Expression analysis of the NR5A2 gene and associations between its polymorphisms and reproductive traits in Jiaxing Black sows

Figures & data

Figure 1. Phylogenetic tree constructed based on the NR5A2 nucleotide sequence of 8 species.

Note: Branches were labelled with species’ names. The number above each branch represented bootstrap values.

Table 1. Genotypic frequency, allelic frequency and diversity parameter in the exons of the NR5A2 gene in JXB sows (MEAN ± SD).

SNPs	Genotypic frequencies			Allelic frequencies		P-value	Population parameters
	GG	GA	AA	G	A		He	Ne	PIC
g.84609G > A	0.125	0.539	0.336	0.404	0.596	0.102	0.482	1.929	0.366
	GG	GT	TT	G	T
g.135751G > T	0.586	0.398	0.016	0.785	0.215	0.041	0.337	1.509	0.280
g.138806G > T	0.734	0.203	0.063	0.836	0.164	0.003	0.274	1.378	0.237
	TT	TA	AA	T	A
g.136703T > A	0.805	0.141	0.055	0.875	0.125	5.33E-05	0.219	1.280	0.195
	AA	AT	TT	A	T
g.136706A > T	0.109	0.508	0.383	0.363	0.637	0.269	0.463	1.861	0.356
	GG	GC	CC	G	C
g.136759G > C	0.438	0.500	0.063	0.688	0.313	0.064	0.430	1.753	0.337
	CC	CT	TT	C	T
g138771C > T	0.109	0.320	0.570	0.270	0.730	0.003	0.394	1.650	0.316
g.138933C > T	0.008	0.055	0.938	0.035	0.965	0.028	0.068	1.073	0.066
	TT	TC	CC	T	C
g.138802T > C	0.039	0.281	0.680	0.180	0.820	0.603	0.295	1.418	0.251
	AA	AG	GG	A	G
g.138864A > G	0.734	0.227	0.039	0.848	0.152	0.165	0.258	1.348	0.225

Notes: SNPs: single nucleotide polymorphism sites. P-value: the χ² test of Hardy–Weinberg equilibrium: p > 0.05 suggested the population conformed to Hardy–Weinberg equilibrium. PIC: polymorphism information content. PIC > 0.5 meant highly polymorphic, 0.25 < PIC < 0.5 signified moderate polymorphism, PIC < 0.25 showed low polymorphism. He: heterozygosity. Ne: effective number of alleles.

Figure 2. Analysis of blocks with 5 SNPs in the NR5A2 gene in JXB sows.

Note: The values in the squares indicate the paired linkage disequilibrium (LD) values (D’) of the SNPs. When D’ = 1, the values will not be displayed. The redder the square, the stronger the LD. The haplotype block was defined using the default setting of the Haploview software.

Table 2. Haplotypes based on the block 1 and frequencies in JXB sows.

Haplotypes	g.84609G > A	g.136706A > T	g.136759G > C	g.138802T > C	g.138864A > G	Frequency
H1	G	A	G	T	A	0.024
H2	G	A	G	T	C	0.004
H3	G	A	G	C	A	0.016
H4	G	A	G	C	C	0.012
H5	G	A	C	T	C	0.008
H6	G	T	G	T	A	0.028
H7	G	T	C	T	A	0.036
H8	G	T	C	C	A	0.432
H9	A	A	G	T	C	0.136
H10	A	A	C	T	A	0.024
H11	A	T	G	T	A	0.108
H12	A	T	C	T	A	0.164
H13	A	T	C	T	C	0.004
H14	A	T	C	C	A	0.004

Table 3. Association of five SNPs of the NR5A2 gene with reproductive traits in Jiaxing Black sows (MEAN ± SD).

SNPs	Traits/Number	Genotypes (mean ± SD)
g.84609G > A		GG	GA	AA
	N	16	69	43
	TNB	12.83 ± 1.61	12.87 ± 1.72	13.08 ± 1.25
	NBA	12.01 ± 1.99	12.23 ± 1.79	12.46 ± 1.32
	LWB (kg)	13.42 ± 2.87	13.9 ± 2.36	13.85 ± 2.05
	NSB	1.91 ± 1.84	1.37 ± 1.20	1.38 ± 1.45
g.136706A > T		AA	AT	TT
	N	14	65	49
	TNB	12.72 ± 1.69	12.81 ± 1.70	13.17 ± 1.27
	NBA	11.8 ± 12.04	12.19 ± 1.84	12.56 ± 1.28
	LWB (kg)	13.32 ± 3.04	14.06 ± 2.63	13.84 ± 1.92
	NSB	2.08 ± 1.89	1.35 ± 1.23	1.37 ± 1.35
g.136759G > C		GG	GC	CC
	N	56	64	8
	TNB	13.24 ± 1.22^a	12.83 ± 1.72^ab	11.78 ± 1.57^b
	NBA	12.61 ± 1.23^a	12.15 ± 1.88^ab	11.20 ± 2.20^b
	LWB (kg)	13.92 ± 2.02	13.97 ± 2.54	13.09 ± 3.93
	NSB	1.46 ± 1.28	1.42 ± 1.29	1.50 ± 2.45
g.138802T > C		TT	TC	CC
	N	5	36	87
	TNB	12.14 ± 1.70	12.89 ± 1.76	13.01 ± 1.45
	NBA	11.20 ± 1.14	12.02 ± 2.08	12.46 ± 1.48
	LWB (kg)	12.29 ± 2.30	13.62 ± 2.19	14.10 ± 2.50
	NSB	1.76 ± 1.71	1.63 ± 1.69	1.34 ± 1.20
g.138864A > G		AA	AG	GG
	N	94	29	5
	TNB	13.07 ± 1.44	12.66 ± 1.83	12.14 ± 1.70
	NBA	12.50 ± 1.47^a	11.79 ± 2.19^b	11.20 ± 1.14^ab
	LWB (kg)	14.09 ± 2.42	13.54 ± 2.38	12.29 ± 2.30
	NSB	1.37 ± 1.17	1.60 ± 1.85	1.76 ± 1.71

Notes: SNPs: single nucleotide polymorphism sites. TBA, total number of piglets born; NBA, number of piglets born alive; NSB, number of stillborn piglet; LWB, litter weight at birth; N: number of sows. Means with different lowercase superscripts differed significantly (p < 0.05); means with different capital superscripts differed highly significantly (p < 0.01); means with the same letter did not differ significantly (p > 0.05).

Table 4. Association of diplotypes of the NR5A2 gene with reproductive traits in Jiaxing Black sows (MEAN ± SD).

Diplotype	N	Traits (mean ± SD)
		TNB	NBA	LWB (kg)	NSB
H8H12	40	13.10 ± 1.26^ab	12.51 ± 1.31	13.89 ± 2.05	1.37 ± 1.44
H8H11	26	12.51 ± 1.77 ^a	12.06 ± 1.84	13.98 ± 2.78	1.16 ± 0.94
H8H9	24	12.70 ± 1.94 ^ab	11.89 ± 2.14	13.60 ± 2.30	1.39 ± 1.63
H6H8	7	13.43 ± 1.10^ab	12.76 ± 0.97	14.20 ± 2.72	2.04 ± 0.65
H7H8	6	14.06 ± 1.20 ^b	13.32 ± 1.08	13.90 ± 1.50	1.54 ± 1.01

Notes: We deleted diplotypes with a diplotypes frequency of less than 0.03, the frequencies of these 17 diplotypes have been summarised in Table S2 in the supplement. SNPs: single nucleotide polymorphism sites. TBA: total number of piglets born; NBA: number of piglets born alive; NSB: number of stillborn piglet; LWB: litter weight at birth N: number of sows. Means with different lowercase superscripts differed significantly (p < 0.05); means with the same letter did not differ significantly (p > 0.05).

Figure 3. Relative expression levels of pig NR5A2 mRNA in 11tissues with the average ΔCt value of heart as the calibrator.

Note: Data were shown as the mean ± SD for 5 pigs. Columns ‘**’showed highly significant difference (p < 0.01).

Figure 4. Relative expression levels of the pig NR5A2 mRNA in ovary with different genotypes.

Note: In the loci of g.136759G > C, g.138864A > G with the average ΔCt value of CC and AG genotype as the calibrator, respectively. Data were shown as the mean ± SD for 5 pigs of each genotype. The column with ‘**’ showed a significant difference (p < 0.01).