Association study and expression analysis of GPC1 gene copy number variation in Chinese Datong yak (Bos grunniens) breed

Figures & data

Table 1. Primers designed for qPCR based on bovine genome sequences.

Level	Accession no.	Gene name	Primers Sequence (5′->3′)	Product length, bp	Annealing temperature, °C
DNA	XM_014480020.1	GPC1	F: GCTTTGCTTTTCCTCACGGG	86	57.45
			R: ACATGGTTGGCGTGTTTGTG		55.40
	NM_001025314.2	BTF3	F:AACCAGGAGAAACTCGCCAA	166	55.40
			R: TTCGGTGAAATGCCCTCTCG		57.45
mRNA	XM_015462903.1	GPC1	F: CTGCAGAAGCTGGTCTCCGAA	90	59.76
			R: CTTCTCACTGCACAGCGTTCC		59.76
	NM_001034034.2	GAPDH	F: ATGAAAGGGCCATCACCATC	204	55.85
			R: GTGGTTCACGCCCATCACA		60.00

Figure 1. Distributions of the CNV of the GPC1 gene in five yak breeds. (A) Scatter plot of CNV of the GPC1 gene in five yak breeds (n = 30). (B) The frequency of copy numbers (0 and 1 = loss, 2= normal and >2= gain copy number types) in five yak populations. CNV: copy number variation.

Table 2. Analysis of the association between CNVs in the GPC1 gene and growth traits in Datong yak breeds.

Age	Growth trait	CNV type (Mean ± SE)			p-value
		Loss (n = 100)	Normal (n = 120)	Gain (n = 133)
6 months (n = 353)	Body height, cm	91.6 ± 0.40^ab	92.4 ± 0.30^a	90.6 ± 0.40^b	.0020
	Body length, cm	90.0 ± 0.30^a	89.4 ± 0.30^b	88.3 ± 0.40^b	.0030
	Chest girth, cm	120.8 ± 0.50^a	120.2 ± 0.60^a	118.3 ± 0.60^b	.0090
	Cannon width, cm	12.1 ± 0.03	12.1 ± 0.03	12.1 ± 0.03	.7700
	Body weight, kg	88.7 ± 1.10^b	95.7 ± 0.80^a	87.2 ± 1.10^b	.0001
		Loss (n = 17)	Normal (n = 26)	Gain (n = 140)
5 years (n = 183)	Body height, cm	111.8 ± 0.3^a	109.9 ± 0.5^b	108.9 ± 0.30^b	.0020
	Body length, cm	128.3 ± 2.1^a	122.7 ± 0.6^b	122.9 ± 0.30^b	.0001
	Chest girth, cm	161.4 ± 2.9^a	152.9 ± 1.3^b	154.6 ± 0.60^b	.0010
	Cannon width, cm	16.4 ± 0.4	16.2 ± 0.1	16.2 ± 0.07	.7300
	Body weight, kg	236.2 ± 13.6^a	204.3 ± 3.8^b	208.2 ± 2.10^b	.0010

Note: Different letters (^a,b) indicate significant differences (p < .05).CNV: copy number variation; SE: standard error.

Figure 2. Expression profiling of the GPC1 gene at two ages of Datong yak. (A) Expression pattern of the GPC1 gene in foetal yak. (B) Expression Pattern of the GPC1 gene in the adult yak. (C) Comparison of expression of GPC1 gen in two ages. The error bar indicated the standard deviation (SD). Different letters indicate significant difference (p < .05). CNV: copy number variation.