Implication of digestive functions and microbiota in the establishment of muscle glycogen differences between divergent lines for ultimate pH

The quality levels of both chicken meat and chicks are influenced by breast muscle glycogen reserves. To study the role of digestive metabolism in establishing this muscular phenotype, we compared two divergent chicken lines for the ultimate pH (pHu) of breast meat, a proxy for glycogen reserves. Males aged 4 weeks had twice the breast muscle glycogen content in the pHu- line (low pHu) than in the pHu+ line (high pHu). An increase in glycogen reserves (pHu-) was associated with a greater relative weight of the proventriculus and gizzard, as well as better apparent ileal digestibility of nitrogen and calcium. The diversity of the caecal microbiota was comparable, but three bacterial genera (Lachnospira, Lachnospiraceae UCG-010, and Caprociproducens) varied between the lines. The differences observed could lead to the downregulation of carbon fixation in prokaryotes and of the citrate cycle in the pHu+ line. RNA-seq analysis of the jejunum, the major site of nutrient absorption, revealed 149 genes that were differentially expressed (DE) between the lines, including several genes linked to immunity, hormonal response and circadian rhythms that were expressed at lower levels in pHu+ animals. Other genes involved in cell migration and proliferation, and more generally tissue morphogenesis, also differed between the lines. Among the DE genes, several colocalized with quantitative trait loci (QTLs) controlling pHu and selection signatures were identified in the divergent lines, such as the gene coding for ghrelin, a hormone regulating appetite.