Genetic variability of Nero Lucano pig breed at IGF2, LEP, MC4R, PIK3C3, RYR1 and VRTN loci

Figures & data

Table 1. Primer sequences and restriction enzymes used for genotyping Nero Lucano pig DNA samples.

Gene	Polymorphic site	Primers (5’→3’)	Restriction enzymes
IGF2^a	−366G>A	F: CCTCTCTGCTCTCGCCACATC R: GTAGGCGGCTGGGATGAGTG	PstI
	−225C>G	F: CAGGTTGCCCCCAGTTTAGAC R: TTCTCCACTCCGACGCAG	Eco0109I
	−209G>C		MboI
	−182T>C		Dra III
LEP^b	2728G>A	F: GGTTGGGCAGGGAGTTCA R: ACAAAACCTGGCACTATGGCT	HindIII
	3469T>C	F: CACGCCAGCCCAAGGAGTT R: GTTCCATCTCCAGCTCACCGC	HinfI
MC4R^c	892A>G	F: GCCATAGCCAAGAACAAGA R: AAATGGGGACAGAGGAGAC	TaqI
PIK3C3^d	2058A>G	F: TGTGATGTCAATGCCAGTTA R: TACTAACAGGTGGAAATGCTC	BsrSI
	2604C>T	F: GAAGAGGCAGTCCATTACATAC R: GTGTGGCAGAGGTCTTGA	NlaIII
RYR1^e	8413C>T	F: GTTCCCTGTGTGTGTGCAATGGTG R: ATTACTGAGAACTTGCTCCCTGGCC	CfoI
VRTN^f	19034A>C	F: TGACCCCTGACAAAAGCAT R: AGTTGGCTGTAGACGGTCC	MaeIII
	del/ins291	F: GAGGCCAACCCATCTACCA R: GCATTCATTCACCCCTTGG	‒

^a Aslan et al. (2012);

^b Kennes et al. (2001); Stratil et al. (1997);

^c Fan et al. (2009);

^d Kim et al. (2005a, 2005b);

^e Fujii et al. (1991);

^f Fan et al. (2013).

Table 2. Genotype distribution and allele frequencies at nine polymorphic sites in Nero Lucano pig.

Gene	Polymorphic site	N	Genotypes			Allele frequencies		χ^2	p-value
IGF2	−366G>A	227	GG = 0	GA = 18	AA = 209	fG = 0.0396	fA = 0.9604	1.0590	.3034
	−225C>G	229	CC = 0	CG = 18	GG = 211	fC = 0.0393	fG = 0.9607	1.0590	.3034
	−182T>C	226	TT = 0	TC = 18	CC = 208	fT = 0.0398	fC = 0.9602	1.0590	.3034
LEP	2728G>A	227	GG = 29	GA = 120	AA = 78	fG = 0.3921	fA = 0.6079	2.7900	.0948
	3469T>C	227	TT = 103	TC = 103	CC = 21	fT = 0.6806	fC = 0.3194	0.3740	.5408
MC4R	892A>G	227	AA = 0	AG = 10	GG = 217	fA = 0.0220	fG = 0.9780	1.0050	.3161
PIK3C3	2604C>T	218	CC = 53	CT = 121	TT = 44	fC = 0.5206	fT = 0.4794	2.5610	.1035
VRTN	19034 A>C	217	AA = 195	AC = 22	CC = 0	fA = 0.9493	fC = 0.0507	1.0480	.3059
	del/ins291	217	del/del = 195	del/ins = 22	ins/ins = 0	fdel = 0.9493	fins = 0.0507	1.0480	.3059

Table 3. Comparison among allele frequencies at nine polymorphic sites in five pig breeds.

Breeds	IGF2				LEP				MC4R		PIK3C3		RYR1		VRTN
	−366G>A		−182T>C		2728G>A		3469T>C		892A>G		2604C>T		1843C>T		del/ins291		19034A>C
	G	A	T	C	G	A	T	C	A	G	C	T	C	T	del	ins	A	C
Nero Lucano	0.040	0.960	0.040	0.960	0.392	0.608	0.680	0.320	0.022	0.978	0.521	0.479	1	0	0.949	0.051	0.949	0.051
Pietrain	0.990^a	0.010^a	0.990^a	0.010^a	na	na	0.750^c	0.250^c	0.076^e	0.924^e	na	na	0.971^h	0.029^h	0.500^j	0.500^j	na	na
Duroc	0.964^a	0.036^a	0.956^a	0.044^a	0.910^b	0.090^b	0.768^d	0.232^d	0.879^d	0.121^d	0.715^d	0.285^d	0.917^i	0.083^i	0.460^k	0.540^k	0.460^k	0.540^k
Large White	0.400^a	0.600^a	0.321^a	0.679^a	na	na	0.820^c	0.180^c	0.694^f	0.306^f	0.425^g	0.575^g	0.981^i	0.019^i	0.340^k	0.660^k	0.340^k	0.660^k
Landrace	na	na	na	na	0.850^b	0.150^b	0.940^b	0.060^b	0.188^f	0.812^f	0.600^g	0.400^g	0.972^i	0.028^i	0.290^k	0.710^k	0.290^k	0.710^k

^a Aslan et al. (2012);

^b Kennes et al. (2001);

^c Stratil et al. (1997);

^d Hirose et al. (2014);

^e Piorkowska et al. (2010);

^f Davoli et al. (2012);

^g Kim et al. (2005b);

^h Ilie et al. (2014);

ⁱ Ruan et al. (2013);

^j Burgos et al. (2012);

^k Fan et al. (2013);

Data for IGF2 -209G>C, IGF2 -225C>G and PIK3C3 2058A>G are not shown since unavailable for all cosmopolitan breeds.

na: not available.

Figure 1. UPGMA phylogenetic tree obtained according to genetic distances (Nei et al. 1983) estimated by considering the allele frequencies at the IGF2, LEP, MC4R, PIK3C3, RYR1 and VRTN loci of Nero Lucano, Large White, Landrace, Pietrain and Duroc pig breeds. Bootstrap values (1000 replicates) are reported on the nodes.

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