Investigation of a Short Interspersed Nuclear Element Polymorphic Site in the Porcine Vertnin Gene: Allele Frequencies and Association Study With Meat Quality, Carcass and Production Traits in Italian Large White pigs

Figures & data

Table 1. Genotype and allele frequencies of the VRTN g.20311_20312ins291 polymorphism in different pig breeds and in Italian wild boars.

Breeds/subspecies	N of genotyped	Genotypes – n of pigs			Allele frequencies
	animals	Q/Q	Q/WT	WT/WT	Q^°	WT^°
Italian Large White^#	824	132	324	368	0.357	0.643
Italian Duroc	22	7	10	5	0.545	0.455
Italian Landrace	21	13	5	3	0.738	0.262
Cinta Senese	21	2	1	18	0.119	0.881
Mora Romagnola	22	5	11	6	0.477	0.523
Casertana	22	4	8	10	0.364	0.636
Nero Siciliano	20	0	2	18	0.050	0.950
Apulo Calabrese	20	0	5	15	0.125	0.875
Italian Wild Boar	22	0	0	22	0.000	1.000

°Q and WT alleles are as defined in Materials and methods;

^#pigs used in the association studies.

Table 2. Association between the VRTN g.20311_20312ins291 polymorphism (Q and WT alleles) and several meat quality and production traits in the 270 Italian Large White pigs. Least square means±standard errors of the different genotypes are presented.

	Genotypes			P
	Q/Q n=44	Q/WT n=85	WT/WT n=141
Traits
EBV ADG, g	32.364 ± 4.025	33.106±2.896	33.901±2.248	0.939
EBV LC, kg	2.293±0.279	1.938±0.200	1.949±0.156	0.520
EBV BFT, mm	-2.475±0.573	-1.694±0.412	2.184±0.320	0.483
EBV HW, kg	0.409±0.093	0.553±0.066	0.656±0.050	0.054
EBV FGR	-0.135±0.023	-0.148±0.017	-0.153±0.013	0.792
RR ADG, g	-1.588±11.947	-7.547±8.497	1.541±6.597	0.700
RR LC, kg	0.390±0.409	-0.136±0.291	-0.042±0.226	0.559
RR BFT, mm	-0.638±0.772	0.181±0.549	-0.073±0.426	0.689
RR HW, kg	-0.293±0.199	-0.125±0.140	0.163±0.106	0.071^°
RR FGR	0.014±0.049	0.014±0.035	0.025±0.027	0.960
pH1	5.942±0.0370	5.923±0.027	5.922±0.022	0.882
pHu	5.624±0.031	5.655±0.023	5.665±0.019	0.485
Glycogen, μmol	50.315±3.505	48.057±2.633	48.347±2.193	0.843
Lactate, μmol	52.880±2.344	58.108±1.729	57.214±1.359	0.170
GP, μmol	103.100±3.545	106.270±2.654	105.490±2.188	0.739
Catb, nmol	1.159±0.022	1.185±0.027	1.140±0.022	0.368

EBV, Estimated Breeding Value; ADG, average daily gain; LC, lean cuts; BFT, back fat thickness; HW, ham weight; FGR, feed:gain ratio; RR, Random Residuals; pH₁, pH at 2 h post-mortem; pH_u, pH at 24 h post-mortem; glycogen and lactate (μmol of lactic acid equivalent per g of fresh muscle); GP, glycolytic potential (μmol of lactic acid equivalent per g of fresh muscle); Catb, cathepsin B activity (nmol of 7-amino-4-methylcoumarin released/min/g muscle).

°P<0.10.

Table 3. Distribution of VRTN genotypes and alleles in the two groups of Italian Large White pigs with extreme and divergent (negative and positive tails) estimated breeding values for back fat thickness. Chi square tests compare genotype and allele distributions in the two tails.

	Genotypes, n of animals (frequency)			Alleles, n (frequency)
	Q/Q	Q/WT	WT/WT	Q^°	WT^°
BFT EBV tails/test
Negative	38 (0.138)	118 (0.429)	119 (0.433)	194 (0.353)	356 (0.647)
Positive	50 (0.179)	121 (0.434)	108 (0.387)	221 (0.396)	337 (0.604)
Chi square (P)	0.337	0.136

BFT, back fat thickness; EBV, Estimated Breeding Value.

°Q and WT alleles are as defined in Materials and methods.

Table 4. Probability, least square means±standard errors obtained in the association study by general linear model procedure between the VRTN polymorphism and estimated breeding values, and random residuals for average daily gain, feed gain ratio, ham weight and lean cuts in the tails of pigs with extreme and divergent estimated breeding values for back fat thickness.

Tail^°	Genotype (n of pigs)	ADG-EBV	FGR-EBV	HW-EBV	LC-EBV	ADG-RR	FGR-RR	HW-RR	LC-RR
Negative	Q/Q (38)	37.6329±4.618	-0.1445±0.0276	0.489±0.093	4.532±0.245	-0.021±0.013	0.077±0.057	0.235±0.192	1.989±0.442
	Q/WT (118)	38.1448±2.621	-0.196±0.016	0.619±0.053	4.299±0.139	-0.006±0.007	-0.054±0.032	0.113±0.105	1.578±0.242
	WT/WT (119)	40.6813±2.609	-0.196±0.0156	0.798±0.053	4.309±0.138	0.010±0.007	-0.110±0.0301	0.638±0.102	1.801±0.236
Positive	Q/Q (50)	6.820±4.0259	-0.008±0.024	0.043±0.081	-1.329±0.214	-0.002±0.010	0.047±0.046	-0.495±0.105	-1.741±0.359
	Q/WT (121)	6.587±2.588	-0.037±0.015	0.108±0.052	-1.449±0.137	-0.004±0.007	0.089±0.030	-0.342±0.101	1.762±0.234
	WT/WT (108)	8.602±2.739	-0.051±0.0164	0.220±0.055	-1.409±0.145	0.005±0.007	0.037±0.033	-0.314±0.109	-1.596±0.251
P		0.923	0.275	0.006^#	0.914	0.170	0.043^#	0.007^#	0.897

ADG, average daily gain; EBV, estimated breeding values; FGR, feed gain ratio; HW, ham weight; LC, lean cuts; RR, random residuals.

°Data are reported for each genotype within tail (tails are constituted by pigs with extreme and divergent back fat thickness EBV);

^# significant results.