SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

Gebrehiwot, Netsanet Z.; Strucken, Eva M.; Marshall, Karen; Aliloo, Hassan; Gibson, John P.

doi:10.1186/s12711-021-00615-4

Genetics Selection Evolution

Table 1 Animal populations, numbers, and sources

From: SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

Breed	Breed group	Geographical location	Origin/country	Number of animals	Array (Illumina)	Genotype source
Reference samples
Ayrshire	EuB.t	Canada	Canada	20	BovineHD	Canadian Dairy Network
Friesian	EuB.t	European	UK	25	BovineHD	SRUC
Guernsey	EuB.t	USA and UK	USA and UK	20	BovineHD	Bovine HapMap et al. [32]
Holstein	EuB.t	USA and NZ	USA and NZ	20	BovineHD	Bovine HapMap consortium et al. [32]
Jersey	EuB.t	USA and NZ	USA and NZ	20	BovineHD	Bovine HapMap consortium et al. [32]
Pooled Bos indicus	B.i	Indian	India	105	BovineHD	Strucken et al.^a
Baoule	AfB.t	West African	Burkina Faso	9	BovineHD	GRRFAC
N’Dama	AfB.t	West African	Guinea	20	BovineHD	Bovine HapMap consortium et al. [32]
N’Dama	AfB.t	West African	Senegal	7	BovineHD	GRRFAC
Montbeliarde	EuB.t	European	France	20	BovineSNP50	Decker et al. [18]
N’Dama1	AfB.t	West African	Cote d’Ivoire	14	BovineSNP50	Decker et al. [18]
Baoule	AfB.t	West African	Burkina Faso	20	BovineSNP50	Decker et al. [18]
Lagune	AfB.t	West African	Benin	20	BovineSNP50	Decker et al. [18]
Somba	AfB.t	West African	Togo	20	BovineSNP50	Decker et al. [18]
Target populations
Sheko1	Sanga	East African	Ethiopia	18	BovineHD	Bovine HapMap consortium et al. [32]
Ankole	Sanga	East African	Uganda	35	BovineHD	DGEA [15]
SEAZ	zebu	East African	Kenya	21	BovineHD	DGEA [15]
Danakil-Harar	zebu	East African	Ethiopia	30	BovineHD	DGEA [15]
Begait-Barka	zebu	East African	Ethiopia	27	BovineHD	DGEA [15]
Boran	zebu	East African	Ethiopia	28	BovineHD	DGEA [15]
Boran	zebu	East African	Kenya	28	BovineHD	DGEA [15]
Fogera	zebu	East African	Ethiopia	28	BovineHD	DGEA [15]
Iringa-Red	zebu	East African	Tanzania	11	BovineHD	DGEA [15]
Singida-White	zebu	East African	Tanzania	22	BovineHD	DGEA [15]
Central Highland	zebu	East African	Ethiopia	9	BovineHD	DGEA [15]
Kenyan crossbred	Crossbred	East African	Kenya	1378	BovineHD	DGEA [15]
Uganda crossbred	Crossbred	East African	Uganda	555	BovineHD	DGEA [15]
Ethiopia crossbred	Crossbred	East African	Ethiopia	545	BovineHD	DGEA [15]
Tanzania crossbred	Crossbred	East African	Tanzania	462	BovineHD	DGEA [15]
Sheko	Sanga	East African	Ethiopia	17	BovineSNP50	Decker et al. [18]
Madagascar-zebu	zebu	Madagascar	Madagascar	20	BovineSNP50	Decker et al. [18]
Lagunaire	AfB.t	West African	West Africa	5	BovineHD	Bovine HapMap consortium et al. [32]
Senegal crossbreed	Crossbred	West African	Senegal	141	BovineHD	CTLGH
N’Dama2	AfB.t	West African	Southeast Burkina Faso	14	BovineSNP50	Decker et al. [18]
N’Dama3	AfB.t	West African	Southwest Burkina Faso	17	BovineSNP50	Decker et al. [18]
Djakore	zebu	West African	Senegal	7	BovineSNP50	Marshall et al. [28]
Gobra	zebu	West African	Senegal	118	BovineSNP50	Marshall et al. [28]
Maure	zebu	West African	Senegal	12	BovineSNP50	Marshall et al. [28]
Gobra x Maure	zebu	West African	Senegal	10	BovineSNP50	Marshall et al. [28]
Bororo	zebu	West African	Chad	20	BovineSNP50	Decker et al. [18]
Fulani	zebu	West African	Benin	20	BovineSNP50	Decker et al. [18]
Kuri	AfB.t	West African	Chad	20	BovineSNP50	Decker et al. [18]
Borgou	zebu	West African	Benin	20	BovineSNP50	Decker et al. [18]
Senegal crossbreed	Crossbred	West African	Senegal	253	BovineSNP50	Marshall et al. [28]
Total				4231

EuB.t = European Bos taurus, AfB.t = African Bos taurus, B.i = Bos indicus, USA = United States of America, UK = United Kingdom, NZ = New Zealand. All the indigenous and crossbred populations were used for total dairy proportion estimation, while only crossbreds were used for the parentage assignment study
^apersonal communication: Strucken EM, Gebrehiwot, NZ, Swaminathan M, Joshi S, Al kalaldeh M, and JP Gibson. Genetic diversity and effective population sizes of thirteen Indian cattle breeds

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ISSN: 1297-9686

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