Sire Variation in the Severity of the Ham Halo Condition

A study was conducted to examine genetic variation in the ham halo condition. The distal portion of the biceps femoris was sampled by taking cores (2.54-cm diameter) from progeny (n = 1,016) from a Duroc meat quality–focused line. Commission Internationale de l ́Éclairage (CIE; “International Commission on Illumination”) color-space values (L*, a*, and b*) and myoglobin concentration were measured on the halo (“Halo”) and inside (“Inside”) portion of each core. The Halo portion of the biceps femoris had greater L* and b* and lesser a* and myoglobin content (all P < 0.001) than the Inside portion. Sires with 11 or more progeny were compared. The sire × muscle-location interaction affected (P < 0.001), L*, a*, and myoglobin concentration. Sire progeny groups differed for each trait in both portions of the muscle, but differences in the Halo portion of the muscle were not mirrored in the Inside portion of the muscle. Similarly, sire group affected the magnitude of the difference in L* (P = 1.4 × 10−4) and a* (P = 9.0 × 10−6) between the Halo and Inside portions of the muscle and tended (P = 0.08) to affect myoglobin content. However, the largest sire-group differences were not necessarily seen in the sires with the highest means for these attributes. Thus, selecting for myoglobin concentration, L*, or a* content in the Halo portion of the biceps femoris muscle would be an effective strategy for reducing the severity of the ham halo condition

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 proteincoding, 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′-RNAseq 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 \u3e 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

Evaluation of genotype quality parameters for \u3ci\u3eSowPro90\u3c/i\u3e, a new genotyping array for swine

Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations. Animals from research and commercial populations (n = 2,586) were genotyped for 103,476 SNPs included in SowPro90. To assess the quality of data generated, genotype concordance was evaluated between the SowPro90 and Porcine SNP60 BeadArray using a subset of common SNP (n = 44,708) and animals (n = 277). The mean genotype concordance rate per SNP was 98.4%. Differences in distribution of data quality were observed between the platforms indicating the need for platform specific thresholds for quality parameters. The optimal thresholds for SowPro90 (≥97% SNP and ≥93% sample call rate) were obtained by analyzing the data quality distribution and genotype concordance per SNP across platforms. At ≥97% SNP call rate, there were 42,151 SNPs (94.3%) retained with a mean genotype concordance of 98.6% across platforms. Similarly, ≥94% SNPs and ≥85% sample call rates were established as thresholds for Porcine SNP60 BeadArray. At ≥94% SNPs call rate, there were 41,043 SNPs (91.8%) retained with a mean genotype concordance of 98.6% across platforms. Final evaluation of SowPro90 array content (n = 103,476) at ≥97% SNPs and ≥93% sample call rates allowed retention of 89,040 SNPs (86%) for downstream analysis. The findings and strategy for quality control could be helpful in identifying consistent, high-quality genotypes for genomic evaluations, especially when integrating genotype data from different platforms

Genomic regions associated with kyphosis in swine

<p>Abstract</p> <p>Background</p> <p>A back curvature defect similar to kyphosis in humans has been observed in swine herds. The defect ranges from mild to severe curvature of the thoracic vertebrate in split carcasses and has an estimated heritability of 0.3. The objective of this study was to identify genomic regions that affect this trait.</p> <p>Results</p> <p>Single nucleotide polymorphism (SNP) associations performed with 198 SNPs and microsatellite markers in a Duroc-Landrace-Yorkshire resource population (U.S. Meat Animal Research Center, USMARC resource population) of swine provided regions of association with this trait on 15 chromosomes. Positional candidate genes, especially those involved in human skeletal development pathways, were selected for SNP identification. SNPs in 16 candidate genes were genotyped in an F2 population (n = 371) and the USMARC resource herd (n = 1,257) with kyphosis scores. SNPs in <it>KCNN2 </it>on SSC2, <it>RYR1 </it>and <it>PLOD1 </it>on SSC6 and <it>MYST4 </it>on SSC14 were significantly associated with kyphosis in the resource population of swine (<it>P </it>≤ 0.05). SNPs in <it>CER1 </it>and <it>CDH7 </it>on SSC1, <it>PSMA5 </it>on SSC4, <it>HOXC6 </it>and <it>HOXC8 </it>on SSC5, <it>ADAMTS18 </it>on SSC6 and <it>SOX9 </it>on SSC12 were significantly associated with the kyphosis trait in the F2 population of swine (<it>P </it>≤ 0.05).</p> <p>Conclusions</p> <p>These data suggest that this kyphosis trait may be affected by several loci and that these may differ by population. Carcass value could be improved by effectively removing this undesirable trait from pig populations.</p

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.Fil: Bernal Rubio, Yeni Liliana. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Producción Animal; Argentina. Michigan State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gualdron Duarte, Jose Luis. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bates, R. O.. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Producción Animal; ArgentinaFil: Ernst, C. W.. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Producción Animal; ArgentinaFil: Nonneman, D.. United States Department of Agriculture. Agricultural Research Service; Estados UnidosFil: Rohrer, G. A.. United States Department of Agriculture. Agricultural Research Service; Estados UnidosFil: King, A.. United States Department of Agriculture. Agricultural Research Service; Estados UnidosFil: Shackelford, S. D.. United States Department of Agriculture. Agricultural Research Service; Estados UnidosFil: Wheeler, T. L.. United States Department of Agriculture. Agricultural Research Service; Estados UnidosFil: Cantet, Rodolfo Juan Carlos. Michigan State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Steibel, J. P.. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Producción Animal; Argentina. Michigan State University; Estados Unido

Transcriptomic Analysis for Pork Color—The Ham Halo Effect in Biceps Femoris

Pork color is a major indicator of product quality that guides consumer purchasing decisions. Recently, industryhas received an increase in consumer complaints about the lightness and nonuniformity of ham color, primarily lighter colorin the periphery termed “ham halo” that is not caused by manufacturing procedures. This effect is seen in fresh and processed hams and the outer lighter muscle is associated with lower myoglobin concentration, pH, and type I fibers. The objective of this study was to identify differences in gene expression profiles between light and normal-colored portions of the biceps femoris muscle from pork hams. RNA-sequencing (RNA-seq) was performed for paired light and normal-colored muscle samples from 10 animals showing the ham halo effect. Over 50 million paired-end reads (2×75 bp) per library were obtained. An average of 99.74% of trimmed high-quality reads was mapped to the Sscrofa 11.1 genome assembly. Differentially expressed genes (DEGs) were identified using both the DESeq2 and GFOLD software packages. A total of 14,049 genes were expressed in the biceps femoris; 13,907 were expressed in both light and normal muscle, while 56 and 86 genes were only expressed in light and normal muscle, respectively. Analysis with DESeq2 identified 392 DEGs with 359 genes being more highly expressed in normal-colored muscle. A total of 61 DEGs were identified in the DESeq2 analysis and identified in at least 7 of the 10 individual animal analyses. All 61 of these DEGs were up-regulated in normal-colored muscle. Gene Ontology enrichment analysis of DEGs identified the transition between fast and slow fibers and skeletal muscle adaptation and contraction as the most significant biological process terms. The evaluation of gene expression by RNA-seq identified DEGs between regions of the biceps femoris with the ham halo effect that are associated with variation in pork color

Synaptogyrin-2 influences replication of Porcine circovirus 2

Porcine circovirus 2 (PCV2) is a circular single-stranded DNA virus responsible for a group of diseases collectively known as PCV2 Associated Diseases (PCVAD). Variation in the incidence and severity of PCVAD exists between pigs suggesting a host genetic component involved in pathogenesis. A large-scale genome-wide association study of experimentally infected pigs (n = 974), provided evidence of a host genetic role in PCV2 viremia, immune response and growth during challenge. Host genotype explained 64% of the phenotypic variation for overall viral load, with two major Quantitative Trait Loci (QTL) identified on chromosome 7 (SSC7) near the swine leukocyte antigen complex class II locus and on the proximal end of chromosome 12 (SSC12). The SNP having the strongest association, ALGA0110477 (SSC12), explained 9.3% of the genetic and 6.2% of the phenotypic variance for viral load. Dissection of the SSC12 QTL based on gene annotation, genomic and RNA-sequencing, suggested that a missense mutation in the SYNGR2 (SYNGR2 p.Arg63Cys) gene is potentially responsible for the variation in viremia. This polymorphism, located within a protein domain conserved across mammals, results in an amino acid variant SYNGR2 p.63Cys only observed in swine. PCV2 titer in PK15 cells decreased when the expression of SYNGR2 was silenced by specific-siRNA, indicating a role of SYNGR2 in viral replication. Additionally, a PK15 edited clone generated by CRISPR-Cas9, carrying a partial deletion of the second exon that harbors a key domain and the SYNGR2 p.Arg63Cys, was associated with a lower viral titer compared to wildtype PK15 cells (\u3e24 hpi) and supernatant (\u3e48hpi)(P \u3c 0.05). Identification of a non-conservative substitution in this key domain of SYNGR2 suggests that the SYNGR2 p.Arg63Cys variant may underlie the observed genetic effect on viral load

Synaptogyrin-2 influences replication of Porcine circovirus 2

Porcine circovirus 2 (PCV2) is a circular single-stranded DNA virus responsible for a group of diseases collectively known as PCV2 Associated Diseases (PCVAD). Variation in the incidence and severity of PCVAD exists between pigs suggesting a host genetic component involved in pathogenesis. A large-scale genome-wide association study of experimentally infected pigs (n = 974), provided evidence of a host genetic role in PCV2 viremia, immune response and growth during challenge. Host genotype explained 64% of the phenotypic variation for overall viral load, with two major Quantitative Trait Loci (QTL) identified on chromosome 7 (SSC7) near the swine leukocyte antigen complex class II locus and on the proximal end of chromosome 12 (SSC12). The SNP having the strongest association, ALGA0110477 (SSC12), explained 9.3% of the genetic and 6.2% of the phenotypic variance for viral load. Dissection of the SSC12 QTL based on gene annotation, genomic and RNA-sequencing, suggested that a missense mutation in the SYNGR2 (SYNGR2 p.Arg63Cys) gene is potentially responsible for the variation in viremia. This polymorphism, located within a protein domain conserved across mammals, results in an amino acid variant SYNGR2 p.63Cys only observed in swine. PCV2 titer in PK15 cells decreased when the expression of SYNGR2 was silenced by specific-siRNA, indicating a role of SYNGR2 in viral replication. Additionally, a PK15 edited clone generated by CRISPR-Cas9, carrying a partial deletion of the second exon that harbors a key domain and the SYNGR2 p.Arg63Cys, was associated with a lower viral titer compared to wildtype PK15 cells (\u3e24 hpi) and supernatant (\u3e48hpi)(P \u3c 0.05). Identification of a non-conservative substitution in this key domain of SYNGR2 suggests that the SYNGR2 p.Arg63Cys variant may underlie the observed genetic effect on viral load

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 (P \u3c 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 (P \u3c 0.01), birth weight (P \u3c 0.01), preweaning growth rate (P \u3c 0.01), and parity (P \u3c 0.01). Backfat accretion was positively associated with preweaning growth rate (P \u3c 0.01), number weaned (P\u3c 0.05), and parity (P \u3c 0.05). Age at puberty was associated with birth weight (positive; P \u3c 0.01) and preweaning growth rate (negative; P \u3c 0.01). Total uterine length was positively associated with only birth weights (P \u3c 0.05). Mammary gland protein was negatively associated with preweaning growth (P\u3c 0.01). Mammary gland fat was positively associated with birth weight and number of piglets weaned (P \u3e 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

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