Transcriptome Analysis of Post-Hatch Breast Muscle in Legacy and Modern Broiler Chickens Reveals Enrichment of Several Regulators of Myogenic Growth

Abstract

Agriculture provides excellent model systems for understanding how selective pressure, as applied by humans, can affect the genomes of plants and animals. One such system is modern poultry breeding in which intensive genetic selection has been applied for meat production in the domesticated chicken. As a result, modern meat-type chickens (broilers) exhibit enhanced growth, especially of the skeletal muscle, relative to their legacy counterparts. Comparative studies of modern and legacy broiler chickens provide an opportunity to identify genes and pathways affected by this human-directed evolution. This study used RNA-seq to compare the transcriptomes of a modern and a legacy broiler line to identify differentially enriched genes in the breast muscle at days 6 and 21 post-hatch. Among the 15,945 genes analyzed, 10,841 were expressed at greater than 0.1 RPKM. At day 6 post-hatch 189 genes, including several regulators of myogenic growth and development, were differentially enriched between the two lines. The transcriptional profiles between lines at day 21 post-hatch identify 193 genes differentially enriched and still include genes associated with myogenic growth. This study identified differentially enriched genes that regulate myogenic growth and differentiation between the modern and legacy broiler lines. Specifically, differences in the ratios of several positive (IGF1, IGF1R, WFIKKN2) and negative (MSTN, ACE) myogenic growth regulators may help explain the differences underlying the enhanced growth characteristics of the modern broilers.

RNA sequencing for global gene expression associated with muscle growth in a single male modern broiler line compared to a foundational Barred Plymouth Rock chicken line

“…This is a very significant skew (binomial P value < 0.000001) implying the PeM birds have a lowered mitochondrial content. Recently, a breast muscle transcriptomic analyses using RNAseq method was reported on the comparison between the broiler pedigree Ross and a legacy Illinois chicken line [7]. When raw sequencing data, which is available on Gene Expression Omnibus (GEO), were reanalyzed for gene expression, the 608 genes encoding proteins localized to the mitochondrion were differentially expressed as 251 and 357 were up- and downregulated, respectively, in the 21 day old Ross chickens compared to Illinois chickens (data not shown; Seo et al, manuscript in preparation).…”

“…The expression of ACE, in combination with angiotensin II and AGTR1 (angiotensin II type 1 receptor), can produce muscle atrophy [23], indicating that down-regulation of ACE in PeM muscle may contribute to muscle hypertrophy compared to BPR chickens. Davis et al [7] also observed elevated ACE in a heritage (Illinois) broiler compared to modern broiler (Ross) and hypothesized that this would play a role in lowering protein synthesis and muscle development in the slower growing Illinois broiler.…”

“…The qPCR of MSTN was consistent with RNAseq result (Table 1) and no single nucleotide polymorphisms (SNP) altering an amino acid residue were found in MSTN cDNA sequences in both PeM and BPR chickens (data not shown). According to a recent RNAseq report comparing a modern pedigree broiler (ROSS) muscle and to that in heritage chicken (Illinois) muscles, MSTN expression was very similar in both chicken lines and showed relatively high expression levels (~30 RPKMs) in both lines, though slightly higher expression was observed in pedigree broiler muscles than heritage chicken muscles [7]. Similarly, the MSTN expression in this study showed relatively abundant expression levels in both BPR (range of 380 – 1000 raw read counts) and in PeM (range of 1000 – 2100 raw read counts) breast muscles (data not shown).…”

“…Several global expression studies showed that production efficiency may be associated with various cellular mechanisms including mitochondrial oxidative stress, inflammatory response, protein degradation, stress responses, growth hormone signaling, cell cycle, apoptosis and fatty acid transportation. A recent study on the transcriptome analyses of breast muscles in modern pedigree broiler chicken and legacy chicken lines reported that the transcriptional profile of differentially enriched genes on day 6 and day 21 in modern broiler muscles includes genes for enhanced myogenic growth and differentiation [7]. …”

WFIKKN1 and WFIKKN2: “Companion” proteins regulating TGFB activity

“…The expression of Wfikkn2 was also upregulated in hyperplasic growth zones of the late trout embryo myotome compared with adult myotomal muscle as shown by Rescan et al using laser capture microdissection and Agilent trout microarray [45]. Another study demonstrated that WFIKKN2 is more expressed in a chicken line that has been selected for 60 years for rapid growth of the skeletal muscle tissue (Ross 708 broiler bird) than in a legacy chicken line (Illinois bird) [46]. The concentration of WFIKKN1 in the serum also decreased with age in a Duchenne muscular dystrophy patient while it increased with age in controls [47].…”