Physiological and genomic insight into neuroendocrine regulation of puberty in gilts.

The timing of pubertal attainment in gilts is a critical factor for pork production and is an early indicator of future reproductive potential. Puberty, defined as age at first standing estrus in the presence of a boar, is brought about by an escape from estrogen inhibition of the GnRH pulse generator, which allows for increasing LH pulses leading to the onset of cyclicity. The biological mechanisms that control the timing of these events is related to decreasing inhibitory signals with a concomitant increase in stimulatory signals within the hypothalamus. The roles of gamma-aminobutyric acid, endogenous opioid peptides, and gonadotropin-inhibitory hormone in negatively regulating gonadotropin secretion in gilts is explored. Developmental changes in stimulatory mechanisms of glutamatergic and kisspeptin neurons are important for increased LH pulsatility required for the occurrence of puberty in pigs. Age at first estrus of gilts is metabolically gated, and numerous metabolites, metabolic hormones, and appetite-regulating neurotransmitters have been implicated in the nutritional regulation of gonadotropin secretion. Leptin is an important metabolic signal linking body energy reserves with age at puberty in gilts. Leptin acting through neuropeptide Y and proopiomelanocortin neurons in the hypothalamus has important impacts on the function of the reproductive neurosecretory axis of gilts. Age at puberty in swine is heritable, and genomic analyses reveal it to be a polygenic trait. Genome-wide association studies for pubertal age in gilts have revealed several genomic regions in common with those identified for age at menarche in humans. Candidate genes have been identified that have important functions in growth and adiposity. Numerous genes regulating hypothalamic neuronal function, gonadotropes in the adenohypophysis, and ovarian follicular development have been identified and illustrate the complex maturational changes occurring in the hypothalamic-pituitary-ovarian axis during puberty in gilts.

Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data.

BACKGROUND: Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig. RESULTS: Across tissues, a total of 67,746 unique transcripts were observed, including 60.5% predicted protein-coding, 36.2% long non-coding RNA and 3.3% nonsense-mediated decay transcripts. On average, 90% of the splice junctions were supported by RNA-seq within tissue. A large proportion (80%) represented novel transcripts, mostly produced by known protein-coding genes (70%), while 17% corresponded to novel genes. On average, four transcripts per known gene (tpg) were identified; an increase over current EBI (1.9 tpg) and NCBI (2.9 tpg) annotations and closer to the number reported in human genome (4.2 tpg). Our new pig genome annotation extended more than 6000 known gene borders (5' end extension, 3' end extension, or both) compared to EBI or NCBI annotations. We validated a large proportion of these extensions by independent pig poly(A) selected 3'-RNA-seq data, or human FANTOM5 Cap Analysis of Gene Expression data. Further, we detected 10,465 novel genes (81% non-coding) not reported in current pig genome annotations. More than 80% of these novel genes had transcripts detected in > 1 tissue. In addition, more than 80% of novel intergenic genes with at least one transcript detected in liver tissue had H3K4me3 or H3K36me3 peaks mapping to their promoter and gene body, respectively, in independent liver chromatin immunoprecipitation data. CONCLUSIONS: These validated results show significant improvement over current pig genome annotations.

Porcine single nucleotide polymorphisms and their functional effect: an update.

OBJECTIVE: To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was published in 2017. This communication extends our previous work not only by utilizing genomic sequence from additional animals, but also by the use of the newly released Sscrofa 11.1 reference genome. RESULTS: A total of 26,850,263 high confidence SNP were identified, including 19,015,267 reported in our previously published results. Variation was detected in the coding sequence or untranslated regions (UTR) of 78% of the genes in the porcine genome: 1729 loss-of-function variants were predicted in 1162 genes, 12,686 genes contained 64,232 nonsynonymous variants, 250,403 variants were present in UTR of 15,739 genes, and 15,284 genes contained 90,939 synonymous variants. In total, approximately 316,000 SNP were classified as being of high to moderate impact (i.e. loss-of-function, nonsynonymous, or regulatory). These high to moderate impact SNP will be the focus of future genome-wide association studies.

A survey of single nucleotide polymorphisms identified from whole-genome sequencing and their functional effect in the porcine genome.

Genetic variants detected from sequence have been used to successfully identify causal variants and map complex traits in several organisms. High and moderate impact variants, those expected to alter or disrupt the protein coded by a gene and those that regulate protein production, likely have a more significant effect on phenotypic variation than do other types of genetic variants. Hence, a comprehensive list of these functional variants would be of considerable interest in swine genomic studies, particularly those targeting fertility and production traits. Whole-genome sequence was obtained from 72 of the founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the founding boars (12 Duroc and 12 Landrace) and 48 Yorkshire-Landrace composite sows. Sequence reads were mapped to the Sscrofa10.2 genome build, resulting in a mean of 6.1 fold (×) coverage per genome. A total of 22 342 915 high confidence SNPs were identified from the sequenced genomes. These included 21 million previously reported SNPs and 79% of the 62 163 SNPs on the PorcineSNP60 BeadChip assay. Variation was detected in the coding sequence or untranslated regions (UTRs) of 87.8% of the genes in the porcine genome: loss-of-function variants were predicted in 504 genes, 10 202 genes contained nonsynonymous variants, 10 773 had variation in UTRs and 13 010 genes contained synonymous variants. Approximately 139 000 SNPs were classified as loss-of-function, nonsynonymous or regulatory, which suggests that over 99% of the variation detected in our pigs could potentially be ignored, allowing us to focus on a much smaller number of functional SNPs during future analyses.

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.

Meta-analysis of genome-wide association from genomic prediction models.

Genome-wide association (GWA) studies based on GBLUP models are a common practice in animal breeding. However, effect sizes of GWA tests are small, requiring larger sample sizes to enhance power of detection of rare variants. Because of difficulties in increasing sample size in animal populations, one alternative is to implement a meta-analysis (MA), combining information and results from independent GWA studies. Although this methodology has been used widely in human genetics, implementation in animal breeding has been limited. Thus, we present methods to implement a MA of GWA, describing the proper approach to compute weights derived from multiple genomic evaluations based on animal-centric GBLUP models. Application to real datasets shows that MA increases power of detection of associations in comparison with population-level GWA, allowing for population structure and heterogeneity of variance components across populations to be accounted for. Another advantage of MA is that it does not require access to genotype data that is required for a joint analysis. Scripts related to the implementation of this approach, which consider the strength of association as well as the sign, are distributed and thus account for heterogeneity in association phase between QTL and SNPs. Thus, MA of GWA is an attractive alternative to summarizing results from multiple genomic studies, avoiding restrictions with genotype data sharing, definition of fixed effects and different scales of measurement of evaluated traits.

Implementing meta-analysis from genome-wide association studies for pork quality traits.

Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to small sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implemented by combining -scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [] and calpastatin []), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated, γ 3 noncatalytic subunit []). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial []) and for the objective measure of muscle redness, CIE a* (glycogen synthase 1, muscle [] and ferritin, light polypeptide []). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.

Age at puberty, ovulation rate, and uterine length of developing gilts fed two lysine and three metabolizable energy concentrations from 100 to 260 d of age.

The objective of this study was to determine the effect of ad libitum feeding diets differing in standard ileal digestible (SID) lysine and ME concentrations that bracket those fed to developing gilts in U.S. commercial settings. Average SID lysine and ME concentrations in diets currently fed to developing gilts were obtained from a poll of the U.S. commercial swine industry. Crossbred Large White × Landrace gilts (n = 1,221), housed in groups, were randomly allotted to 6 corn-soybean diets in a 2 × 3 factorial arrangement formulated to provided 2 SID lysine and 3 ME concentrations. Gilts received grower diets formulated to provide 1.02% (control = survey average) or 0.86% (control minus 15%) SID lysine and 2.94, 3.25, or 3.57 (survey average ME ± 10%) Mcal of ME/kg from 100 d of age until approximately 90 kg BW. Then, gilts were fed finisher diet containing 0.85% (control = survey average) or 0.73% (control minus 15%) SID lysine and 2.94, 3.26, or 3.59 (control ± 10%) Mcal of ME/kg until 260 d of age. Gilts were weighed, and backfat thickness and loin muscle area were recorded at the beginning of the trial and then every 28 d. Starting at 160 d of age, gilts were exposed daily to vasectomized boars and observed for behavioral estrus. At approximately 260 d of age, gilts were slaughtered and their reproductive tract was collected. Each reproductive tract was examined to determine whether the gilt was cyclic, the stage of estrus cycle, ovulation rate, and uterine length. Data were evaluated for normality and analyzed using mixed model methods. Average age at puberty was 193 d of age with a range from 160 to 265 d. When all gilts on trial at 160 d of age were included in the analysis, 91.0% reached puberty as determine by observation of standing estrus. Differences between dietary treatments on age at puberty or measurements of the reproductive tract were not detected. Growth rates to 160 d were not limiting for attainment of puberty in response to daily boar stimulation from 160 d.

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.

Genomewide association and identification of candidate genes for ovulation rate in swine.

Reproductive efficiency has a great impact on the economic success of pork production. Ovulation rate is an early component of reproduction efficiency and contributes to the number of pigs born in a litter. To better understand the underlying genetics of ovulation rate, a genomewide association study was undertaken. Samples of DNA were collected and tested using the Illumina Porcine SNP60 BeadChip from 1,180 females with ovulation measurements ranging from never farrowed to measurements taken after parity 2. A total of 41,848 SNP were tested using the Bayes C option of GenSel. After the Bayes C analysis, SNP were assigned to sliding windows of 5 consecutive SNP by chromosome-position order beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on SSCX. The 5-SNP windows were analyzed using the Predict option of GenSel. From the Predict analysis, putative QTL were selected having no overlap with other 5-SNP window groups, no overlap across chromosomes, and the highest genetic variation. These putative QTL were submitted to statistical testing using the bootstrap option of GenSel. Of the putative QTL tested, 80 were found to be statistically significant (P < 0.01). Ten QTL were found on SSC1, 12 on SSC2, 4 on SSC3, 8 on SSC4, 3 on SSC5, 3 on SSC6, 3 on SSC7, 4 on SSC8, 2 on SSC9, 4 on SSC10, 1 on SSC12, 4 on SSC13, 2 on SSC14, 4 on SSC15, 4 on SSC16, 6 on SSC17, 4 on SSC18, and 1 on SSCX. Sixteen QTL were found to be statistically significant at the P < 0.001 level. Six additional QTL were significant at the P = 0.001 level. These 22 QTL accounted for 71.10% of the total genetic variance. The most compelling candidate genes in these regions include Estrogen receptor 1, growth differentiation factor 9, and inhibin ßA. 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.

Genome-wide association with delayed puberty in swine.

An improvement in the proportion of gilts entering the herd that farrow a litter would increase overall herd performance and profitability. A significant proportion (10-30%) of gilts that enter the herd never farrow a litter; reproductive reasons account for approximately a third of gilt removals, with anestrous and failure to conceive the most common reasons for culling. Tools to select gilts for reproductive longevity through genomics or alternative phenotypes would be of great benefit to the producer. Ninety-one gilts that failed to display behavioral estrus by 240 days (cases) and 127 pubertal littermates (controls) were genotyped with the Illumina Porcine SNP60 Beadchip. One hundred and seventy-four SNPs with the most significant associations were genotyped in an additional 86 cases and 103 controls. Twelve of these associations were significant in the final analysis. The most significant (P < 1.5 × 10(-14) ) region associated with failure to attain puberty was on chromosome 4 surrounding the NHLH2 gene. Delayed pubertal development and age at first estrus have been associated with NHLH2 in mice. Because attainment of puberty is a complex trait, identifying genes that affect pubertal age would greatly contribute to our knowledge of reproductive development as well as overall fertility.

Genome-wide association of meat quality traits and tenderness in swine.

Pork quality has a large impact on consumer preference and perception of eating quality. A genome-wide association was performed for pork quality traits [intramuscular fat (IMF)], slice shear force (SSF), color attributes, purge, cooking loss, and pH] from 531 to 1,237 records on barrows and gilts of a Landrace-Duroc-Yorkshire population using the Illumina PorcineSNP60 BeadChip. Associations were detected using MTDFREML for all traits. Intramuscular fat had the greatest number of SNP associations, followed by pH, purge, cooking loss, shear force, and color. Two regions contained associations for multiple traits; one on SSC1 at 255 Mb near calcineurin subunit B (PPP3R2) was associated with SSF, moisture loss, and pH, and one on SSC6 from 28 to 29.5 Mb for purge and IMF containing the candidate genes glucose-6-phosphate isomerase (GPI) and KCTD15. Some of the other compelling candidate genes in regions associated with meat quality include CEBPA, SNAI1, and FAM132A for IMF, CAPN1 for SSF, GLUL for pH, and PRKAG3 and ITGB1 with cooking loss.

Effects of nesfatin-1 on food intake and LH secretion in prepubertal gilts and genomic association of the porcine NUCB2 gene with growth traits.

Nesfatin-1, a product of the nucleobindin 2 (NUCB2) gene, purportedly plays important roles in whole-body energy homeostasis. Experiments were conducted to determine how NUCB2 expression in fat depots may be controlled in the pig and to test the hypothesis that nesfatin-1 regulates appetite and LH secretion in the gilt. Prepubertal gilts were used to study expression of NUCB2 in fat and the effects of intracerebroventricular (i.c.v.) injection of nesfatin-1 on food intake and pituitary hormone secretion. Growing pigs (gilts and barrows at 22 wk of age, n = 1,145) or sexually mature gilts (n = 439) were used to test association of SNP in the NUCB2 gene with growth traits. The expression of NUCB2 was similar for subcutaneous fat compared with perirenal fat. An i.c.v. injection of the melanocortin-4 receptor agonist [Nle4, d-Phe7]-α-melanocyte-stimulating hormone did not alter expression of NUCB2 mRNA in the hypothalamus but reduced (P = 0.056) NUCB2 mRNA expression in subcutaneous fat. Short-term (7 d) submaintenance feeding reduced (P < 0.05) BW and did not alter expression of mRNA for NUCB2, visfatin, or leptin but increased (P < 0.05) expression of adiponectin mRNA in fat. Central injection of nesfatin-1 suppressed (P < 0.001) feed intake. Secretion of LH was greater (P < 0.01) after i.c.v. injection of nesfatin-1 than after saline. Single nucleotide polymorphisms in the porcine NUCB2 gene were not associated with adiposity of growing pigs or age at puberty in gilts but were associated (P < 0.05) with BW at puberty. These data indicate that NUCB2 is expressed in fat depots of the pig and that the level of expression is sensitive to stimulation of appetite-regulating pathways in the hypothalamus. It is confirmed herein that nesfatin-1 can regulate appetite in the pig and affect the gonadotropic axis of the prepubertal pig. Association of SNP in the porcine NUCB2 gene with BW at puberty suggests that regulation of appetite by nesfatin-1 in the pig affects growth, which may have important consequences for adult phenotypes.

The relationship of plasma urea nitrogen with growth traits and age at first estrus in gilts.

Gilts that reach puberty at an earlier age with more backfat have greater lifetime productivity. Increased growth rates generally promote earlier age at first estrus; however, an association of age at first estrus with discrete measures of body fatness remains controversial. We tested the hypothesis that metabolic state as determined by concentrations of plasma urea nitrogen (PUN), which reflect lean tissue growth, were correlated with age at first estrus. Blood samples were collected from gilts (n = 337) at 102, 123, and 145 d of age during development. Concentrations of albumin, creatinine, glucose, and PUN were determined. Body weight and backfat thickness were determined at each time point. From 130 to 240 d of age, gilts were monitored for first pubertal estrus. Concentrations of creatinine increased whereas concentrations of glucose decreased with increasing age (P < 0.0001). Concentrations of albumin and PUN remained relatively stable throughout development. Average daily BW gain (r = 0.22) and change in backfat thickness (r = 0.29) had a positive phenotypic correlation (P < 0.0001) with PUN at 145 d of age. Concentrations of PUN at 102 and 123 d of age were not phenotypically correlated with pubertal age, but there was a moderately negative phenotypic correlation (r = -0.22; P < 0.0001) of PUN at 145 d of age with age at first estrus along with a negative genetic correlation (r = -0.42). The relationship of PUN with age at first estrus shifted from liner to quadratic with advancing age. These data demonstrate that near the age at which gilts are selected for entry into the breeding unit, those with greater PUN have increased BW and backfat thickness and display pubertal estrus earlier but that PUN does not account for additional variation in age at first estrus beyond growth rate or backfat. It is concluded that PUN can be used to select gilts with increased efficiency of nutrient use without negatively impacting pubertal development.

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.

Association of single nucleotide polymorphism (SNP) markers in candidate genes and QTL regions with pork quality traits in commercial pigs.

Numerous reports have described genetic markers or genomic regions (QTL) associated with pork quality and/or palatability but few validation studies have been reported. Therefore, 156 SNP markers from 45 candidate genes and eight QTL regions were analyzed for association with pork quality and palatability traits from 888 pork loins. Loins were collected at three slaughter facilities and selected to represent a wide range of pork color, pH and marbling. Phenotypic data recorded included objective and subjective measures of color and marbling, purge loss, shear force, and cooking loss. Data were analyzed with SAS PROC MIXED where loin was fit as a random effect. Results indicated some of the markers tested should be useful in industry, while others are not segregating in all populations or linkage disequilibrium between markers and causative genetic variation fluctuates among populations limiting their universal utility. Genes with the largest effects on pork quality were MC4R, IGF2, CAST and PRKAG3.

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.

Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace × Chinese-European crossbred population.

Several quantitative trait loci (QTL) for different meat quality traits have been localized on the q arm of porcine chromosome 2 at position 55-78 cM. Association analyses were performed in a commercial Landrace × Chinese-European (LCE) crossbred population (n = 446) slaughtered at approximately 127 kg and an average age of 198 days with records for performance (growth, fat and meat accretion) and meat quality [intramuscular fat (IMF), Minolta L*, Minolta a*, Minolta b* and pH at 45 m]. Polymorphisms within positional candidate genes cloned from homologous regions on human chromosome 19, ubiquitin-like 5 (UBL5- AM950288:g.566G>A), resistin (RETN- AM157180:g.1473A>G causing substitution p.Ala36Thr), insulin receptor (INSR- AM950289:g.589T>C) and complement factor D (adipsin) (CFD- AM950287:g. 306C>T) were located at positions 62.1, 64.0, 68.0 and 70.7 cM respectively on the current USDA USMARC map of porcine chromosome 2 and had the following allele frequencies in the LCE: UBL5 566G - 0.57; RETN 1473G - 0.84; INSR 589C - 0.70; and CFD 306C - 0.73. The effects of alleles within the candidate genes on the recorded traits were estimated using an animal model. Significant effects (P < 0.05) were found for pH(45) in m. semimembranosus (m. sm.) (UBL5), IMF (RETN) and Minolta L* (RETN, CFD). Differences between phenotypic means of homozygotes at UBL5, RETN and either RETN or CFD explained 0.34 SD for pH(45) in m. sm., 0.47 SD for IMF and 0.68 SD for Minolta L* respectively. Suggestive effects (P < 0.10) on IMF (UBL5, CFD), Minolta a* (INSR, CFD) and Minolta b* (INSR) were also observed. Our results support the localization of further QTL for meat quality traits in this region and suggest that there are several genes affecting different meat quality traits.

Validation and fine mapping of a QTL for ovulation rate on swine chromosome 3.

Ovulation rate (OR) is an important component of litter size, but mutation(s) in gene(s) underlying OR QTL have yet to be identified in pigs. Markers within an OR QTL on SSC3 were genotyped in three white composite lines selected for ten generations for increased OR or uterine capacity (UC), with one line being an unselected control. Numbers of corpora lutea (CL) and UC (number of fully formed fetuses) were collected at approximately 105 days of gestation, as well as ovary weight (OW), uterine length (UL) and uterine weight (UW) measurements at 160 d of age in generation 12 and 13 females from all three lines. Six microsatellites and ten single nucleotide polymorphisms (SNPs; 0-42 cM) were genotyped in pigs from all lines of generations 11 through 13. The allele frequencies of 24269.1, SW2429, 7907.2 and 7637.2 were different (P < 0.01) in the OR line compared to the control line. A significant (P < 0.05) association of CL with 24269.1 (additive effect 0.65 ± 0.32) was detected, and additive genotypic effects approached significance for markers at 28 through 35 cM (16963.2, 27514.1 and SWR1637). Haplotyping of 7637.2 and 16963.2 (31 through 32 cM) identified a significant additive association of haplotype 1 with CL (-0.62 ± 0.30). These markers were also associated with OW (24296.1 and SWR1637), UL (16963.2, 27514.1 and haplotypes of 7637.2/16963.2) and UW (haplotypes of 7637.2/16963.2). This study verifies an OR QTL on SSC3. However, based on the data, it was concluded that there may be two genes, at 13 through 18 cM and 28 through 35 cM, controlling OR on SSC3p.