Selecting the hologenome to breed for an improved feed efficiency in pigs—A novel selection index

Abstract

Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect mi of the microbiota composition on the breeding value gi of an animal i is the conditional expectation of its breeding value, given the vector ϕi with microbiota frequencies, that is mi=E(gi/ϕi) The breeding value gi of an animal can therefore be decomposed into a heritable contribution mi that arises from an altered microbiota composition and a heritable contribution pi that arises from altered metabolic pathways within the animal, so gi=mi+pi Instead of selecting for breeding value (Formula presented.), an index comprising the two components (Formula presented.) and (Formula presented.) with appropriate weights, that is (Formula presented.), can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.