The completion of the first draft of the domesticated pig genome represents an important landmark in the ongoing efforts to exploit and understand the genetic variation of this important agricultural species. Simultaneous efforts to identify genetic variants in pig breeds have resulted in the development of a DNA chip with over 60,000 genetic variants (SNPs).

Why Sequence a Complete Genome?

The availability of the sequence of the complete genome provides enormous opportunities to understand and exploit the genetic control of complex traits to the benefit of livestock, the consumer and the environment. A complete genome sequence is an important reference to further characterise genetic variation in other individuals and to study how this variation affects phenotypic variation of economically important traits.

The pig, Sus scrofa domesticus, was domesticated from Sus scrofa, the wild boar, 9,000 years ago in multiple regions of the world. Since then, the pig has been selected for a variety of traits and it has become an important source of animal proteins in many parts of the world. The availability of the new genomic tools allows more efficient selection and it opens up new ways to improve traits related to animal health and meat quality. This is nicely illustrated by the immediate use of these new tools within other activities of SABRE, e.g. the identification of genomic regions containing genes affecting boar taint.

Research for Improved Genomic Tools

The aim was to provide a set of improved bioinformatics tools and concurrent information that is needed to reduce boar taint, improve egg shell quality or understand fertility. This set of tools includes the in silico mining of SNPs, and the validation and exchange of information on SNPs.

Not Just the Pig

Whereas the majority of the activities within ‘Genomics and Bioinformatics’ of SABRE were directed to improve the genomic tools in the pig, other species were not forgotten. The group was also actively involved in the further improvement of the genomic tools in chicken and cattle, whose draft genome sequences were already available at the start of the project. A good example is the validation of a large number of chicken SNPs in a variety of breeds. These results were used to select an optimal set of SNPs to be used for the genetic analysis of eggshell quality.

Some Numbers

Similar to the genome of other mammals like man and cow, the genome of the pig is made up of close to three billion base pairs. These three billion base pairs are divided over the 19 different chromosomes of the pig and they contain the information for around 20,000 different genes. These genes are present in any individual and although they are roughly 99.9 per cent identical between individuals, the small 0.1 per cent difference strongly contributes to the wide variety of breeds and individual variation within breeds we observe in our livestock today. These genomic differences underlie the phenotypic differences we observe and for which we select.

Both the porcine genome sequence and the development of the ‘Pig SNP60 iSelect Beadchip’ are excellent examples of large international collaborations. While developing the porcine SNP chip, the group already identified 400,000 variants in a variety of commercially import breeds and the genome sequencing efforts have resulted in the identification of an additional two million of such variants (SNPs). Currently, the number of identified SNPs continues to increase daily, with many millions of SNPs identified in all major livestock species (pig, chicken, cow). These genomic tools and genome information will enable unprecedented possibilities to further explore, use and understand genetic variation in these important species.

Further Reading

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You can view the previous article from the SABRE report by clicking here.

January 2012