Comparison of Four Italian Beef Cattle Breeds by Means of Functional Genes

Figures & data

Table 1. Information on the single nucleotide polymorphisms studied.

Gene	Chromosome	SNP name	Location	Accession No. and base position	SNP
GH	BTA19	GH	Promoter	AY445811:g.358	C>T
GHR	BTA20	GHR-2	Promoter	AF126288:g.149	G>A
GHR	BTA20	GHR-3	Intron IV	AY643807:g.300	A>G
GDF8	BTA2	GDF8-1	Promoter	AJ438578:g.843	T>A
GDF8	BTA2	GDF8-3	Exon I	AY725215:g.229	A>C
GHRL	BTA22	GHRL	Intron III	AY455980:g.446	A>G
LEP	BTA4	LEP-1	Promoter	AB070368:g.528	C>T
LEP	BTA4	LEP-2	Promoter	AB070368:g.1759	G>C
LEP	BTA4	LEP-3	Exon II	AY138588:g.305	T>C
MYF5	BTA5	MYF5	Intron II	M95684:g.1948	A>G
IGF2	BTA29	IGF2	Exon II	AY237543:g.150	C>T
LEPR	BTA3	LEPR	Exon XX	AJ580801:g.115	C>T
NPY	BTA14	NPY-1	Intron II	AY491054:g.284	A>G
NPY	BTA4	NPY-2	Intron II	AY491054:g.666	A>G
NPY	BTA4	NPY-3	Intron II	AY491054:g.3032	C>T
POMC	BTA11	POMC	Intron II	J00021:g.254	C>T
UCP2	BTA15	UCP2	Intron V	AY14782:g.380	G>C
UCP3	BTA15	UCP3	Intron III	AF127030:g.1099	G>A

SNP, single nucleotide polymorphism.

Table 2. Frequencies of alleles in the single nucleotide polymorphisms studied.

SNP name	Alleles		Breeds			FST
		CHI	MAR	PIE	ROM
GDF8-1	A	0.247	0.171	0.000	0.099	0.074
GDF8-3	C	1.000	1.000	1.000	1.000	-
GH	C	1.000	1.000	1.000	1.000	-
GHR-2	A	0.496	0.620	0.462	0.215	0.087
GHR-3	A	0.752	0.682	0.665	0.720	0.005
GHRL	A	0.857	0.932	0.797	0.952	0.037
IGF2	C	0.787	0.669	0.749	0.765	0.010
LEP-1	C	0.937	0.833	0.597	0.633	0.105
LEP-2	C	0.781	0.633	0.137	0.399	0.238
LEP-3	C	0.210	0.407	0.830	0.541	0.204
LEPR	C	0.563	0.529	0.926	0.403	0.159
MYF5	A	0.416	0.560	0.426	0.424	0.014
NPY-1	A	0.097	0.060	0.232	0.129	0.036
NPY-2	C	0.267	0.178	0.311	0.491	0.061
NPY-3	A	1.000	1.000	1.000	1.000	-
POMC	C	0.802	0.924	0.819	0.956	0.039
UCP2	C	0.930	0.917	0.810	0.853	0.022
UCP3	A	0.625	0.581	0.774	0.426	0.064

SNP, single nucleotide polymorphism; CHI, Chianina breed; MAR, Marchigiana breed; PIE, Piemontese breed; ROM, Romagnola breed; F_ST, fixation index. Only one allele per SNP is reported.

Table 3. Mean observed and expected heterozygosity and inbreeding coefficient within population in the studied breeds.

	Ho	He	FIS
CHI	0.35 (0.13)	0.34 (0.13)	-0.027 (-0.057-0.001)
MAR	0.34 (0.159	0.34 (0.15)	0.005 (-0.039-0.043)
PIE	0.34 (0.14)	0.33 (0.14)	-0.022 (-0.061-0.013)
ROM	0.36 (0.16)	0.36 (0.15)	-0.008 (-0.051-0.029)

Ho, observed heterozygosity; He, expected heterozygosity; F_IS, inbreeding coefficient within population; CHI, Chianina breed; MAR, Marchigiana breed; PIE, Piemontese breed; ROM, Romagnola breed. Values in parentheses represent 95% confidence interval.

Table 4. Haplotype frequencies.

Gene	Haplotype		Breeds
		CHI	MAR	PIE	ROM
GHR [GHR-2, GHR-3]	AA	0.49574	0.61981	0.43393	0.20685
AG	0.00004	0.00002	0.02708	0.01064
GA	0.25426	0.06200	0.22891	0.51288
GG	0.24996	0.31816	0.31008	0.26963
LEP [LEP-1, LEP-2, LEP-3]	CCC	0.03602	0.03427	0.00485	0.00493
CCT	0.74430	0.59319	0.13779	0.38868
CGC	0.11462	0.20449	0.45569	0.24038
CGT	0.04133	0.00000	0.00020	0.00045
TCC	0.00000	0.00515	0.00022	0.00014
TCT	0.00014	0.00018	0.00000	0.00012
TGC	0.06183	0.16273	0.36683	0.29229
TGT	0.00178	0.00000	0.03443	0.07302
NPY [NPY-1, NPY-2]	AC	0.00034	0.00037	0.00025	0.00020
AT	0.09715	0.05955	0.23017	0.12760
GC	0.26707	0.17731	0.30851	0.49307
GT	0.63544	0.76277	0.46108	0.37913

CHI, Chianina breed; MAR, Marchigiana breed; PIE, Piemontese breed; ROM, Romagnola breed.

Table 5. Pairwise and global fixation index.

	CHI	MAR	PIE	ROM
CHI	-
MAR	0.0296	-
PIE	0.1877	0.1403	-
ROM	0.1029	0.0786	0.1189	-
Global FST		0.0848 (P=0.001)

CHI, Chianina breed; MAR, Marchigiana breed; PIE, Piemontese breed; ROM, Romagnola breed; F_ST, fixation index. After Bonferroni’s correction all the values are significant.

Table 6. Percentage of animals assigned to each breed.

	Assigned to			Mean probability of assignment
	CHI	MAR	PIE	ROM
CHI	70.8	15.9	5.8	7.5	79.3
MAR	31.4	47.5	10.8	10.3	69.5
PIE	3.5	5.3	87.6	3.6	91.0
ROM	15.4	7.9	11.8	64.9	82.9

CHI, Chianina breed; MAR, Marchigiana breed; PIE, Piemontese breed; ROM, Romagnola breed.