Genome-wide transcriptome profiling reveals the mechanisms underlying muscle group–specific phenotypic changes under different raising systems in ducks

Abstract

Although a number of nongenetic factors have been reported to be able to modulate skeletal muscle phenotypes in meat-type birds, neither the underlying mechanisms nor the muscle group–specific phenotypic and molecular responses have been fully understood. In the present study, a total of 240 broiler ducks were used to compare the effects of floor raising system ( FRS ) and net raising system ( NRS ) on the physicochemical properties and global gene expression profiles of both breast and thigh muscles at the posthatching week 4 ( W4 ), W8, and W13. Our results showed that compared with FRS, NRS generally induced higher pH, lower lightness (L∗) and yellowness (b∗), lower drip loss and cooking loss, and lower shear force in either breast or thigh muscles during early posthatching stages but subsequently showed less pronounced or even reverse effects. Meanwhile, it was observed that the raising system differently changed the myofiber characteristics depending on the muscle group and the developmental stage. Genome-wide transcriptome analysis showed that compared with FRS, NRS induced the most extensive gene expression changes in breast muscle ( BM ) at W4 but in thigh muscle ( TM ) at W13, suggesting the asynchronous molecular responses of BM and TM to the raising system and period. Most of differentially expressed genes in either BM or TM between NRS and FRS were enriched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes terms associated with regulation of muscle cellular functions, metabolic and contractile activities, and tissue remodeling, indicating similar molecular mechanisms principally responsible for the raising system-caused phenotypic changes in both muscle groups. Nevertheless, several crucial pathways (e.g., adipocytokine signaling, AGE-RAGE signaling, and apoptosis) and genes (e.g., ANO6, ACER2, UCP3, DTL, and TMEM120A) were tightly related to the muscle group–specific adaptive remodeling on different raising systems. These data could not only contribute to a better understanding of the molecular mechanisms behind meat quality but also provide novel insights into the molecular causes of the muscle group–specific adaptive remodeling in response to environmental stimuli.

Potential regulator of meat quality in geese: C1QTNF1 implications on cell proliferation and muscle growth

“…This integrated analysis of multi-omics data overcame the limitations of single-omics, and accessed the genetic information of organisms in different dimensions, which is an effective solution to address biological problems nowadays. Numerous scholars have employed this approach to undertake pertinent investigations, elucidating the genetic mechanisms underlying muscle development in mammalian species such as pigs and cattle ( Yang et al, 2021 ; Liang et al, 2022 ), as well as avian species including ducks and pigeons ( Hu et al, 2020 ; Hou et al, 2021 ). It is worth noting that fiber numbers per bundle in birds are fixed before or immediately after birth, and an increase in the bundle size is accompanied by an increased muscle fiber size, resulting in subsequent muscle growth ( Velleman, 2019 ).…”