Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle.

The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil.Article 32

Estimation of linkage disequilibrium, persistence of phase and effective population size of Brazilian Hereford and Braford breeds.

A set of 41,241 SNP genotypes from 2,435 Hereford (HH) and Braford (BO) bovines were analyzed to estimate linkage disequilibrium (LD) levels, persistence of phase and effective population size of these populations. LD levels were estimated using the squared correlation of alleles at two loci (r2) at varying distances. Average r2 between adjacent SNP was 0.21 for HH and 0.16 for BO. Average inter-marker distance was 61 kb in both breeds. Useful LD values (r2>0.2) were observed at 0-60 kb bins in HH and 0-20 kb bins in BO. Breeds demonstrated moderate to strong persistence of phase at all distances (range=0.53-0.97). The greatest phase correlations (r>0.9) were found in 0-50 kb bins. LD estimates decreased rapidly with increasing distances between SNPs, however, useful LD was observed in genomic regions spanning up to ~50 kb

Estimation of linkage disequilibrium, persistence of phase and effective population size of Brazilian Hereford and Braford breeds.

A set of 41,241 SNP genotypes from 2,435 Hereford (HH) and Braford (BO) bovines were analyzed to estimate linkage disequilibrium (LD) levels, persistence of phase and effective population size of these populations. LD levels were estimated using the squared correlation of alleles at two loci (r2) at varying distances. Average r2 between adjacent SNP was 0.21 for HH and 0.16 for BO. Average inter-marker distance was 61 kb in both breeds. Useful LD values (r2>0.2) were observed at 0-60 kb bins in HH and 0-20 kb bins in BO. Breeds demonstrated moderate to strong persistence of phase at all distances (range=0.53- 0.97). The greatest phase correlations (r>0.9) were found in 0-50 kb bins. LD estimates decreased rapidly with increasing distances between SNPs, however, useful LD was observed in genomic regions spanning up to ~50 kb

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

Genome-Wide Linkage Analysis of Global Gene Expression in Loin Muscle Tissue Identifies Candidate Genes in Pigs

BACKGROUND: Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy for revealing candidate genes involves expression QTL (eQTL) mapping, where the mRNA abundance of a set of transcripts is used as the response variable for a QTL scan. METHODOLOGY/PRINCIPAL FINDINGS: We utilized a whole genome expression microarray and an F(2) pig resource population to conduct a global eQTL analysis in loin muscle tissue, and compared results to previously inferred phenotypic QTL (pQTL) from the same experimental cross. We found 62 unique eQTL (FDR <10%) and identified 3 gene networks enriched with genes subject to genetic control involved in lipid metabolism, DNA replication, and cell cycle regulation. We observed strong evidence of local regulation (40 out of 59 eQTL with known genomic position) and compared these eQTL to pQTL to help identify potential candidate genes. Among the interesting associations, we found aldo-keto reductase 7A2 (AKR7A2) and thioredoxin domain containing 12 (TXNDC12) eQTL that are part of a network associated with lipid metabolism and in turn overlap with pQTL regions for marbling, % intramuscular fat (% fat) and loin muscle area on Sus scrofa (SSC) chromosome 6. Additionally, we report 13 genomic regions with overlapping eQTL and pQTL involving 14 local eQTL. CONCLUSIONS/SIGNIFICANCE: Results of this analysis provide novel candidate genes for important complex pig phenotypes

Oligonucleotide Microarray Analysis of Age-Related Gene Expression Profiles in Miniature Pigs

Miniature pigs are useful model animals for humans because they have similar anatomy and digestive physiology to humans and are easy to breed and handle. In this study, whole blood microarray analyses were conducted to evaluate variations of correlation among individuals and ages using specific pathogen-free (SPF) Clawn miniature pigs. Whole blood RNA is easy to handle compared to isolated white blood cell RNA and can be used for health and disease monitoring and animal control. In addition, whole blood is a heterogeneous mixture of subpopulation cells. Once a great change occurs in composition and expressing condition of subpopulations, their associated change will be reflected on whole blood RNA. From 12 to 30 weeks of age, fractions of lymphocytes, monocytes, neutrophils, eosinophils, and basophils in white blood cells showed insignificant differences with age as a result of ANOVA analysis. This study attempted to identify characteristics of age-related gene expression by taking into account the change in the number of expressed genes by age and similarities of gene expression intensity between individuals. As a result, the number of expressed genes was less in fetal stage and infancy period but increased with age, reaching a steady state of gene expression after 20 weeks of age. Variation in gene expression intensity within the same age was great in fetal stage and infancy period, but converged with age. The variation between 20 and 30 weeks of age was comparable to that among 30 weeks individuals. These results indicate that uniformity of laboratory animals is expected for miniature pigs after 20 weeks of age. Furthermore, a possibility was shown that whole blood RNA analysis is applicable to evaluation of physiological state