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

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 $m_i$ of the microbiota composition on the breeding value $g_i$ of an animal $i$ is the conditional expectation of its breeding value, given the vector ${\phi }_i$ with microbiota frequencies, that is $m_i=E\left(g_i|{\phi }_i\right).$ The breeding value $g_i$ of an animal can therefore be decomposed into a heritable contribution $m_i$ that arises from an altered microbiota composition and a heritable contribution $p_i$ that arises from altered metabolic pathways within the animal, so $g_i=m_i+p_i.$ Instead of selecting for breeding value ${\hat{g}}_i$ , an index comprising the two components ${\hat{m}}_i$ and ${\hat{p}}_i$ with appropriate weights, that is $I_i={\lambda }_1{\hat{m}}_i+{\lambda }_2{\hat{p}}_i$ , 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.