Signatures of Selection for Intramuscular Fat in Duroc Pigs

Intramuscular fat (IMF) content is an important trait affecting the quality of pork. Two Duroc populations (Iowa and Spain) selected for IMF were used to identify signatures of selection associated with IMF. The effects of selection were analyzed between two groups representing essentially select and control animals within each population using a discriminant analysis of principal components and Wright’s fixation index (FST) using 60k SNPs. Moreover, extended haplotype homozygosity-based approaches were used to examine the changes in haplotype frequency due to recent selection. New genomic regions have been identified by use of selection signatures and should provide useful information identification of genes involved in IMF and future selection

Identification of signatures of selection for intramuscular fat and backfat thickness in two Duroc populations

Intramuscular fat (IMF) content is an important trait affecting the quality of pork. Two Duroc populations, one under positive selection for IMF and the other selected for decreased backfat but under stabilizing selection for IMF, were used to identify signatures of selection associated with IMF using 60,000 single-nucleotide polymorphism data. The effects of selection were analyzed between 2 lines or groups representing selected and control animals within each population using a discriminant analysis of principal components and Wright’s fixation index (FST). Moreover, extended haplotype homozygosity-based approaches were used to examine the changes in haplotype frequency due to recent selection. Each statistical method identified 10–20 selection signatures. A few haplotype-based signatures of selection agreed with results from a genome-wide association study (GWAS), while FST measures showed a better agreement with GWAS results. Agreement of marker-trait associations and signatures of selection was limited, and further examination will be necessary to understand the effect of selection on IMF and why some regions identified by GWAS did not appear to respond to the selection practiced. The genes in 21 consensus selection signatures were examined. Several genes with an effect on overall fatness were identified, but further research is needed to assess whether or not some of them could have a specific effect on IMF

Genetic differences in the frequency of the hinge variants of porcine IgA is breed dependent

The distribution of the IgAa and IgAb alleles of porcine IgA in over 160 randomly-selected animals revealed an abundance of heterozygotes but only two b/b homozygotes. Since the IgAb allotype is a splice site mutant lacking two-thirds of the hinge, this study tests the hypothesis that pigs with this genotype may be at a selective disadvantage while heterozygous individuals may be at some advantage. This hypothesis was tested by collecting data on 374 animals of known breed and often parentage. We show here that when breed was not considered, young animals of known parentage had genotypic frequencies identical to that expected for Mendelian alleles but that a/b heterozygotes were overrepresented in adults. However, when analyzed with regard to breed, a very strong association between breed and the frequency of the IgAa and IgAb alleles was discovered. Meishan and NIH minipigs were homozygous for IgA while heterozygotes predominated in Berkshire, Chester White, Durocs, Hampshire and Landrace. Animals homozygous for IgAb were best represented in the White Cross line. We show here that this very strong breed dependency of IgA allotypy in swine can produce a sample bias that can explain why only two b/b homozygotes (1.3%) were found in the 160 randomly-selected samples since the original samples came from primarily Landrace and Yorkshire animals. The expected frequency of b/b homozygotes in these breeds would be \u3c3%. Thus, the data presented here reject the hypothesis that swine homozygous for a trait that results in loss of two-thirds of the IgA hinge, are selected against and that heterozygotes are positively selected. Rather, the study shows that IgAa and IgAb appear to be simple, breed-dependent allotypic markers

Genetic Parameters and Chromosomal Regions Associated with Viral Load and Growth in Pigs Infected with Porcine Reproductive and Respiratory Syndrome Virus

Six hundred commercial crossbred piglets were experimentally infected with the Porcine Reproductive and Respiratory Syndrome (PRRS) virus. Blood samples and body weights were collected at least once per week throughout the 6-week test period. Blood samples were used to measure the degree of infection through viral load. Body weight was measured to look at the impact of the PRRS virus on growth. Serum viral load from day 0 to 21 were summarized by area under the curve. Heritability for viral load and weight gain from 0 to 42 days after infection was 0.28 and 0.26, respectively. All piglets were genotyped for over 60,000 genetic markers comprising single nucleotide polymorphisms (SNPs) distributed across the genome. Regions on chromosomes 3, 4, and X appeared to be associated with area under the curve, while regions on chromosomes 1, 4, 7, and 17 appeared to be associated with weight gain. These results are promising to the swine industry, as it shows that there is genetic variation for resistance to PRRS within a population and that selection for resistance or susceptibility to the virus is plausible

Difference in severity of porcine circovirus type two-induced pathological lesions between Landrace and Pietrain pigs

Anecdotal information from the field suggests that there are host genetic differences in susceptibility to porcine circovirus type 2 (PCV2) associated disease among Landrace and Pietrain breeds. The objective of this study was to determine if a difference exists in PCV2 susceptibility between Landrace and Pi-etrain pigs under experimental conditions. Thirty-nine Landrace pigs and 39 Pietrain pigs were blocked by breed, sire, dam, and litter and randomly divided into the following 4 groups: Landrace noninoculated negative control (Landrace-NEG; n = 13), Pietrain noninoculated negative control (Pietrain-NEG; n = 13), Landrace-PCV2 (n = 26; Landrace), and Pietrain-PCV2 (n = 26; Pietrain). After waning of passively acquired anti-PCV2 antibodies, Landrace-PCV2 and Pietrain-PCV2 groups were inoculated with PCV2 isolate ISU-40895. The Landrace-NEG and Pietrain-NEG groups were housed in a separate room, remained noninoculated, and served as negative controls. All pigs in all groups were necropsied at 21 d post PCV2-inoculation. Onset of seroconversion and concentrations of anti-PCV2-IgM, anti-PCV2-IgG, and anti-PCV2 neutralizing antibodies were similar in Landrace-PCV2 and Pietrain-PCV2 groups. Furthermore, the amount of PCV2 DNA and cytokine concentrations in serum and plasma samples were not different between the 2 PCV2-inoculated groups. The severity of PCV2-associated microscopic lesions was different between Landrace and Pietrain pigs; Landrace-PCV2 pigs had significantly (P \u3c 0.05) more severe lymphoid lesions than the Pietrain-PCV2 pigs. Although the pigs originated from the same farm where their dams were commingled, passively acquired anti-PCV2-antibodies waned in Pietrain pigs by approximately 12 wk of age, whereas the majority of the Landrace pigs remained PCV2 seropositive until 18 wk of age and beyond. The results from this study indicate that a genetic difference exists between these 2 breeds of pigs in susceptibility to PCV2-associated lesions

Probing genetic control of swine responses to PRRSV infection: current progress of the PRRS host genetics consortium

<p>Abstract</p> <p>Background</p> <p>Understanding the role of host genetics in resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection, and the effects of PRRS on pig health and related growth, are goals of the PRRS Host Genetics Consortium (PHGC).</p> <p>Methods</p> <p>The project uses a nursery pig model to assess pig resistance/susceptibility to primary PRRSV infection. To date, 6 groups of 200 crossbred pigs from high health farms were donated by commercial sources. After acclimation, the pigs were infected with PRRSV in a biosecure facility and followed for 42 days post infection (dpi). Blood samples were collected at 0, 4, 7, 10, 14, 21, 28, 35 and 42 dpi for serum and whole blood RNA gene expression analyses; weekly weights were recorded for growth traits. All data have been entered into the PHGC relational database. Genomic DNAs from all PHGC1-6 pigs were prepared and genotyped with the Porcine SNP60 SNPchip.</p> <p>Results</p> <p>Results have affirmed that all challenged pigs become PRRSV infected with peak viremia being observed between 4-21 dpi. Multivariate statistical analyses of viral load and weight data have identified PHGC pigs in different virus/weight categories. Sera are now being compared for factors involved in recovery from infection, including speed of response and levels of immune cytokines. Genome-wide association studies (GWAS) are underway to identify genes and chromosomal locations that identify PRRS resistant/susceptible pigs and pigs able to maintain growth while infected with PRRSV.</p> <p>Conclusions</p> <p>Overall, the PHGC project will enable researchers to discover and verify important genotypes and phenotypes that predict resistance/susceptibility to PRRSV infection. The availability of PHGC samples provides a unique opportunity to continue to develop deeper phenotypes on every PRRSV infected pig.</p

Analyses of pig genomes provide insight into porcine demography and evolution

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model

Dissent, debate, and the origins of United States responsiveness to mass killing

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Political Science, 2017.Cataloged from PDF version of thesis.Includes bibliographical references.The United States has developed a reputation for consistently failing to respond to mass killing and genocide throughout history. The conventional wisdom is that the United States has the resources and intelligence to act, but fails to do so because of a lack of political will. However, a closer examination of history reveals that although the modal response of the United States is indeed to refrain from devoting significant resources to these crises, at times the United States reverses course to pursue policies aimed at assisting victims of atrocity. Previous analyses have not fully explained the sources this policy variation. Drawing on extensive archival research, this dissertation proposes a theory explaining when these shifts in US policy occur. I suggest that three factors-the level at which dissent occurs within the government, the degree of congressional pressure, and the direction of a variable that I term political liability-are responsible for shifting US policy toward a more robust response. I illustrate the theory with case studies covering US responsiveness to the following cases: the Holocaust (193 8-1945) under presidents Franklin D. Roosevelt and Harry S. Truman; mass killing in Bosnia (1992-1995) under presidents George H.W. Bush and William J. Clinton; and mass killing in Rwanda (1994) under Clinton. A comparative analysis of US responsiveness to theby Amanda Joan Rothschild.Ph. D