Reproduction in Domestic Animals

86 JA Longor six distinct centres across the geographical range ofthe wild species (Larson et al. 2005).Domestication of cattle has been particularly welldocumented through gene mapping, with clear evidenceof three distinct initial domestication events for threedistinct aurochs (Bos primigenius) subspecies. Bos primigeniusprimigenius and B. p. opisthonomous, are theancestors of the humpless B. taurus cattle of the NearEast and Africa, respectively, with domestication occurringapproximately 9000 years ago (Wendorf and Schild1994). Humped Zebu cattle (B. indicus) are believed tohave been domesticated at a later date, approximately7000–8000 years ago (Loftus et al. 1994; Bradley et al.1996; Bradley and Magee 2006). Finally, the domesticchicken (Gallus domesticus) is descended from the wildred jungle fowl (G. gallus). While previous molecularstudies suggested a single domestic origin in SoutheastAsia (Fumihito et al. 1994, 1996), at least six distinctmaternal genetic lineages have now been identified (Liuet al. 2006).In genetic diversity studies, the most frequently usedmarkers are microsatellites and these are the mostpopular markers in livestock genetic characterizationstudies (Sunnucks 2001). Their high mutation rate andco-dominant nature permit the estimation of within- andbetween-breed genetic diversity, and genetic admixtureamong closely related breeds. There are a few examplesof large-scale analyses of the genetic diversity oflivestock species. For example, chicken and pig diversitythroughout Europe have been reported (Hillel et al.2003; SanCristobal et al. 2006). Sheep diversity wasassessed at a large regional scale in northern Europeancountries (Tapio et al. 2005); while Can˜ on et al. (2006)studied goat diversity in Europe and the Middle East.Probably the most comprehensive study of this type inlivestock is a continent-wide study of African cattle(Hanotte et al. 2002), which revealed the genetic signaturesof the origins, secondary movements and differentiationof African cattle. For most livestock breeds,however, a comprehensive review is still lacking.Single nucleotide polymorphisms (SNPs) are used asan alternative to microsatellites in genetic diversitystudies (Marsjan and Oldenbroek 2007). Single nucleotidepolymorphisms are variations at single nucleotideswhich do not change the overall length of theDNA sequence in the region and occur throughoutthe genome. With this perspective, large-scale projectsare ongoing in several livestock species to identifymillions (Wong et al. 2004) and validate severalthousands of SNPs, and identify haplotype blocks inthe genome.Mitochondrial DNA (mtDNA) polymorphisms havebeen extensively used in phylogenetic and geneticdiversity analyses. The haploid mtDNA, carried by themitochondria in the cell cytoplasm, has a maternal modeof inheritance (individuals inherit the mtDNA fromtheir dams and not from their sires) and a high mutationrate; it does not recombine. These characteristics enablebiologists to reconstruct evolutionary relationshipsbetween and within species by assessing the patterns ofmutations in mtDNA. MtDNA markers may alsoprovide a rapid way of detecting hybridization betweenlivestock species or subspecies (Nijman et al. 2003).An alternative approach to the identification ofgenome regions carrying relevant genes has recentlybeen proposed. It consists of the detection of ‘selectionsignatures’ via a ‘population genomics’ approach (Blacket al. 2001; Luikart et al. 2003). Population genomicsutilizes phenotypic data at the breed level (or subpopulationswithin a breed), rather than at the individuallevel. The population genomics approach also canidentify genes subjected to strong selection pressureand eventually fixed within breeds and, in particular,genes involved in adaptation to extreme environmentsor disease resistance. Population genomics relies on theprinciple that loci across the genome are influenced bygenome-wide evolutionary forces (e.g. genetic drift, geneflow), whereas locus-specific forces, such as selection,imprint a particular pattern of variability on linked locionly (Luikart et al. 2003). By comparing the geneticdiversity of many loci across the genome, it is thenpossible to reveal loci displaying an atypical variationpattern, which are likely to be linked to those genomicregions affected by selection (Black et al. 2001). Therefore,in contrast to candidate-gene-based methods,strategies making use of population genomics do notfocus on a few loci only, but rather depict the effect ofselection over the whole genome (Storz 2005).Another new frontier emerging from the concept ofpopulation genomics is landscape genomics. Livestockby definition are adapted to the landscape (e.g. temperature,altitude, rainfall, disease challenge, nutritionalchallenge and human selection). The aim of landscapegenomics is to learn from the co-evolution of livestockand production systems and use the knowledge gainedto better match different breeds with production circumstances.A novel approach for evaluating populationgenomics is based on a spatial analysis methoddesigned to detect signatures of natural selection withinthe genome of domestic and wild animals (Joost et al.2007). Spatial analysis method goes a step furthercompared to classical approaches, as it is designed toidentify environmental parameters associated withselected markers (FAO 2007). By overlaying populationgenomic analyses (e.g. ‘signatures of selection’) withother sets of information such as agro-ecological mapsor other environmental ⁄ production information, it canbe determined what genetic materials are candidates foruse in which parts of the globe. The concept oflandscape genomics is promising, as this combines georeferencingof breed distributions, spatial ⁄ global geneticdiversity, climatic, ecological, epidemiological and productionsystem information which will facilitate anddirect priority decisions for breed conservation.Future Challenges and OpportunitiesLack of information on the world’s livestock resources,such as what livestock breeds ⁄ populations exist, theirgeographical location and their genetic characteristics, isa major impediment to their sustainable use. The currentdocumented numbers of breeds is likely an underestimation,as a large proportion of indigenous livestockpopulations are in the developing world and have yetto be described at phenotypic and genotypic levels(Hanotte and Jianlin 2005). Additionally, the geneticÓ 2008 No claim to original government works