Transcriptomic profile of leg muscle during early growth in chicken

Abstract

The early growth pattern, especially the age of peak growth, of broilers affects the time to market and slaughter weight, which in turn affect the profitability of the poultry industry. However, the underlying mechanisms regulating chicken growth and development have rarely been studied. This study aimed to identify candidate genes involved in chicken growth and investigated the potential regulatory mechanisms of early growth in chicken. RNA sequencing was applied to compare the transcriptomes of chicken muscle tissues at three developmental stages during early growth. In total, 978 differentially expressed genes (DEGs) (fold change ≥ 2; false discovery rate < 0.05) were detected by pairwise comparison. Functional analysis showed that the DEGs are mainly involved in the processes of cell growth, muscle development, and cellular activities (such as junction, migration, assembly, differentiation, and proliferation). Many of the DEGs are well known to be related to chicken growth, such as MYOD1, GH, IGF2BP2, IGFBP3, SMYD1, CEBPB, FGF2, and IGFBP5. KEGG pathway analysis identified that the DEGs were significantly enriched in five pathways (P < 0.1) related to growth and development: extracellular matrix-receptor interaction, focal adhesion, tight junction, insulin signaling pathway, and regulation of the actin cytoskeleton. A total of 42 DEGs assigned to these pathways are potential candidate genes inducing the difference in growth among the three developmental stages, such as MYH10, FGF2, FGF16, FN1, CFL2, MAPK9, IRS1, PHKA1, PHKB, and PHKG1. Thus, our study identified a series of genes and several pathways that may participate in the regulation of early growth in chicken. These results should serve as an important resource revealing the molecular basis of chicken growth and development.

Fig 1. The actual growth curve and the matching curve of Jinghai Yellow chicken.

Fig 2. Numbers of expressed genes and differentially expressed genes: Results of RNA-Seq.

A: Expressed genes among the three groups. B: Differentially expressed genes among three comparisons, namely, 4W vs. 12W, 4W vs. 16W, and 12W vs. 16W. 4W, 12W, and 16W indicate the chicken groups at 4, 12, and 16 weeks of age, respectively.

Fig 3. Top ten most abundantly expressed genes in chicken leg muscles at 4, 12, and 16 weeks of age.

Fig 4. Differentially expressed genes identified in the comparisons of 4W vs. 12W (A), 4W vs. 16W (B), and 12W vs. 16W (C).

Fig 5. Heatmap of differently expressed genes in the five pathways related to chicken growth.

Rows indicate genes with significant differences in expression among the three stages; columns represent individual samples from three stages (M4W, M12W, and M16W indicate muscle samples at 4, 12, and 16 weeks of age, respectively.).

Fig 6. Expression level of nine DEGs detected by RNA-Seq and validated by qPCR.

Results from RNA-Seq are shown by bar graphs and values are shown on the right y-axis as FPKM. Results from qPCR are shown by line graphs and values are shown on the left y-axis as relative expression level. Data are presented as mean±SE.