# Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching

## TL;DR

This study uses RNA sequencing to explore gene expression in F1 chicken breast muscle and liver, finding that additivity is the main pattern and identifying genes linked to growth and development.

## Contribution

The study reveals additivity as the dominant gene expression pattern in post-hatch F1 chickens and identifies growth-related genes and pathways.

## Key findings

- Additivity is the predominant gene expression pattern in F1 chicken breast muscle and liver.
- GO analysis identified 11 growth and development-related biological processes with key genes like STAT5A and TGFB2.
- KEGG analysis uncovered six growth-related pathways involving genes such as SLC27A4 and GLUL.

## Abstract

Understanding post-hatch gene expression patterns is crucial for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens, which has been rarely studied. Therefore, we conducted gene expression analysis on F1 chicken breast muscle and liver tissues using ssRNA-seq at 28 days. The study revealed additivity as the predominant gene expression pattern in post-hatch muscle and liver. GO analysis identified 11 biological process terms associated with growth and development in differentially expressed gene sets and non-additive gene sets, including key genes like STAT5A and TGFB2. KEGG analysis uncovered six growth-related pathways with genes such as SLC27A4 and GLUL. These findings provide valuable insights for domestic animal crossbreeding.

Heterosis refers to the phenomenon where hybrids exhibit superior performance compared to the parental phenotypes and has been widely utilized in crossbreeding programs for animals and crops, yet the molecular mechanisms underlying this phenomenon remain enigmatic. A better understanding of the gene expression patterns in post-hatch chickens is very important for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens. In this study, breast muscle and liver tissues (n = 36) from full-sib F1 birds and their parental pure lines were selected to identify gene expression patterns and differentially expressed genes (DEGs) at 28 days of age by strand-specific RNA sequencing (ssRNA-seq). This study indicates that additivity is the predominant gene expression pattern in the F1 chicken post-hatch breast muscle (80.6% genes with additivity) and liver (94.2% genes with additivity). In breast muscle, Gene Ontology (GO) enrichment analysis revealed that a total of 11 biological process (BP) terms closely associated with growth and development were annotated in the identified DEG sets and non-additive gene sets, including STAT5A, TGFB2, FGF1, IGF2, DMA, FGF16, FGF12, STAC3, GSK3A, and GRB2. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation presented that a total of six growth- and development-related pathways were identified, involving key genes such as SLC27A4, GLUL, TGFB2, COX17, and GSK3A, including the PPAR signaling pathway, TGF-beta signaling pathway, and mTOR signaling pathway. Our results may provide a theoretical basis for crossbreeding in domestic animals.