Science - March 9, 2010

Comparing 1,200,000,000,000 base pairs

Martien Groenen, professor of the Animal Breeding and Genomics Centre, will use a European Research Grant to determine the DNA sequence of twelve different pig species. These will include European and Chinese pig species, the wild boar, other pig species of Java and Sulawesi, and even archeological DNA samples of pigs.

I want to find out what genetic changes have taken place during species formation and domestication of the pig', says Groenen. The DNA of 120 pigs will go through a gene sequencer. 'We will then have a lot of information. The genome of the pig has about 2.7 billion base pairs and we want to examine each base pair four times to achieve a high accuracy rate. We will therefore be examining ten billion base pairs for each animal. That works out to comparing at least 120 times ten billion base pairs.
Selection process
The pig was domesticated by man nineteen thousand years ago. What changes had the pig genome undergone during the selection process? Groenen hopes to find the answer using DNA fragments of a pig from an archeological dig. The comparison of pig species in various parts of the world would throw light into the genetic process of species formation. Groenen also wants to find out how pig breeding has affected the pig genome. To do this, he will compare the DNA of a present pig population to animals of the same population ten generations ago.
The enormous amount of data which will result will be sorted out by Groenen, two PhD students and two postdocs using bio-informatic programmes. 'We want to find out in which areas of the genome changes have taken place, and which genes are involved in the process.'
Two hundred species
The research team's vast knowledge of the pig genome will come in handy. In the past two years, the Animal Breeding and Genomics Centre had already compared a part of the DNA of more than two hundred pig species. Groenen made use of this knowledge in a powerful research proposal to the European Research Council, which in January gave credit to the proposal by awarding him a personal subsidy of 2.5 million euros for the coming five years. Groenen's research programme has begun on 1 March.
Leaps and bounds
Later this year, a researchers' consortium - including Groenen - will publish the complete pig DNA sequence. That will be a very good foundation on which subsequent research can be built, says Groenen. For example, he wants to know more about the genetic background of growth, fertility and resistance to pig diseases.
Six years ago, Groenen was co-author of the chicken DNA sequence. The amount of DNA information is growing by leaps and bounds. 'You can scan more and more genetic information faster and faster at lower and lower costs. The knowledge of base pairs in the world doubles every five months. This knowledge increase goes faster than the increase in computing capacity of computers.' Groenen will contribute 1.2 trillion base pairs to the gene pool in the coming years. 'We're going to trace the genetic variations. We're very good at that.'