Genetic differentiation between subpopulations of Swedish mountain (Fjäll and Fjällnära) cattle

Figures & data

Table 1. Number of samples from Fjäll and Fjällnära (Fjäll is also divided into old and new samples) and heterozygosity and polymorphic loci. H_o is observed heterozygozity, H_e is expected heterozygosity.

Breed	Total number of samples	Number of males	Number of females	Ho	He	Proportion polymorphic markers
Fjäll (all)	39	19	20	0.3817	0.3727	0.9524
Fjäll (1976–1997)	23	3	20	0.3872	0.3728	0.9422
Fjäll (2000–2015)	16	16	0	0.3738	0.3608	0.9173
Fjällnära	16	2	14	0.3145	0.3727	0.9253

Figure 1. PCA analysis of Fjäll and Fjällnära. The Fjäll samples are divided into the old (SMC_O) samples from animals born 1976-1997 and new (SMC_N) samples from animals born 2000-2015. The Fjällnära samples are divided into the founder farms they originate from. FNC_B (upper right corner) is from Biellojaure, FNC_F (around PC1 0.03, PC2 -0.1) is from Funäsdalen, FNC_K (around PC1 0.05, PC2 -0.15) is from Klövsjö, and FNC_L (around PC2 -0.4) is from Lillhärjåbygget.

Table 2. F_ST values between groups of Fjällnara and old and new Fjäll.

	Fjällnära Biellojaure	Fjällnära Lillhärjåbygget	Fjällnära Funäsdalen	Fjällnära Klövsjö	Fjäll (1976–1997)
Fjällnära Lillhärjåbygget	0.395
Fjällnära Funäsdalen	0.306	0.180
Fjällnära Klövsjö	0.366	0.230	0.154
Fjäll (1976–1997)	0.228	0.140	0.072	0.110
Fjäll (2000–2015)	0.246	0.152	0.083	0.125	0.008

Figure 2. The ADMIXTURE result with K ranging from 2 to 6. The Fjäll samples are divided into the old (SMC_O) samples from animals born 1976–1997 and new (SMC_N,) samples from animals born 2000–2015. The Fjällnära samples are divided into the founder farms they originate from. FNC_B is from Biellojaure, FNC_F is from Funäsdalen, FNC_K is from Klövsjö, and FNC_L is from Lillhärjåbygget.

Table 3. Allele frequencies of SNPs related to functional traits and within parentheses the number of animals being homozygous or heterozygous for the allele.

Breed	BCNAB* (B allele)	Beta lactoglobulin (B allele)	FGF2 (minor allele (A))	Mulefoot (allele A)
Fjäll	5% (4)	60% (34)	42% (8)	1% (1)
Fjällnära	0% (0)	94% (16)	34% (27)	0% (0)
Swedish Red	0% (0)	52% (21)	31% (12)	19% (9)
SH-F**	0% (0)	46% (18)	61% (20)	0% (0)

Notes: *Beta-casein SNP, **Swedish Holstein-Friesian.