A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes

Strillacci, Maria G.; Moradi-Shahrbabak, Hossein; Davoudi, Pourya; Ghoreishifar, Seyed Mohammad; Mokhber, Mahdi; Masroure, Anoar Jamai; Bagnato, Alessandro

doi:10.1186/s12864-021-07604-3

BMC Genomics

Table 5 Common and pop_CNVRs for which genes and QTL annotation were available. Complete list of common and pop_CNVRs and QTL_IDs (referring to Bos taurus species) are reported in Supplementary Table 3. QTL_Terms: Trait Names are grouped in Fig. 3 as Traits Type according to Animal Genome Cattle QTL Database. The Table does not include common_CNVRs reported in Table 3

From: A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes

Breed	Chr	Start	End	State	N	Gene	QTL_Terms: Trait Names
AZE	1	186,836,088	187,487,608	complex	14	PDE9A	Bovine respiratory disease, Milk fat yield susceptibility, Milk protein yield, Milk yield
	1	186,836,088	187,487,608	complex	14	SLC37A1	Milk phosphorus content
	1	20,942,758	21,126,649	loss	16	PRAG1	Bovine tuberculosis susceptibility
	2	57,805,999	58,006,839	gain	18	BIN1	Residual feed intake
	8	26,033,634	26,136,325	complex	13	SNX13	Milk protein percentage
	10	72,266,178	72,898,604	complex	16	FAM184A	Subcutaneous fat
	12	15,024,107	15,144,657	loss	13	TTC27	Milk fat yield
	15	78,109,455	78,335,826	loss	12	COL22A1	Milk fat percentage, Milk protein percentage, Milk fat yield, Milk yield, Milk protein yield
	15	8,242,728	8,744,577	loss	13	DECR1	Fat thickness at the 12th rib
	15	16,595,357	16,770,941	gain	14	STK3	Milk fat yield, Milk protein percentage, Milk protein yield
	16	21,588,533	21,771,264	gain	18	WT1	Carcass weight, Milk fat percentage
KHU	2	70,740,089	70,803,405	gain	5	TTN	Udder cleft
	2	159,382,105	159,476,051	loss	5	SLC11A1	Bovine tuberculosis susceptibility, M. paratuberculosis susceptibility
	3	38,990,851	39,088,431	gain	5	ITGAE	Milk conjugated linoleic acid content
	5	36,870,251	37,136,533	gain	7	SPSB1	Milk protein yield, Somatic cell score
	5	98,013,455	98,218,453	loss	6	ANO5	Milk C14 index, Curd firming rate, Meat texture
	6	26,325,308	26,500,901	gain	8	CD2	Calving to conception interval, Inseminations per conception, Milk fat percentage, Net merit, Somatic cell score
	7	31,368,913	31,752,823	loss	5	RUFY3	Milk protein percentage, Milk protein yield, Milk yield, Residual feed intake, Somatic cell score
	8	116,160,601	116,290,580	gain	6	DPP6	Average daily gain, Body weight (birth), Body weight (weaning), Bovine respiratory disease susceptibility
	9	62,716,777	62,830,823	loss	5	SPOCK1	Body depth, Calving ease (maternal), Calving ease, Conception rate, Daughter pregnancy rate, Feet and leg conformation, Foot angle, Length of productive life, Milk fat percentage, Milk fat yield, Milk protein percentage, Milk protein yield, Milk yield, Net merit, PTA type, Rear leg placement - rear view, Rump width, Somatic cell score, Stillbirth, Udder attachment, Udder depth
	10	90,708,913	91,158,966	gain	5	CD109	First service conception, Inseminations per conception
	15	51,487,540	51,850,347	complex	5	CRH	Average daily gain, Carcass weight, Conformation score, Connective tissue amount, Longissimus muscle area, Marbling score, Muscle pH, Subcutaneous fat
	15	51,487,540	51,850,347	complex	5	TRIM55	Carcass weight
	16	10,532,220	10,757,353	loss	5	ACCS	Serotonin level
						ACCSL	Conception rate, Serotonin level
						ALKBH3	Stayability
	17	17,338,207	17,457,683	gain	6	CIT	First service conception QTL, Inseminations per conception
	17	21,924,791	22,056,117	complex	6	SCARB1	Bovine respiratory disease susceptibility, Milk beta-carotene content, Milk fat percentage, Milk protein percentage
	18	39,524,271	39,714,171	loss	6	HYDIN	Marbling score
	18	64,081,682	64,220,127	complex	5	PEG3	Body depth, Fat cover, Rump width, Stature, Stillbirth
	18	64,081,682	64,220,127	complex	5	PEG3	Angularity, Body depth, Stature, Stillbirth
	19	41,270,588	41,632,848	gain	6	PDZD2	Somatic cell score
	20	61,571,126	61,672,190	gain	8	IGF1R	Age at puberty, Body size, Body weight (birth), Body weight (weaning), Milk protein yield, Milk yield, Milk protein percentage, Milk fat yield, Milk fat percentage, Inseminations per conception, Bovine respiratory disease susceptibility, Body weight (yearling)
	22	4,920,880	5,171,378	gain	5	NEDD4L	Abomasum displacement
MAZ	3	133,069,378	133,117,242	gain	2	LOXL2	Milk fat yield
	6	96,104,850	96,210,725	loss	3	AGBL4	Milk protein yield, Milk yield
	6	81,057,321	81,285,031	loss	2	ROR1	Body depth, Calving ease (maternal), Calving ease, Daughter pregnancy rate, Length of productive life, Milk protein percentage, Net merit, PTA type, Rump width, Somatic cell score, Stature, Stillbirth (maternal), Stillbirth, Strength, Udder attachment, Udder depth, Udder height
	9	15,430,969	15,568,337	gain	2	ELL2	Milk fat yield, Milk protein yield, Milk yield, Somatic cell score
	12	44,167,548	44,199,735	loss	2	SH3RF3	Teat placement
	18	49,428,499	49,811,006	gain	2	NUMBL	Shear force
	18	49,428,499	49,811,006	gain	2	NUMBL	Conception rate, Daughter pregnancy rate
AZE KHU	1	139,476,110	139,719,306	loss	26	FNDC3B	Calving ease (maternal), Daughter pregnancy rate, Length of productive life, Milk protein yield, Rear leg placement - side view, Somatic cell score, Teat length, Dairy form, Dry matter intake, Milk protein percentage, Net merit, Residual feed intake, Stillbirth, Udder cleft, Calving ease
						GHSR	Average daily gain, Body weight (slaughter), Body weight (test end), Carcass weight
						TNFS10	Interval from first to last insemination, Milk fat percentage, Milk fat yield, Milk protein yield
	3	7,562,702	7,799,466	gain	22	ACOX1	Marbling score, Subcutaneous fat, Subcutaneous fat
	3	67,310,421	67,462,093	complex	18	GALNTL6	Bovine tuberculosis susceptibility
	3	68,223,946	68,369,724	gain	23	GALNTL6	Bovine tuberculosis susceptibility
	4	91,862,787	92,034,556	gain	68	GALNT6	Milk linoleic acid content, Udder cleft, Udder texture
	11	12,884,241	13,195,697	complex	20	NRXN3	Milk protein yield
	14	10,786,055	10,971,651	complex	28	HNF4A	Body length, Body weight (24 months), Chest girth, Height (24 months)
	16	30,256,354	30,582,499	complex	46	ARRB1	Bovine respiratory disease susceptibility, Milk fat percentage, Milk fat yield, Milk yield
	16	30,256,354	30,582,499	complex	46	NEU3	Conception rate, Daughter pregnancy rate, Net merit, Length of productive life
	16	75,669,845	75,781,021	complex	42	CNTN5	Body depth, Calving ease (maternal), Calving ease, Feet and leg conformation, Foot angle, Milk fat percentage, Milk fat yield, Milk protein percentage, Milk protein yield, Net merit, PTA type, Rear leg placement - rear view, Residual feed intake, Rump width, Somatic cell score, Stature, Stillbirth, Strength, Udder attachment, Udder depth, Udder height
	18	12,571,250	12,842,177	complex	37	ZCCHC14	Inseminations per conception
	20	40,344,161	40,510,307	gain	69	PCSK6	Metabolic body weight, Residual feed intake, Dry matter intake
	23	16,558,338	16,817,683	complex	26	PDLIM1	Rump angle
	23	18,714,144	18,844,893	complex	30	CRTAC1	Milk C14 index, Milk fat yield, Milk myristoleic acid content
AZE MAZ	8	70,758,890	71,075,937	complex	14	OSBPL3	Fat thickness at the 12th rib
	9	94,954,953	95,685,910	loss	17	ANGPTL8	Body length
	9	94,954,953	95,685,910	loss	17	ARHGEF18	Fat area to ribeye area ratio

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ISSN: 1471-2164

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