Whole genome analysis
During the last decade, animal genetics has moved from analysis of a handful of genetic polymorphisms or candidate gene loci, towards genome scans and whole genome sequencing. The 1,000 human genomes project has put in place the infrastructure for whole genome scale population studies in farm animals (Nature 467: 28 October 2010). This landmark study opens the way for similar analysis of common and rare genetic variants in domestic species. During this important period in agricultural development, analysis of genetic diversity in commercial and marginal breeds will allow identification of millions of potentially informative single nucleotide polymorphisms and thousands of structural variants. As genome sequencing is becoming more technically feasible, the cost is also become much more affordable. This will lead to a ‘democratisation’ of genome data, enabling any country or interested party to analyse and exploit the genome of their own genetic resources.
The use of molecular genetic markers has evolved rapidly since the 1960’s when allozymes (soluble enzyme electrophoresis) were first discovered, and as we have progressed through restriction enzyme polymorphisms in the 1970’s to DNA fingerprinting in the 1980’s and DNA profiling using STR markers in the 1990’s statistical analysis of genetic variation has become very sophisticated and model-driven. In the last decade, the advent of high-density single nucleotide polymorphism (SNP) genome maps in livestock has moved the science along even further and now analysis of more than 50,000 SNPs in a single reaction for cattle and sheep is routine. However, the population genetic analysis of these markers is challenging due to the sheer amount of data and the computational intensity of many current statistical methods. The biggest challenge in the near future will be the development of approaches that optimally utilise the enormous datasets and generate novel information on the evolutionary history of breeds and domestic species.
Archaeological collections of osteological materials of domesticated animals and their wild ancestors, fibre and leather may store genetic information that can provide otherwise unobtainable insights into the past history of domesticated animals. The historic DNA provides information about the heterogeneity and genetic ancestries of past animal populations. For example, ancient DNA analysis has led to insights into the origins of domesticated wild ancestral populations and possible prehistoric backcrossing between domesticated and wild ancestral populations. In addition, ancient DNA analysis is a tool to explore temporal changes in genetic diversity within domesticated animal populations and can provide useful information on the current animal genetic biodiversity.
The archaeogenetics data for domesticated animal studies come typically from analyses of short DNA segments in the hypervariable mitochondrial control region, but the more challenging analysis of nuclear DNA has already been achieved. In general, ancient DNA experiments are demanding. The accepted criteria for ancient DNA work include e.g. reproducibility and the use of negative controls in order to demonstrate that the amplified DNA did not come from contaminants introduced during the experiment.
Phenotypic variation is traditionally divided into components that are under control of genetic and environmental variation, in addition to variation not readily attributable to either. Epigenetic phenomena are likely to contribute to this ‘‘intangible variation’’. Epigenetic effects are caused by chemical modifications to DNA that do not change the DNA sequence but alter the probability of gene transcription. These include methylation of cytosines and modification of the DNA binding proteins, which modulate the accessibility of DNA to transcription complexes. Technologies in epigenomic research include genomic analysis of DNA methylation, chromatin-associated proteins and chromatin higher-order structures. Besides the well-known epigenetic aspects like gene silencing and genomic imprinting, a role of epigenetics has recently been identified in fetal adaptation and transgenerational inheritance of acquired phenotypes. The progressive elucidation of epigenetic molecular mechanisms in different organisms will be a major research goal.