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Researchers Report on Findings from Pig Genome

NEW YORK (GenomeWeb News) – In a set of papers appearing in Nature, the Proceedings of the National Academies of Science online, GigaScience, and other BioMed Central journals today, investigators outlined findings from the newly sequenced pig genome and related research efforts.

For the first of these studies, members of the International Swine Genome Sequencing Consortium detailed efforts to sequence, assemble, and begin analyzing a high-quality draft genome for the domestic Duroc pig, Sus scrofa. Within this pig genome, for instance, they saw expansions to gene families contributing to the animals' ability to smell, along with evidence for rapid evolution of olfactory- and immune-related genes.

"This understanding of the genetic origins of modern pigs is important as we breed pigs to meet growing demand more efficiently and to resist old and emerging diseases," co-corresponding author Alan Archibald, a researcher with the University of Edinburgh's Roslin Institute, said in a statement.

As the international team reports in Nature, its analyses also included comparisons between the domestic pig genome and sequences representing wild boars from different parts of Europe and Asia — work that offered clues about the evolution and domestication of pigs.

"This study marks the beginning of the sequencing of the genomes of hundreds, perhaps even thousands of individual pigs," co-corresponding author Martien Groenen, a researcher with Wageningen University's Animal Breeding and Genomics Centre, said in a statement. "This knowledge will be invaluable for pig breeding and exploring fundamental questions in biology and evolution."

The consortium originally announced the completion of a draft pig genome — based on genomic DNA from a Duroc pig — in 2009.

In the new Nature study, the group presented detailed information on the genome of a female Duroc pig, sequenced using a combination of bacterial artificial chromosome and whole-genome shotgun sequencing.

Around 2.6 billion bases of the pig genome has been assembled onto chromosomes, members of the consortium noted, while almost 212 million more bases of sequence remain as unplaced sequence scaffolds.

Analyses of the domestic pig genome uncovered nearly 3,000 non-coding RNAs, 21,640 predicted protein-coding genes, 380 pseudogenes, and almost 26,500 transcripts.

When they compared swine sequences to those from humans, mice, cows, horses, and dogs, investigators found pig orthologs for thousands of genes present in the other mammals. In addition, the team tracked down variants in specific pig genes that correspond to versions of human genes that have been implicated in obesity, diabetes, or other diseases in the past.

"These porcine variants are of interest," researchers wrote, "as they will allow detailed characterization in an experimental model organism whose physiology is very similar to that of human."

The pig genome may prove medically useful in other ways, too, the team noted. For example, the availability of swine genome data provided the opportunity to look for sequences stemming from retroviruses, which become incorporated into host DNA and are sometimes passed along in the germline as endogenous retroviruses.

Most of the porcine endogenous retroviruses, or PERVs, detected so far appear to be defective. But the authors of the study noted that the presence of PERVs, which have the potential to become re-activated, is something that ought to be taken into account when considering the possibility of transplanting organs or tissue from pigs into humans.

When they focused on fast-evolving pig genes, meanwhile, researchers garnered evidence that immune response and olfaction-related genes have undergone relatively rapid changes in the pig genome, which also contained expanded sets of genes related to the sense of smell. On the other hand, rearrangements to some taste receptor genes in the pig genome may help to explain the animals' lack of sensitivity to bitter tasting food, they noted, while other clues in the genome suggest that pigs likely have altered perceptions of sweet or meaty food flavors as well.

Using genome sequence data from wild boars, the researchers identified more than 17.2 million SNPs that proved useful for exploring the origins of pigs' wild counterpart.

Results of that analysis suggest that wild boars originated in Southeast Asia roughly four million years ago before spreading to other parts of the world, whereas wild boar populations in Asia and Europe appear to have diverged from one another an estimated one million years ago. Those distinct wild boar populations subsequently served as a source for independent pig domestication events in Europe and Asia during the past 10,000 years, it seems, as researchers' phylogenetic analyses of wild boar and domestic pig genomes point to distinct European and Asian lineages.

Because domestication corresponded with changes in everything from body size, shape, and coloring to the animals' behavior and reproductive traits, some investigators are also delving into the genetic alterations that accompanied the development of such traits.

In a study slated to appear online this week in PNAS, for instance, researchers from Uppsala University, the Swedish University of Agricultural Sciences, and elsewhere searched for signals of selection related to the domestication of European pigs. That analysis also pointed to a role for structural changes to the genome during domestication.

In GigaScience, meanwhile, investigators from China and Denmark described the initial findings from the draft genome of the Wuzhishan pig, an extensively inbred miniature pig breed native to China.

Additional data and information on the domestic pig genome is available online through the Swine Genome Consortium's website or ENSEMBL. Data from the Wuzhishan pig genome can be found through a GigaScience database called GigaDB or in NCBI's sequence read archive.