A genome-wide association study for gestation length in swine.

Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska-Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1-GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.

Long-term selection for litter size in swine results in shifts in allelic frequency in regions involved in reproductive processes.

High-density genotype data were analyzed in three lines of swine that express substantial variation in sow fertility to uncover regions of the genome potentially influenced during selection for litter size traits. The experimental lines examined include the Nebraska Index Line (NIL), which has been subjected to long-term selection for litter size; a control line derived from the same population that founded NIL; and a commercial Duroc × Hampshire (D × H) population, in which no selection for litter size was practiced. Regions of the genome potentially affected by selection for litter size traits in NIL were determined by multiple lines of evidence, including altered allelic frequency compared to the other lines, loss of heterozygosity and relative extended haplotype homozygosity. Additionally, a genome-wide association study for litter size traits was conducted in a population based on NIL and commercial maternal line genetics. Several genomic regions identified as putative signatures of selection overlapped with QTL for litter size traits. One of these regions, located on SSC2 (13-14 Mb), includes the candidate gene P2X3R, which plays a role in implantation and sustained release of hormones associated with reproductive processes. Sequencing identified synonymous SNPs in P2X3R that are fixed in NIL but polymorphic with nearly equal frequencies in the D × H line, indicating a potential role of P2X3R in sow fertility. These results suggest that data derived from these lines can help to uncover and understand a portion of the genetic variance associated with fertility traits in swine.

Evaluation of reduced subsets of single nucleotide polymorphisms for the prediction of age at puberty in sows.

Genomic information could be used efficiently to improve traits that are expensive to measure, sex limited or expressed late in life. This study analyzed the phenotypic variation explained by major SNPs and windows for age at puberty in gilts, an indicator of reproductive longevity. A genome-wide association study using 56, 424 SNPs explained 25.2% of the phenotypic variation in age at puberty in a training set (n = 820). All SNPs from the top 10% of 1-Mb windows explained 33.5% of the phenotypic variance compared to 47.1% explained by the most informative markers (n = 261). In an evaluation population, consisting of subsequent batches (n = 412), the predictive ability of all SNPs from the major 1-Mb windows was higher compared to the variance captured by the most informative SNP from each of these windows. The phenotypic variance explained in the evaluation population varied from 12.3% to 36.8% when all SNPs from major windows were used compared to 6.5-23.7% explained by most informative SNPs. The correlation between phenotype and genomic prediction values based on SNP effects estimated in the training population was marginal compared to their effects retrained in the evaluation population for all (0.46-0.81) or most informative SNPs (0.30-0.65) from major windows. An increase in genetic gain of 20.5% could be obtained if genomic selection included both sexes compared to females alone. The pleiotropic role of major genes such as AVPR1A could be exploited in selection of both age at puberty and reproductive longevity.

An application of MeSH enrichment analysis in livestock.

An integral part of functional genomics studies is to assess the enrichment of specific biological terms in lists of genes found to be playing an important role in biological phenomena. Contrasting the observed frequency of annotated terms with those of the background is at the core of overrepresentation analysis (ORA). Gene Ontology (GO) is a means to consistently classify and annotate gene products and has become a mainstay in ORA. Alternatively, Medical Subject Headings (MeSH) offers a comprehensive life science vocabulary including additional categories that are not covered by GO. Although MeSH is applied predominantly in human and model organism research, its full potential in livestock genetics is yet to be explored. In this study, MeSH ORA was evaluated to discern biological properties of identified genes and contrast them with the results obtained from GO enrichment analysis. Three published datasets were employed for this purpose, representing a gene expression study in dairy cattle, the use of SNPs for genome-wide prediction in swine and the identification of genomic regions targeted by selection in horses. We found that several overrepresented MeSH annotations linked to these gene sets share similar concepts with those of GO terms. Moreover, MeSH yielded unique annotations, which are not directly provided by GO terms, suggesting that MeSH has the potential to refine and enrich the representation of biological knowledge. We demonstrated that MeSH can be regarded as another choice of annotation to draw biological inferences from genes identified via experimental analyses. When used in combination with GO terms, our results indicate that MeSH can enhance our functional interpretations for specific biological conditions or the genetic basis of complex traits in livestock species.

Genome-wide analysis of TNF-alpha response in pigs challenged with porcine circovirus 2b.

Tumor necrosis factor alpha (TNF-α) is a pro-inflammatory cytokine with a role in activating adaptive immunity to viral infections. By inhibiting the capacity of plasmacytoid dendritic cells to produce interferon-α and TNF-α, porcine circovirus 2 (PCV2) limits the maturation of myeloid dendritic cells and impairs their ability to recognize viral and bacterial antigens. Previously, we reported QTL for viremia and immune response in PCV2-infected pigs. In this study, we analyzed phenotypic and genetic relationships between TNF-α protein levels, a potential indicator of predisposition to PCV2 co-infection, and PCV2 susceptibility. Following experimental challenge with PCV2b, TNF-α reached the peak at 21 days post-infection (dpi), at which time a difference was observed between pigs that expressed extreme variation in viremia and growth (P < 0.10). A genome-wide association study (n = 297) revealed that genotypes of 56,433 SNPs explained 73.9% of the variation in TNF-α at 21 dpi. Major SNPs were identified on SSC8, SSC10 and SSC14. Haplotypes based on SNPs from a SSC8 (9 Mb) 1-Mb window were associated with variation in TNF-α (P < 0.02), IgG (P = 0.05) and IgM (P < 0.13) levels at 21 dpi. Potential overlap of regulatory mechanisms was supported by the correlations between genomic prediction values of TNF-α and PCV2 antibodies (21 dpi, r > 0.22), viremia (14-21 dpi, P > 0.29) and viral load (r = 0.31, P < 0.0001). Characterization of the QTL regions uncovered genes that could influence variation in TNF-α levels as well as T- and B-cell development, which can affect disease susceptibility.

Genomic analysis of the differential response to experimental infection with porcine circovirus 2b.

Porcine circovirus type 2 (PCV2) is the etiological agent of a group of associated diseases (PCVAD) that affect production efficiency and can lead to mortality. Using different crossbred lines of pigs, we analyzed host genetic variation of viral load, immune response and weight change following experimental infection with a PCV2b strain (n = 386). Pigs expressed variation in the magnitude and initiation of viremia and immune response recorded weekly until 28 days post-infection. A higher viral load was correlated with weight gain (r = -0.26, P < 0.0001) and presence of PCV2-specific antibodies (IgM, r = 0.26-0.34, P < 0.0001; IgG, r = 0.17-0.20, P < 0.01). In genome-wide association analyses of the responses at different time points, the proportions of phenotypic variation explained by combined effects of 56 433 SNPs were 34.8-59.4% for viremia, 10.1-59.5% for antibody response and 5.6-14.9% for weight change. Relationships between genomic prediction of overall viral load and weight gain during the first weeks of challenge were negative (-0.21 and -0.24 respectively, P < 0.0001). Individuals that carried more favorable alleles across three SNPs on SSC9 (0.60 Mb) and SSC12 (6.8 and 18.2 Mb) partially explained this relationship, having lower viral load (P < 0.0001); lower viremia at day 14 (P < 0.0001), day 21 (P < 0.01) and day 28 (P < 0.05) and greater overall average daily gain during infection (ADGi ; P < 0.01), ADGi at week 3 (P < 0.001) and week 4 (P < 0.01). These additive genetic relationships could lead to molecular solutions to improve animal health and reduce production costs.

Genome-wide prediction of age at puberty and reproductive longevity in sows.

Traditional selection for sow reproductive longevity is ineffective due to low heritability and late expression of the trait. Incorporation of DNA markers into selection programs is potentially a more practical approach for improving sow lifetime productivity. Using a resource population of crossbred gilts, we explored pleiotropic sources of variation that influence age at puberty and reproductive longevity. Of the traits recorded before breeding, only age at puberty significantly affected the probability that females would produce a first parity litter. The genetic variance explained by 1-Mb windows of the sow genome, compared across traits, uncovered regions that influence both age at puberty and lifetime number of parities. Allelic variants of SNPs located on SSC5 (27-28 Mb), SSC8 (36-37 Mb) and SSC12 (1.2-2 Mb) exhibited additive effects and were associated with both early expression of puberty and a greater than average number of lifetime parities. Combined analysis of these SNPs showed that an increase in the number of favorable alleles had positive impact on reproductive longevity, increasing number of parities by up to 1.36. The region located on SSC5 harbors non-synonymous alleles in the arginine vasopressin receptor 1A (AVPR1A) gene, a G-protein-coupled receptor associated with social and reproductive behaviors in voles and humans and a candidate for the observed effects. This region is characterized by high levels of linkage disequilibrium in different lines and could be exploited in marker-assisted selection programs across populations to increase sow reproductive longevity.

A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei.

Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r(2)), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r(2) increased with decreasing inter-marker distance from approximately 80 cm, and increased more rapidly from approximately 30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.

A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei).

Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r(2)-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of L. vannamei.

Progress in reducing the pale, soft and exudative (PSE) problem in pork and poultry meat.

Research in the area of the pale, soft and exudative (PSE) pork and poultry meat is reviewed in this article with an emphasis on genetic, biochemical and metabolic factors contributing to the problem. Over the past five decades, there has been much more work in the pork meat area where a few genetic markers have been identified, and are currently used to remove susceptible animals from the herd. Some of the markers are linked to aberrant calcium regulation in the early postmortem muscle. The poultry industry is still not at the point of using genetic marker(s); however, some recent work has revealed several potential markers. The review also discusses environmental factors such as antemortem stress and early postmortem processing practices (e.g. chilling rate) that can influence the development and severity of the PSE phenomenon. Some of these factors are known to cause protein denaturation at the early stage of postmortem and directly contribute to poor water-holding capacity and inferior texture in fresh meat and later in processed products. A newer hypothesis suggesting that variation in protein oxidation, in response to antemortem stress and early postmortem tissue environment, can contribute to development of PSE pork is also discussed. Finally, a few recommendations for future work are proposed.

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 ( = 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 high-ranked 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 ( = 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 < 0.05) between gilts that became pubertal early (<155 d of age) and late (>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 (), 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 ( < 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.

New alleles in calpastatin gene are associated with meat quality traits in pigs.

Suggestive QTL affecting raw firmness scores and average Instron force, tenderness, juiciness, and chewiness on cooked meat were mapped to pig chromosome 2 using a three-generation intercross between Berkshire and Yorkshire pigs. Based on its function and location, the calpastatin (CAST) gene was considered to be a good candidate for the observed effects. Several missense and silent mutations were identified in CAST and haplotypes covering most of the coding region were constructed and used for association analyses with meat quality traits. Results demonstrated that one CAST haplotype was significantly associated with lower Instron force and cooking loss and higher juiciness and, therefore, this haplotype is associated with higher eating quality. Some of the sequence variation identified may be associated with differences in phosphorylation of CAST by adenosine cyclic 3', 5'-monophosphate-dependent protein kinase and may in turn explain the meat quality phenotypic differences. The beneficial haplotype was present in all the commercial breeds tested and may provide significant improvements for the pig industry and consumers because it can be used in marker-assisted selection to produce naturally tender and juicy pork without additional processing steps.

Genetic variation in two conserved local Romanian pig breeds using type 1 DNA markers.

Analysis of the genetic variation of an endangered population is an important component for the success of conservation. Animals from two local Romanian pig breeds, the Mangalitsa and Bazna, were analysed for variation at a number of genetic loci using PCR-based DNA tests. Polymorphism was assessed at loci which 1) are known to cause phenotypic variation, 2) are potentially involved in trait differences or 3) are putative candidate genes. The traits considered are disease resistance, growth, coat colour, meat quality and prolificacy. Even though the populations are small and the markers are limited to specific genes, we found significant differences in five of the ten characterised loci. In some cases the observed allele frequencies were interesting in relation to gene function and the phenotype of the breed. These breeds are part of a conservation programme in Romania and marker information may be useful in preserving a representative gene pool in the populations. The use of polymorphisms in type 1 (gene) markers may be a useful complement to analysis based on anonymous markers.