Novel copy number variations of the CHRM3 gene associated with gene expression and growth traits in Chinese Datong yak (Bos grunniens)

Figures & data

Table 1. qPCR primers designed based on bovine genomic sequences.

Level	Accession No.	Gene Name	Primer Sequence (5′–>3′)	Product Length (bp)	Annealing Temperature (°C)
DNA	NM_174270.2	CHRM3	F: AGGGCTTCAGAACTATGGACAG	149	58.13
			R: AGCTAGGATGCCCGGGATTG		59.5
	NM_001025314.2	BTF3	F: AACCAGGAGAAACTCGCCAA	166	55.40
			R: TTCGGTGAAATGCCCTCTCG		57.45
mRNA	NM_174270.2	CHRM3	F: GGCTATCCATTGACTACGTGG	124	57.80
			R: GCTCGCTTTGTTGTTCGT		54.00
	NM_001034034.2	GAPDH	F: ATGAAAGGGCCATCACCATC	204	55.85
			R: GTGGTTCACGCCCATCACA		60.00

Table 2. An association analysis of the copy number variations of the CHRM3 gene with growth traits in the Datong yak breed.

Age	Growth traits	CNV type (Mean ± SE)			p-Value
		Loss (n = 32)	Normal (n = 61)	Gain (n = 129)
6 months(n = 222)	Body height (cm)	90.4 ± 0.8^b	90.9 ± 0.5^b	92.8 ± 0.2^a	0.001
	Body length (cm)	88.2 ± 0.8^b	88.8 ± 0.5^b	90.4 ± 0.3^a	0.001
	Chest girth (cm)	116.3 ± 1.3b	118.7 ± 0.8^b	121.5 ± 0.7^a	0.0001
	Cannon width (cm)	12.2 ± 0.07	12.1 ± 0.03	12.1 ± 0.03	0.44
	Body weight (kg)	83.9 ± 2.2b	88.3 ± 1.5^b	93.2 ± 0.9^a	0.0001
3 years (n = 70)		Loss (n = 4)	Normal (n = 18)	Gain (n = 50)
	Body height (cm)	103.1 ± 1.5	103.7 ± 0.7	104.6 ± 0.5	0.53
	Body length (cm)	114.4 ± 3.6	114.1 ± 0.9	111.8 ± 0.7	0.78
	Chest girth (cm)	141.5 ± 3.8	147.7 ± 1.4	148.4 ± 0.9	0.12
	Cannon width (cm)	16.3 ± 0.3	16.4 ± 0.1	16.5 ± 0.07	0.62
	Body weight (kg)	163.6 ± 12.3	177.1 ± 3.9	175.7 ± 4.4	0.68
5 years (n = 93)		Loss (n = 16)	Normal (n = 17)	Gain (n = 60)
	Body height (cm)	108.9 ± 0.7	108.9 ± 0.7	110.1 ± 0.4	0.2
	Body length (cm)	120.8 ± 0.7^b	122.4 ± 0.7^a	124.6 ± 0.6^a	0.003
	Chest girth (cm)	150.8 ± 1.8	152.7 ± 1.2	155.7 ± 1	0.05
	Cannon width (cm)	16.1 ± 0.1	16.2 ± 0.2	16.2 ± 0.1	0.81
	Body weight (kg)	195.3 ± 5.1^b	202.8 ± 2.8^a	217.9 ± 4.1^a	0.008

Note: Different letters (^a,b) indicate significant differences (p < 0.05); SE: Standard error; n: number of observations.

Figure 1. Distributions of the CNV of the CHRM3 gene in five yak breeds. (A) Box plot of CNV distributions of the CHRM3 gene in five yak breeds (n=30). (B) Relative frequency of copy numbers classified as the loss (0 and 1), normal (2), and gain (>2) types in five yak populations. Copy numbers were determined by rounding to the nearest integer.