The pig genome project has plenty to squeal about

Genetic Diversity and Ancestral Study for Korean Native Pigs Using 60K SNP Chip

Simple Summary

Assessing and understanding the genetic resources of indigenous livestock populations is necessary to address issues associated with conservation and domestic supply, etc. This study examined the Korean native pig (KNP; Sus scrofa coreanus), which is among the native porcine breeds in South Korea, in terms of its overall genetic diversity and ancestry. According to 60K single-nucleotide polymorphism (SNP) BeadChip analyses, the KNP pig showed similarity to Western breeds than to Chinese breeds. This conclusion runs contrary to popular belief as a Chinese origin of KNP pigs, as suggested by previous historical and genetic studies. We also describe the possibility of potential biases in the analysis results.

Abstract

The Korean native pig (KNP; Sus scrofa coreanus) is an indigenous porcine breed in South Korea considered as a valuable but dwindling genetic resource. Studies using diverse methodologies and genetic markers suggest that this population originated from the Manchu province of Northeastern China and migrated approximately 3000 years ago into the Korean peninsula. This study aimed to verify those findings by performing diversity and ancestral analyses using the 60K single-nucleotide polymorphism (SNP) BeadChip on 891 pigs of 47 breeds worldwide. We also performed principal component analysis (PCA), ancestry analyses, phylogenetic tree analysis using SNPhylo, and linkage disequilibrium analysis. Furthermore, we generated heatmap, obtained Nei’s genetic distance and F_ST values, and explored the heterozygosity of commercial and native Korean pigs. The results demonstrated that KNP pigs are more closely related to European breeds than to Chinese breeds. In addition, as previous studies have suggested, our admixture analyses indicated that KNP pigs showed distinguishable genetic structure.

One world, one health: the threat of emerging swine diseases. A North American perspective

The predicted expansion of global livestock populations to meet the food and fibre demands of the growing human population raises numerous concerns, including the implications for disease emergence. The evolution of animal production in developed countries has been marked by substantial reduction in farm numbers with correspondingly larger herd sizes, specialization of enterprises, concentration or ownership and vertical integration. Innovations in the structure and operations of swine production have been largely driven by efforts to improve swine health, and the impact of several important swine diseases has declined. Productivity in swine production and the safety of pork products have increased markedly. The most significant emerging infectious diseases of pigs over the last decades have been highly host-specific viruses rather than multihost pathogens. While some bacterial pathogens of pigs have increased in importance in modern systems, improved management systems and biosecurity have enabled herd sizes to increase without negative impact on swine health. The most vulnerable scenario for disease emergence in swine, particularly for zoonotic agents, may be rapid expansion and intensification of swine industries in developing countries without incorporating the stringent biosecurity measures and veterinary oversight that have helped maintain the health and productivity of large herds in North America. Factors that may influence disease emergence in the long term include regulatory measures (particularly related to antimicrobial use), genetics and feeding practices.

Transcriptome profiling identifies differentially expressed genes in postnatal developing pituitary gland of miniature pig

In recent years, Tibetan pig and Bama pig are popularly used as animal models for medical researches. However, little genomic information is available for the two breeds, particularly regarding gene expression pattern at the whole-transcriptome level. In this study, we characterized the pituitary transcriptome profile along their postnatal developmental stages within and between the two breeds in order to illustrate the differential dynamics and functions of differentially expressed genes. We obtained a total of ∼300 million 80-bp paired-end reads, detected 15 715 previously annotated genes. Most of the genes (90.33%) were shared between the two breeds with the main functions in metabolic process. Four hormone genes (GH, PRL, LHB, and FSHB) were detected in all samples with extremely high levels of expression. Functional differences between the three developmental stages (infancy, puberty and adulthood) in each breed were dominantly presented by the gene expressions at the first stage. That is, Bama pig was over-represented in the genes involved in the cellular process, while Tibetan pig was over-represented in the genes represented by the reproductive process. The identified SNPs indicated that the divergence between the miniature pig breeds and the large pig (Duroc) were greater than that between the two miniature pig breeds. This study substantially expands our knowledge concerning the genes transcribed in the pig pituitary gland and provides an overview of pituitary transcriptome dynamics throughout the period of postnatal development.

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation

Given the relevance of the pig proteome in different studies, including human complex maladies, a statistical validation of the annotation is required for a better understanding of the role of specific genes and proteins in the complex networks underlying biological processes in the animal. Presently, approximately 80% of the pig proteome is still poorly annotated, and the existence of protein sequences is routinely inferred automatically by sequence alignment towards preexisting sequences. In this article, we introduce SUS-BAR, a database that derives information mainly from UniProt Knowledgebase and that includes 26 206 pig protein sequences. In SUS-BAR, 16 675 of the pig protein sequences are endowed with statistically validated functional and structural annotation. Our statistical validation is determined by adopting a cluster-centric annotation procedure that allows transfer of different types of annotation, including structure and function. Each sequence in the database can be associated with a set of statistically validated Gene Ontologies (GOs) of the three main sub-ontologies (Molecular Function, Biological Process and Cellular Component), with Pfam functional domains, and when possible, with a cluster Hidden Markov Model that allows modelling the 3D structure of the protein. A database search allows some statistics demonstrating the enrichment in both GO and Pfam annotations of the pig proteins as compared with UniProt Knowledgebase annotation. Searching in SUS-BAR allows retrieval of the pig protein annotation for further analysis. The search is also possible on the basis of specific GO terms and this allows retrieval of all the pig sequences participating into a given biological process, after annotation with our system. Alternatively, the search is possible on the basis of structural information, allowing retrieval of all the pig sequences with the same structural characteristics.

Database URL:http://bar.biocomp.unibo.it/pig/

Novel approach for deriving genome wide SNP analysis data from archived blood spots

Background

The ability to transport and store DNA at room temperature in low volumes has the advantage of optimising cost, time and storage space. Blood spots on adapted filter papers are popular for this, with FTA (Flinders Technology Associates) Whatman™^TM technology being one of the most recent. Plant material, plasmids, viral particles, bacteria and animal blood have been stored and transported successfully using this technology, however the method of porcine DNA extraction from FTA Whatman™^TM cards is a relatively new approach, allowing nucleic acids to be ready for downstream applications such as PCR, whole genome amplification, sequencing and subsequent application to single nucleotide polymorphism microarrays has hitherto been under-explored.

Findings

DNA was extracted from FTA Whatman™^TM cards (following adaptations of the manufacturer’s instructions), whole genome amplified and subsequently analysed to validate the integrity of the DNA for downstream SNP analysis. DNA was successfully extracted from 288/288 samples and amplified by WGA. Allele dropout post WGA, was observed in less than 2% of samples and there was no clear evidence of amplification bias nor contamination. Acceptable call rates on porcine SNP chips were also achieved using DNA extracted and amplified in this way.

Conclusions

DNA extracted from FTA Whatman cards is of a high enough quality and quantity following whole genomic amplification to perform meaningful SNP chip studies.

Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome

The analysis of interaction networks is crucial for understanding molecular function and has an essential impact for genomewide studies. However, the interactomes of most species are largely incomplete and computational strategies that take into account sequence homology can help compensating for this lack of information using cross-species analysis. In this work we report the construction of a porcine interactome resource. We applied sequence homology matching and carried out bi-directional BLASTp searches for the currently available protein sequence collections of human and pig. Using this homology we were able to recover, on average, 71% of the proteins annotated for human pathways for the pig. Porcine protein-protein interactions were deduced from homologous proteins with known interactions in human. The result of this work is a resource comprising 204,699 predicted porcine interactions that can be used in genome analyses in order to enhance functional interpretation of data. The data can be visualized and downloaded from http://cpdb.molgen.mpg.de/pig.

Biotechnologies for the management of genetic resources for food and agriculture

In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.

Advances in assay of complement function and activation

The main function of the complement system is pattern recognition of danger. Typical exogenous danger signals are pathogen associated molecular patterns inducing a protective inflammatory response. Other examples are exposure to foreign surfaces of biomedical materials including nanoparticles, which principally induce the same inflammatory response. If a surface is "foreign" to the host, it induces complement activation. Development of monoclonal antibodies to neoepitopes on complement activation products introduced an entirely new set of methods for assay of complement activation. Activation of complement by a surface occurs by impairment of the fine balance of the control system, e.g. by preferred binding of factor B at the expense of factor H. Sensitive methods to detect complement activation on surfaces and in the fluid phase are a prerequisite for investigation of the biocompatibility of artificial materials. This information can be used to develop new materials with enhanced biocompatibility. Here we review available methods to study human and animal complement function and activation in vitro and in vivo.