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.
Highlights
The advent of modern agriculture in the early 20th century led to intensive genetic selection for meat and egg production traits in the domesticated chicken
A total of 15,945 genes were analyzed for their expression level, expressed in reads per kilobase of transcript per million mapped reads (RPKM), in breast muscle tissue from both Ross 708 and Illinois birds; of these, 10,841 genes were expressed with an RPKM > 0.1, the threshold that corresponds to reliable results when assayed by quantitative RT-PCR (Fig 1)
Comparing the RPKM values for all genes from the Ross and Illinois birds at day 6 and day 21 shows a high relationship between the samples (Day 6 R2 = 0.948 and Day 21 R2 = 0.986) (Fig 2A and 2B) and hierarchical clustering segregated the data first by line by day (Fig 2C)
Summary
The advent of modern agriculture in the early 20th century led to intensive genetic selection for meat (broiler) and egg (layer) production traits in the domesticated chicken. In the Illinois birds, the normalized breast muscle mass (breast muscle mass/bird mass) remained constant after day 14 whereas the Ross 708 normalized breast muscle mass continued to increase [8] Given these observations, we hypothesized that genes affecting muscle growth and differentiation along with ones affecting energy metabolism would be differentially regulated between the breast muscle of the Ross 708 and Illinois lines, and that the transcriptomes would have different relationships before and after the growth-inflection point of day 14. We hypothesized that genes affecting muscle growth and differentiation along with ones affecting energy metabolism would be differentially regulated between the breast muscle of the Ross 708 and Illinois lines, and that the transcriptomes would have different relationships before and after the growth-inflection point of day 14 To test this hypothesis, RNA-seq was used to compare the gene expression patterns of the breast muscle from Ross 708 and Illinois birds bracketing the 14-day post-hatch period. The transcript levels of 15,945 genes were analyzed in the breast muscle of post-hatch day 6 (D6) and day 21 (D21) Illinois and Ross 708 chickens
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