Genetic Resources, Genome Mapping and Evolutionary Genomics of the Pig (Sus scrofa)

Abstract

The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.

Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication

“…Unlike most other domestic animals, the wild ancestors of domesticated pigs and a number of outgroup species are still present in the world, which is convenient for examining ancestral and derived mutations as well as inferring the processes of artificial selection (Chen et al, 2007). Moreover, the origin and history of Chinese domestic pigs have been deciphered.…”

Human–carnivore conflict over livestock in the eastern part of the Serengeti ecosystem, with a particular focus on the African wild dogLycaon pictus

“…H uman-carnivore conflict over livestock presents a challenge for both wildlife conservationists and farmers (Diamond, 1997;Chen et al, 2007;Kissui, 2008;Driscoll et al, 2009). It is a global problem (Ciucci & Boitani, 1998;Røskaft et al, 2003Røskaft et al, , 2007Treves & Karanth, 2003;Rodney & Rinchen, 2004;Woodroffe et al, 2005) and the decline of many large wild carnivore species is at least partly attributable to revenge killing as a result of predation on livestock .…”

Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies

“…There are over 730 distinct pig breeds worldwide, of which two thirds reside in Europe and China (Chen et al 2007), whose diverse phenotypes are shaped by the combined effects of local adaptation and artificial selection (Ai et al 2015). Efforts have been made to characterize the genetic variation that underlies this phenotypic diversity using resequencing data and the genome of the European domestic Duroc pig as a reference Rubin et al 2012;Choi et al 2015;Moon et al 2015).…”