Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

BMC Genomics

Table 1 Characterization of the association CNVs

CNV	Supported by		P value after FDR correction							Overlap with
CNV	PennCNV	HapMap	WG	PW	PY	CW	CY	MW	MY	Gene symbol	QTL ID	QTL phenotype
CNV17	Yes	Yes	0.6589	0.0068	0.0036	0.8175	0.5368	0.0010	0.0035	SETD4, CBR1
CNV79	Yes	No	0.2911	0.1268	0.0450	0.1043	0.0580	0.0826	0.1497	DYNC1LI1
CNV93	Yes	Yes	0.0438	0.0002	0.0017	0.0752	0.0484	0.0054	0.0063		22866	Intramuscular fat
CNV95	Yes	Yes	0.0157	0.8172	0.8042	0.0002	0.0000	0.8961	0.8287	PRAME
CNV96	Yes	Yes	0.2910	0.9430	0.8805	0.0382	0.0643	0.9529	1.0000	ZNF280B, HSFY2	19024	Clinical mastitis
CNV97	Yes	Yes	0.0376	0.0015	0.0027	0.0453	0.0191	0.0089	0.0081		19024	Clinical mastitis
CNV98	Yes	Yes	0.0439	0.0011	0.0052	0.0789	0.0637	0.0057	0.0155	EPHB3
CNV99	Yes	No	0.0927	0.3515	0.3329	0.1864	0.0491	0.3428	0.1107	FANCC, TSPY
CNV100	No	No	0.0093	0.0000	0.0000	0.0109	0.0001	0.0000	0.0000	KCNJ12	22873	Intramuscular fat
CNV107	Yes	No	0.6665	0.0074	0.0033	0.9921	0.9579	0.0064	0.0315		20642	Iron content
CNV121	Yes	No	0.0918	0.2194	0.5162	0.0784	0.3762	0.0379	0.4378	COL26A1	15219	Calf size
CNV137	Yes	Yes	0.3419	0.0276	0.0126	0.8045	0.5354	0.0211	0.0434
CNV146	Yes	Yes	0.0132	0.9858	0.8931	0.0663	0.0546	0.9304	0.8783
CNV167	No	No	0.0390	0.7426	0.8412	0.0674	0.1045	0.8952	0.9391		22873	Intramuscular fat
CNV175	Yes	Yes	0.2494	0.1736	0.0704	0.5176	0.0921	0.0772	0.0160
CNV195	Yes	Yes	0.1181	0.1798	0.2897	0.1032	0.2477	0.0371	0.1585		15419	Gestation length
CNV204	Yes	Yes	0.0892	0.9530	1.0000	0.0270	0.0712	0.9434	1.0000	GBP6, GBP4

Note: PennCNV: We applied PennCNV analysis using the same samples. HapMap: The previous study using the Bovine HD microarray data from 27 cattle breeds [18]

ISSN: 1471-2164