Detection of selective sweeps in cattle using genome-wide SNP data

Ramey, Holly R; Decker, Jared E; McKay, Stephanie D; Rolf, Megan M; Schnabel, Robert D; Taylor, Jeremy F

doi:10.1186/1471-2164-14-382

BMC Genomics

Table 6 Potential causal genes underlying selective sweep regions and their associated function or phenotype

From: Detection of selective sweeps in cattle using genome-wide SNP data

SNP50 discovery breed(s)	AFFXB1P discovery breed(s)	BTA	Sweep position (Mb)	Potential causative gene(s)	Gene or region type^*	Associated function or phenotype
SNP50 Specific Sweep Regions
Hereford	---	6	70.65-70.87	spotted ¹	---¹	white points on face, underline, feet & tail in cattle [8]
Angus, Salers, Shorthorn, Simmental	---	12	25.87-26.23	NBEA	PC	autism spectrum disorder in human [35, 36]
Angus, Salers, Shorthorn, Simmental	---	12	25.87-26.23	MAB21L1	PC	psychiatric disorders in human [37]
Angus, Hanwoo, Hereford, Holstein, Limousin, Simmental	---	24	0.06-0.32	LOC10013911	PS	olfactory receptor-like variants
				LOC783097	PS	olfactory receptor-like variants
				LOC100337172	PS	olfactory receptor-like variants
Co-Discovered Regions (SNP50 and AFFXB1P)
Angus	Angus	1	1.67-2.02	POLL ²	---²	presence or absence of horns in cattle [5, 6, 38]
Holstein	Wagyu	13	15.49-15.74	DGKZ	PC	leptin signaling – linked to human obesity [39]
Angus, Hereford, Jersey, Holstein, Limousin, Simmental	Angus, Simmental	16	45.39-45.65	RERE	PC	embryogenesis and embryonic survival [40–42]
Hanwoo	Simmental, Wagyu	16	52.63-52.86	AGRN	PC	cell adhesion between embryo & maternal tissues [43]
				HES4	PC	oscillation and repression of embryogenesis [44]
				ISG15	PC	acknowledgement & maintenance of pregnancy [45, 46]
Hanwoo	Angus, Simmental	18	14.72-14.97	MC1R	PC	black coat colour in cattle [7]
AFFXB1P Specific Sweep Regions
---	Simmental	1	83.46-83.68	HTR3E	PC	serotonin receptors – social cognition (tameness)
---	Simmental	1	83.46-83.68	HTR3C	PC	in foxes and dogs [47–50]
---	Angus	1	111.66-111.90	LEKR1 CCNL1	PC	reduced birth weight in humans [51]
---	Angus	3	28.19-28.40	TSPAN2	PC	oligodendrocyte signaling & maturation [52, 53]
---	Brahman	5	48.68-48.90	MSRB3	PC	ear floppiness and morphology in dogs [54, 55]
---	Angus, Hanwoo, Simmental, Wagyu	6	5.64-5.99	MAD2L1	PC	proper onset of anaphase during cell division
---	Angus, Simmental, Wagyu	6	106.84-107.30	RGS12	PC	positional candidate for ovulation rate in swine [56]
---	Wagyu	11	33.02-33.26	NRXN1	PC	synaptic function – linked to autism spectrum disorders [57, 58]
---	Simmental	13	66.46-66.70	SAMHD1	PC	innate immune response [59]
---	Angus	14	24.63-25.17	PLAG1	PC	variation in human height [60] and cattle stature [61]
---	Angus, Simmental	16	44.69-44.88	PIK3CD	PC	immune response
---	Angus, Simmental	16	44.69-44.88	SPSB1	PC	immune regulation [62]
---	Simmental, Wagyu	17	73.76-73.97	VpreB	PC	B cell development
---	Simmental, Wagyu	17	73.76-73.97	PRODH	PC	schizophrenia [63]
---	Angus, Simmental	20	71.67-72.01	IgCgamma	PC	immune response
---	Angus, Simmental	20	71.67-72.01	PDCD6	PC	T cell receptor-induced apoptosis
---	Angus, Hanwoo	21	70.11-71.28	AHNAK2	PC	skeletal muscle fiber organization [64]
				IGHE	other	immune response
				CRIP1	PC	immune regulation [65, 66]
				CRIP2	PC	immune regulation [65, 66]
---	Brahman	22	10.70-10.96	TRANK1	PC	bipolar disorder in humans [67]
				DCLK3	PC	brain development [68]
				GOLGA4	PC	golgi identity/structure [69]
				ITGA9	PC	gamete interaction & reduced fertilization success [70]
---	Wagyu	22	49.08-49.45	TLR9	PC	innate immunity
---	Simmental	25	26.43-26.74	HSA16³	HO	autism spectrum disorders [71–73]
---	Angus, Hanwoo Simmental, Wagyu	26	0.21-0.45	OR5D18	PC	olfactory receptor [74]
---	Angus, Hanwoo Simmental, Wagyu	26	0.21-0.45	various loci⁴	PS	olfactory receptor-like variants
---	Wagyu	27	17.91-18.11	CBX1	PC	epigenetic reprogramming of embryo/gene expression [75–77]
---	Simmental	28	30.48-30.71	ADK	PC	physiological state – blood flow, neurotransmission in brain [78]
---	Hanwoo, Simmental, Wagyu	29	0.32-0.56	ANKRD26P3	PS	ncRNA regulatory activity
---	Hanwoo, Simmental, Wagyu	29	0.32-0.56	CCDC144C	PS	ncRNA regulatory activity

*Gene and region types are defined as: PC protein coding, PS pseudogene, HO human orthologue, other = known type, unspecific.
¹The causal mutation has not yet been identified but the locus has been fine mapped to this region, see reference.
²The POLL locus in cattle has been identified but is characterised by allelic heterogeneity among breeds.
³This region is orthologous to human chromosome 16 (HSA16).
⁴There are 13 loci identified as olfactory receptor-like variants which have been determined to be pseudogenes.

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ISSN: 1471-2164

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