绵羊SMAD1基因组织表达及其多态性与产羔数关联分析

doi:10.3864/j.issn.0578-1752.2019.04.015

Abstract

Abstract:

【Objective】Sheep litter size is a very complex trait influenced by many factors. Ovulation is one of the most important factors. SMAD protein plays an important role in the mammalian follicular development as well as growth and differentiation process of granulosa cell. To reveal the relationship between the SMAD family member 1 (SMAD1) gene and the litter size of sheep and its mechanism affecting litter size, meanwhile to provide a scientific basis for sheep molecular breeding, we researched the expression pattern of SMAD1 in Small Tail Han sheep with different fertility and analyzed the relationship between polymorphism and the litter size in sheep, based on the previous sheep genome resequencing data. 【Method】First, reverse transcription PCR was used to detect the expression of SMAD1 gene in Small Tail Han sheep (brain, cerebellum, hypothalamus, pituitary, uterus, ovary, oviduct, heart, liver, spleen, lung, kidney, adrenal glands, thyroid, large intestine, small intestine, pancreas, rumen, and kidney fat) tissues with different lambing abilities. Then, Real-time PCR was performed to investigate the expression of SMAD1 gene in Small Tail Han sheep reproduction tissues (hypothalamus, pituitary, uterus, ovary, and oviduct) with different lambing abilities. Multiparous (Small Tail Han sheep (n=380), Hu sheep (n=101), Cele black sheep (n=52)) and uniparous (Sunite (n=21), Tan sheep (n=22), Prairie Tibetan sheep (n=161)) sheep breeds were selected and Sequenom MassARRAY ^?SNP assay was applied to genotype five single nucleotide polymorphism sites (SNPs) of SMAD1 gene. Then the association was analyzed between SMAD1 and litter size in Small Tail Han sheep by using SPSS 19.0. 【Result】The results of RT-PCR revealed that SMAD1 gene expressed in 19 tissues. The qPCR showed that the expression of SMAD1 was higher in ovary (P<0.01), hypothalamus (P<0.05) and pituitary (P<0.05) of uniparous Small Tail Han sheep than that in multiparous sheep. From genotyping, this study found that the genotype frequencies and allele frequencies of the g.12485895A>G, g.12487558G>A and g.12487190G>T of SMAD1 gene were significantly different between uniparous and multiparous sheep (P<0.05). However, g.12508874T>C and g.12487467A>G had no significantly different between uniparous and multiparous sheep (P>0.05). Population genetic analysis indicated that g.12485895A>G, g.12487558G>A, g.12508874T>C, g.12487467A>G, and g.12487190G>T loci were at moderate polymorphism (0.25<PIC<0.5) in Small Tail Han sheep, Hu sheep, Prairie Tibetan sheep, Cele black sheep, Sunite and Tan sheep, while g.12508874T>C was at low polymorphism (PIC<0.25) in Tan sheep. The χ ² test indicated that the g.12485895A>G and g.12487467 A>G were not under Hardy-Weinberg equilibrium (P<0.05) in Small Tail Han sheep and Prairie Tibetan sheep. g.12487558 G>A was not under Hardy-Weinberg equilibrium (P<0.05) in Small Tail Han sheep and Hu sheep. g.12487190 G>T was not under Hardy-Weinberg equilibrium (P<0.05) in Prairie Tibetan sheep. Other loci were under Hardy-Weinberg equilibrium (P>0.05) in six sheep breeds. Association analysis indicated that the polymorphism of g.12487190 G>T had significant correlation with the litter size in Small Tail Han sheep, while the litter size of TT was higher than GT and GG in the first three births (P<0.05). However, the polymorphism of g.12485895A>G, g.12487558G>A, g.12508874T>C and g.12487467A>G had no significant correlation with the litter size in Small Tail Han sheep. The combination of SMAD1 gene g.12487190G>T and FecB (A746G) gene showed that the number of lambs in AA-GG, AA-GT, AA-TT genotypes was significantly low than that of other genotypes (P<0.05), respectively. 【Conclusion】Therefore, it could be concluded that SMAD1 might be the key gene for litter size and the g.12487190G>T locus might provide a basis for litter size trait selection in sheep.

Key words: sheep, SMAD1 gene, tissue expression, SNP genotyping, litter size

TIAN ZhiLong,TANG JiShun,SUN Qing,WANG YuQin,ZHANG XiaoSheng,ZHANG JinLong,CHU MingXing. Tissue Expression and Polymorphism of Sheep SMAD1 Gene and Their Association with Litter Size[J].Scientia Agricultura Sinica, 2019, 52(4): 755-766.

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Figures/Tables 9

Table 1

Fig. 1

Fig. 2

Fig. 3

Fig. 4

Table 2

Table 3

Population genetic analysis of different loci at SMAD1 gene"

位点 Locus	品种 Breed	基因型频率 Genotype frequency			基因频率 Allele frequency		多态信息含量（PIC） Polymorphism information content	杂合度（HE） Heterozygosity (HE)	有效等位基因数 Effective number of allele (NE)	卡方值（P） χ² test (P value)
g.12485895A>G		AA	AG	GG	A	G
	小尾寒羊 Small Tail Han sheep	0.33	0.44	0.23	0.55	0.45	0.37	0.49	1.98	0.02
	湖羊 Hu sheep	0.35	0.54	0.11	0.62	0.38	0.36	0.47	1.89	0.12
	草原型藏羊 Prairie Tibetan sheep	0.58	0.32	0.10	0.73	0.27	0.31	0.39	1.64	0.02
	策勒黑羊 Cele black sheep	0.06	0.50	0.44	0.31	0.69	0.34	0.43	1.74	0.21
	苏尼特羊 Sunite sheep	0.29	0.48	0.23	0.52	0.48	0.37	0.50	2.00	0.83
	滩羊 Tan sheep	0.27	0.41	0.32	0.48	0.52	0.37	0.50	2.00	0.40
g.12487558G>A		AA	GA	GG	A	G
	小尾寒羊 Small Tail Han sheep	0.25	0.43	0.32	0.47	0.53	0.37	0.50	1.99	0.01
	湖羊 Hu sheep	0.18	0.34	0.48	0.36	0.64	0.35	0.46	1.85	0.00
	草原型藏羊 Prairie Tibetan sheep	0.10	0.40	0.50	0.30	0.70	0.33	0.42	1.73	0.60
	策勒黑羊 Cele black sheep	0.35	0.52	0.13	0.61	0.39	0.36	0.48	1.91	0.53
位点 Locus	品种 Breed	基因型频率 Genotype frequency			基因频率 Allele frequency		多态信息含量（PIC） Polymorphism information content	杂合度（HE） Heterozygosity (HE)	有效等位基因数 Effective number of allele (NE)	卡方值（P） χ² test (P value)
	苏尼特羊 Sunite sheep	0.33	0.29	0.38	0.48	0.52	0.37	0.50	2.00	0.05
	滩羊 Tan sheep	0.41	0.45	0.14	0.64	0.36	0.36	0.46	1.86	0.93
g.12508874T>C		CC	CT	TT	C	T
	小尾寒羊 Small Tail Han sheep	0.61	0.34	0.05	0.78	0.22	0.29	0.35	1.53	0.64
	湖羊 Hu sheep	0.34	0.50	0.16	0.59	0.41	0.37	0.48	1.94	0.67
	草原型藏羊 Prairie Tibetan sheep	0.56	0.38	0.06	0.75	0.25	0.31	0.38	1.60	0.94
	策勒黑羊 Cele black sheep	0.58	0.38	0.04	0.77	0.23	0.29	0.36	1.55	0.55
	苏尼特羊 Sunite sheep	0.57	0.38	0.05	0.76	0.24	0.30	0.36	1.57	0.82
	滩羊 Tan sheep	0.73	0.27	0.00	0.86	0.14	0.21	0.24	1.31	0.46
g.12487467A>G		AA	GA	GG	A	G
	小尾寒羊 Small Tail Han sheep	0.54	0.30	0.16	0.69	0.31	0.34	0.43	1.75	0.00
	湖羊 Hu sheep	0.62	0.33	0.05	0.78	0.22	0.28	0.34	1.52	0.84
	草原型藏羊 Prairie Tibetan sheep	0.65	0.25	0.10	0.78	0.22	0.28	0.34	1.52	0.00
	策勒黑羊 Cele black sheep	0.22	0.55	0.23	0.49	0.51	0.37	0.50	2.00	0.46
	苏尼特羊Sunite sheep	0.43	0.38	0.19	0.62	0.38	0.36	0.47	1.88	0.42
	滩羊 Tan sheep	0.29	0.38	0.33	0.48	0.52	0.37	0.50	2.00	0.28
g.12487190G>T		GG	GT	TT	G	T
	小尾寒羊 Small Tail Han sheep	0.45	0.41	0.14	0.65	0.35	0.35	0.45	1.83	0.08
	湖羊 Hu sheep	0.61	0.34	0.05	0.78	0.22	0.28	0.34	1.52	0.90
	草原型藏羊 Prairie Tibetan sheep	0.62	0.29	0.09	0.77	0.23	0.29	0.35	1.55	0.00
	策勒黑羊 Cele black sheep	0.19	0.58	0.23	0.48	0.52	0.37	0.50	2.00	0.26
	苏尼特羊 Sunite sheep	0.38	0.48	0.14	0.62	0.38	0.36	0.47	1.89	0.96
	滩羊 Tan sheep	0.27	0.41	0.32	0.48	0.52	0.37	0.50	2.00	0.40

Table 3

Table 4

Table 5

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引物及探针名称 Primer names	引物序列 Primer sequences	退火温度 Annealing temperature (℃)	扩增片段(bp) Product size	用途 Usage
SMAD1	F: TGGTTCCAAGACACAGCGAAT R: GGTGTATCTGCTGGCATCTGA	60	253	半定量RT-PCR semi-quantitative RT-PCR
SMAD1Q	F: CCCGAGTGGGTGTAGTTT R: TCCTGGCGGTGGTATTCT	60	162	荧光定量PCR qPCR
GAPDH	F: TGACGCTCCCATGTTTGTGA R: TCATAAGTCCCTCCACGATGC	60	149	半定量RT-PCR 和荧光定量PCR semi-quantitative RT-PCR and qPCR
FecB-Taqman	F: CCAGCTGGTTCCGAGAGACA R: CTTATACTCACCCAAGATGTTTTCATG	60	73	FecB-Taqman分型 FecB-Taqman genotyping
FecB-Taqman P-G FecB-Taqman P-A	AAATATATCGGACGGTGTT-MGB AAATATATCAGACGGTGTTG-MGB	60	73	FecB-Taqman分型 FecB-Taqman genotyping

位点 Locus	基因型 Genotype	第一胎样本数 Number of the first parity	第一胎产羔数 Litter size of the first parity	第二胎样本数 Number of the second parity	第二胎产羔数 Litter size of the second parity	第三胎样本数 Number of the third parity	第三胎产羔数 Litter size of the third parity
g.12485895A>G	AA	114	2.11±0.08	109	2.33±0.09	45	2.80±0.15
	GG	80	2.14±0.09	74	2.24±0.11	27	2.93±0.20
	GA	144	2.12±0.07	139	2.37±0.08	55	2.70±0.14
g.12487190G>T	GG	157	2.08±0.07a	150	2.28±0.07a	57	2.67±0.14a
	GT	144	2.16±0.07a	138	2.34±0.08a	60	2.72±0.13a
	TT	51	2.39±0.12b	46	2.65±0.13b	16	3.75±0.25b
g.12487467A>G	AA	159	2.11±0.06	152	2.29±0.07	56	2.70±0.13
	GG	48	2.35±0.12	43	2.47±0.14	15	2.80±0.24
	GA	67	2.17±0.09	85	2.31±0.10	36	2.67±0.16
g.12487558G>A	AA	92	2.28±0.09	87	2.43±0.10	35	2.91±0.17
	GG	107	2.06±0.08	99	2.31±0.09	44	2.82±0.15
	GA	142	2.16±0.07	138	2.38±0.08	50	2.64±0.14
g.12508874T>C	CC	204	2.10±0.06	193	2.40±0.07	66	2.82±0.13
	CT	120	2.27±0.08	113	2.35±0.09	54	2.82±0.14
	TT	18	2.11±0.02	19	2.21±0.21	9	2.56±0.35

基因型 Genotype	第一胎样本数 Number of the first parity	第一胎产羔数 Litter size of the first parity	第二胎样本数 Number of the second parity	第二胎产羔数 Litter size of the second parity	第三胎样本数 Number of the third parity	第三胎产羔数 Litter size of the third parity
AA-GG	23	1.00±0.16a	23	1.00±0.18a	23	1.04±0.19a
AA-GT	14	1.36±0.21a	14	1.36±0.22a	14	1.07±0.24a
AA-TT	10	1.10±0.25a	10	1.30±0.27a	10	1.10±0.29a
AG-GG	77	2.04±0.09b	75	2.40±0.10b	27	2.67±0.18b
AG-GT	70	2.07±0.09b	67	2.16±0.10b	34	2.65±0.16b
AG-TT	27	2.14±0.15b	24	2.50±0.17b	10	3.40±0.29b
GG-GG	57	2.33±0.21b	53	2.38±0.12b	22	3.00±0.19b
GG-GT	60	2.40±0.10b	57	2.67±0.11b	18	3.22±0.21b
GG-TT	14	2.29±0.10b	13	2.31±0.23b	6	3.33±0.37b

Tissue Expression and Polymorphism of Sheep SMAD1 Gene and Their Association with Litter Size

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位点 Locus	基因型 Genotype	多羔基因型频率 Genotype frequency in multiparous sheep	单羔基因型频率 Genotype frequency in uniparous sheep	卡方检验 χ² test (P value)	等位基因 Allele	多羔中基因频率 Allele frequency in multiparous sheep	单羔中基因频率 Allele frequency in uniparous sheep	卡方检验 χ² test (P value)
g.12485895A>G	AA	0.30(167)	0.52 (104)	0.00	A	0.54	0.68	0.00
	GA	0.47 (254)	0.34 (70)		G	0.46	0.32
	GG	0.23 (124)	0.14 (29)
g.12487558G>A	AA	0.25 (139)	0.15 (32)	0.00	A	0.48	0.36	0.00
	GA	0.45 (248)	0.40 (81)		G	0.52	0.64
	GG	0.30(161)	0.45 (91)
g.12508874T>C	CC	0.56 (307)	0.58 (118)	0.69	C	0.74	0.76	0.50
	CT	0.37 (203)	0.37 (75)		T	0.26	0.24
	TT	0.07 (39)	0.05(11)
g.12487467A>G	AA	0.51 (249)	0.59 (111)	0.15	A	0.69	0.73	0.11
	GA	0.35 (169)	0.28 (52)		G	0.31	0.27
	GG	0.14 (68)	0.13 (24)
g.12487190G>T	GG	0.44 (250)	0.56 (115)	0.01	G	0.66	0.72	0.01
	GT	0.43 (239)	0.32 (65)		T	0.34	0.28
	TT	0.13 (73)	0.12(24)

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