin basic protein. There was also a Gromega × zinc supplementation interaction (P < 0.05) on brain stem high molecular weight myelin basic protein in which the combined treatment was greater than the control or each supplement alone. Zinc treatment decreased stillbirth rate during prolonged farrowing and subsequent preweaning survival of low birth weight piglets. Gromega increased overall stillbirth rate and increased the stillbirth rate during prolonged farrowing. There were no relationships between myelin measurements and preweaning survival. In conclusion, combined Gromega and zinc supplementation appeared to improve myelination, but zinc alone improved stillbirth and preweaning survival.