The DNA of individual plants and animals is a random order of DNA blocks inherited from their ancestors. But what to do if you find a plant or animal with interesting characteristics but do not know from which of the ancestors the genes of this organism come from? This is where the new software tool RABBIT (Reconstructing Ancestry Blocks Bit By Bit), developed by Wageningen UR, can help – even if it is from a randomly mating and multi-parent population and you have no idea how the different generations of plants or animals mated during your breeding experiments.
As most organisms inherit DNA from their two parents, their DNA is unique. After this has gone on for generations, individuals have a randomly mixed order of DNA blocks that originate from their great-great-grandparents.
Wageningen UR developed RABBIT to establish from which ancestors the randomly mixed DNA comes from in breeding populations (not association panels). In scientific terms, the tool performs haplotype reconstruction: it links individuals’ genomes to their founder parents.
The model Wageningen UR developed is unique: it can be used for both plant and animal (diploid) populations, no matter whether the individuals are inbred or outbred. In the last scientific publication about the model, the scientists compared it with other models such as HAPPY and GAIN packages. This showed that the RABBIT reconstructions are more accurate and more robust to data errors and population types.
The hidden Markov model framework
To develop RABBIT, the scientists used the hidden Markov model, which is a way to reconstruct hidden ancestral blocks from DNA marker data observed in the plant or animal with interesting characteristics. Along individual genomes, the block patterns follow Markov processes, which are specified a priori by population designs.
This research is mainly funded by Stichting Technische Wetenschappen (STW; Technology Foundation) (grant no. STW-Rijk Zwaan project 12425), which is part of NWO, the Netherlands Organisation for Scientific Research. It is partly funded by the Netherlands Ministry of Economic Affairs.