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Breast muscle growth rate and intramuscular fat (IMF) content show apparent differences between fast-growing broilers and slow-growing indigenous chickens. However, the underlying genetic basis of these phenotypic characteristics remains elusive. In this study, we investigate the dynamic alterations of three-dimensional genome architecture and chromatin accessibility in breast muscle across four key developmental stages from embryo to starter chick in Arbor Acres (AA) broilers and Yufen (YF) indigenous chickens. The limited breed-specifically up-regulated genes (Bup-DEGs) are embedded in breed-specific A compartment, while a majority of the Bup-DEGs involving myogenesis and adipogenesis are regulated by the breed-specific TAD reprogramming. Chromatin loops allow distal accessible regions to interact with myogenic genes, and those loops share an extremely low similarity between chicken with different growth rate. Moreover, AA-specific loop interactions promote the expression of 40 Bup-DEGs, such as IGF1, which contributes to myofiber hypertrophy. YF-specific loop interactions or distal accessible regions lead to increased expression of 5 Bup-DEGs, including PIGO, PEMT, DHCR7, TMEM38B, and DHDH, which contribute to IMF deposition. These results help elucidate the regulation of breast muscle growth and IMF deposition in chickens. A Hi-C study reveals the dynamic chromatin architecture of breast muscle and gene expression affected by breed-specific 3D genome architecture that may influence muscle growth and intramuscular fat deposition between fast-growing and slow-growing chickens. [ABSTRACT FROM AUTHOR]

Simple Summary: In poultry production, fasting can remodel ovarian function and thereby delay the aging process of chickens. However, this approach may induce various stresses on the intestinal health of chickens. So, intestinal injury, the microbiome, and the metabolome were analyzed individually and integrated to elucidate the impact of the intestinal flora on intestinal injury during fasting-induced molting (FIM). The findings revealed that fasting led to intestinal villus atrophy, inflammation in the intestines, and disruption of gut microbiota and metabolites. During the fasting period, intestinal injury is associated with an increased abundance of Escherichia_Shigella and related metabolites Citrulline and Sterobilin, as well as a decreased abundance of Ruminococcaceae_UCG-013 and Lactobacillus and related metabolites Lanthionine and reduced Glutathione. This provides an experimental basis for improving the gut microbiota and reducing intestinal inflammation during the FIM process. Fasting-induced molting (FIM) is a common method used to improve the laying performance of aged laying hens. Nevertheless, this approach may impose various stresses on chickens, such as disruptions in intestinal flora and inflammation issues within the intestines. However, the impact of an imbalance in intestinal flora on intestinal health during the FIM process remains elusive. Therefore, intestinal injury, the microbiome, and the metabolome were analyzed individually and integrated to elucidate the impact of the intestinal flora on intestinal health during the FIM process. The findings indicated that fasting resulted in a notable reduction in villus height and villus/crypt ratio, coupled with elevated levels of intestinal inflammation and permeability. During the fasting period, microbiota compositions changed. The abundance of Escherichia_Shigella increased, while the abundance of Ruminococcaceae_UCG-013 and Lactobacillus decreased. Escherichia_Shigella was positively correlated with Citrinin and Sterobilin, which lead to intestinal inflammation. Ruminococcaceae_UCG-013 and Lactobacillus exhibited positive correlations with Lanthionine and reduced Glutathione, thereby reducing intestinal inflammation. This study screened the intestinal probiotics, Ruminococcaceae UCG-013 and Lactobacillus, that influence gut health during the fasting period, providing an experimental basis for improving gut microbiota and reducing intestinal inflammation during the FIM process. [ABSTRACT FROM AUTHOR]

Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens. We identified two muscle tissue specific expression lncRNAs. In addition, the target genes of these lncRNAs were significantly enriched in certain biological processes and molecular functions, as demonstrated by Gene Ontology (GO) analysis, and these target genes participate in five signaling pathway, as revealed by an analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Taken together, these data suggest that different lncRNAs might be involved in regulating chicken muscle development and growth and provide new insight into the molecular mechanisms of lncRNAs. Key words: lncRNA, RNA-Seq, chicken, muscle development. La qualité du muscle chez le poulet est un des facteurs les plus importants pour déterminer la valeur économique de la volaille, et le développement et la croissance musculaires sont affectés par la génétique, l'environnement et la nutrition. Cependant, peu de choses sont connues au sujet des mécanismes de régulation moléculaire opérant via des longs ARN non-codants (lncRNA) lors du développement des muscles squelettiques chez le poulet. Cette étude visait à mieux comprendre le développement musculaire chez les poulets et d'ainsi améliorer la qualité de la viande. Dans ce travail, une approche RNA-Seq Ribo-Zero a été employée pour étudier les différences dans les profils d'expression des gènes liés au développement et sentiers associés chez les poulets Gushi (GS) et Arbor Acres (AA). Les auteurs ont identifié deux lncRNA dont l'expression était spécifique aux tissus musculaires. De plus, les gènes ciblés par ces lncRNA étaient significativement enrichis pour certains processus biologiques et fonctions moléculaires, tel que démontré par une analyse ontologique GO, et ces gènes ciblés participent à cinq sentiers de signalisation sur la base d'une analyse de la base de données KEGG (Kyoto Encyclopedia of Genes and Genomes). Ensemble, ces données suggèrent que différents lncRNA seraient impliqués dans la régulation du développement et de la croissance musculaires chez le poulet, et elles apportent un éclairage sur les mécanismes moléculaires des lncRNA. [Traduit par la Rédaction] Mots-clés : lncRNA, RNA-Seq, poulet, développement du muscle., Introduction In recent decades, poultry research has made significant progress in genetic improvement and feedstuff optimization. Due to its high protein, low calorie, and low cholesterol content, chicken meat has [...]