Structural identification of trait associated chromosomal segments and of causal mutations for quantitative traits in pooled F2 crosses using next-generation sequencing technologies and innovative statistical methods

• Applicants: Professor Dr. Jörn Bennewitz; Professor Dr. Georg Thaller
• Subject Area: Animal Breeding, Animal Nutrition, Animal Husbandry
• Term: from 2014 to 2018
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 261898836

The aim of the research project is to structurally identify short chromosomal regions harbouring causal mutations of quantitative traits for growth, carcass and meat quality in pigs and to test the polymorphisms within the segments for structural causality. Four existing and phenotypically very well characterised porcine F2 crosses are pooled into a powerful joint design consisting of 3 466 F2 individuals. The crosses are analysed jointly using next generation sequencing technologies as well as bioinformatic, statistical and genomic methods and models. The project includes complete SNP genotyping of founder animals by re-sequencing, a chip-based SNP-genotyping of F1 and F2 individuals, and the imputation of sequence in the F1 and F2 individuals. Chromosomal regions with strongest evidence for trait associations are indentified and subsequently screened for haplotypes and mutations. These are tested for structural causality. Special focus is set on gene variants that segregate within the Piétrain founder breed, because it is the most important population from a breeding perspective, and mapping resolution is highest for the Piétrain related mutations. Additive as well as non-additive gene effects and gametic imprinting are considered and the interrelationships between these gene effects are investigated using the identified causal polymorphisms. The design of functional follow-up studies is the last step of the project. The results of the project contribute to the genetic dissection of quantitative traits in crossbred designs and provide valuable contributions to the exploration of similar trait complexes in segregating populations.

• DFG Programme: Research Grants