Impact of GC content on gene expression pattern in chicken

Table 2 Relationship between GC content and expression pattern in three chromosome groups

Chr group	GC content	Expression level		Expression breadth		Maximum expression
Macro (1–5)	5^′ UTR	r = 0.2161	P < 0.0001	r = 0.2770	P < 0.0001	r = 0.1169	P < 0.0001
	CDS	r = − 0.0538	P = 0.0014	r = − 0.0623	P = 0.0003	r = − 0.0080	P = 0.7233
	intron	r = − 0.0455	P = 0.0208	r = − 0.0482	P = 0.0021	r = − 0.0442	P = 0.2358
	GC₃	r = − 0.0596	P = 0.0342	r = − 0.0968	P < 0.0001	r = − 0.0223	P = 0.4972
Interm (6–10)	5^′ UTR	r = 0.1978	P < 0.0001	r = 0.1400	P < 0.0001	r = 0.0624	P < 0.0001
	CDS	r = − 0.1689	P < 0.0001	r = − 0.1549	P < 0.0001	r = − 0.1377	P < 0.0001
	intron	r = − 0.1283	P < 0.0001	r = − 0.0923	P < 0.0001	r = − 0.0229	P = 0.0223
	GC₃	r = − 0.1826	P < 0.0001	r = − 0.1786	P < 0.0001	r = − 0.1453	P < 0.0001
Micro (11–38)	5^′ UTR	r = 0.1234	P < 0.0001	r = 0.2040	P < 0.0001	r = 0.1374	P < 0.0001
	CDS	r = − 0.1647	P < 0.0001	r = − 0.1850	P < 0.0001	r = − 0.1172	P < 0.0001
	intron	r = − 0.0961	P < 0.0001	r = − 0.1294	P < 0.0001	r = − 0.0562	P < 0.0001
	GC₃	r = − 0.1719	P < 0.0001	r = − 0.1974	P < 0.0001	r = − 0.1171	P < 0.0001

Based on reference[23], the chicken autosomes were divided into five pairs of macro-chromosomes (Macro = GGA1–5), five pairs of intermediate chromosomes (Interm = GGA6–10) and 28 pairs of micro-chromosomes (Micro = GGA11–38); for each gene, the GC contents in CDS, introns, and 5^′ UTR were determined; GC₃ were calculated by codonW 1.4.2.; correlation analyses were performed by SAS Proprietary Software Release 8.1; significance tests were corrected for multiple testing by the Bonferroni step-down correction.

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