Abstract
Chicken growth performance provides direct economic benefits to the poultry industry. However, the underlying genetic mechanisms are unclear. The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRRh, WRRl) and Xinghua chickens (XHh, XHl). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRRh vs. WRRl, XHh vs. XHl, WRRh vs. XHh and WRRl vs. XHl, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated. FBXO32 was predominantly expressed in leg muscle, heart and breast muscle. After decreased FBXO32 expression, growth-related genes such as PDK4, IGF2R and IGF2BP3 were significantly down-regulated (P < 0.05). FBXO32 was significantly (P < 0.05) associated with carcass and meat quality traits, but not growth traits. FOXO3 was predominantly expressed in breast and leg muscle. In both of these tissues, the FOXO3 mRNA level in XH was significantly higher than that in WRR chickens with normal body weight (P < 0.05). In DF-1 cells, siRNA knockdown of FOXO3 significantly (P < 0.01) inhibited the MYOD expression and significantly up-regulated (P < 0.01 or P < 0.05) the expression of growth-related genes including CEBPB, FBXO32, GH, GHR, IGF1R, IGF2R, IGF2BP1, IGF2BP3, INSR, PDK1 and PDK4. Moreover, 18 SNPs were identified in FOXO3. G66716193A was significantly (P < 0.05) associated with growth traits. The sites C66716002T, C66716195T and A66716179G were significantly (P < 0.05) associated with growth or carcass traits. These results demonstrated that FOXO3 is a candidate gene influencing chicken growth. Our observations provide new clues to understand the molecular basis of chicken growth.
Highlights
Chicken growth, an important economic trait, is determined by genetic, nutritional and environmental factors
Skeletal muscle increase occurs mainly due to muscle hypertrophy accompanied by satellite cell proliferation to incorporate new myonuclei into existing myofibers [11]
The comparison with the highest number of differentially expressed genes (DEGs) resulted in the most Gene ontology (GO) biological process terms, and terms of development process, cell differentiation and cell adhesion were present in multiple comparisons
Summary
An important economic trait, is determined by genetic, nutritional and environmental factors. Heritability estimates showed that chicken growth could be enhanced by genetic improvement [1, 2]. This trait is controlled by multiple genes. Many studies have been performed to find genetic factors affecting growth. Genomewide associate study (GWAS) analysis found that two FOXO1A single-nucleotide polymorphisms (SNPs) were strongly associated with chicken growth [5]. The genetic mechanisms of chicken growth are unclear, and a more systematic picture of the genes responsible for this trait is needed. Generation sequencing provided an important opportunity for the genome-wide characterization of genes and pathways involved in growth [6,7,8]
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