CRISP3 gene SNP identification and its impact on reproductive traits in Kela pigs

doi:10.3969/j.issn.1004-1524.20230951

Acta Agriculturae Zhejiangensis ›› 2024, Vol. 36 ›› Issue (6): 1270-1278.DOI: 10.3969/j.issn.1004-1524.20230951

• Animal Science • Previous Articles Next Articles

CRISP3 gene SNP identification and its impact on reproductive traits in Kela pigs

XIANG Jin(), WANG Chunyuan, WU Yan, TAN Yuancheng, YANG Suan, ZHANG Yiyu^*()

Key Laboratory of Genetic Breeding and Reproduction of Plateau and Mountain Animals, Ministry of Education, Guizhou Provincial Key Laboratory of Animal Genetic Breeding and Reproduction, Institute of Swine, College of Animal Science, Guizhou University, Guiyang 550025, China

Received:2023-08-07 Online:2024-06-25 Published:2024-07-02

Abstract

Abstract:

To analyze the impact of single nucleotide polymorphism (SNP) loci in the Cysteine Rich Secretory Protein 3 (CRISP3) gene on reproductive traits of Kele pigs, Sanger sequencing was used to detect SNP mutations in the CRISP3 gene of 250 healthy and prolific Kele sows. SPSS 22.0 software was utilized to analyze the association between SNP loci and six reproductive traits in Kele pigs, including total number of piglets born, primary litter weight, average birth weight, weaning litter weight, number of weaned piglets, and average weaning weight. The result showed that in the CRISP3 gene of Kele pigs, three SNP mutations were identified in the fourth intron (g.43796318T>C, g.43796424T>A, and g.43796425G>T), each having three genotypes. The dominant genotypes for g.43796318T>C and g.43796424T>A were TT, with the dominant alleles being T, while the dominant genotype for g.43796425G>T was GG, with the dominant allele being G. The χ² test revealed that the genotype distribution of g.43796318T>C was in Hardy-Weinberg equilibrium (P>0.05), whereas the genotype distributions of g.43796424T>A and g.43796425G>T significantly (P<0.01) deviated from Hardy-Weinberg equilibrium. All three SNP loci exhibited moderate polymorphism with polymorphism information content (PIC) ranging from 0.25 to 0.50. Linkage disequilibrium analysis showed strong linkage disequilibrium between g.43796424T>A and g.43796425G>T. The association analysis demonstrated that the TT and CC genotypes of g.43796318T>C were significantly (P<0.05) higher in primary litter weight and average birth weight than those of the TC genotype. The TA genotype of g.43796424T>A had significantly (P<0.05) higher number of piglets born alive, primary litter weight, and number of weaned piglets compared to the TT and AA genotypes. The GT genotype of g.43796425G>T showed significantly (P<0.05) higher number of piglets born alive, primary litter weight, and number of weaned piglets than those of the GG and TT genotypes. In the diplotype analysis, individuals with the H2H4 (CCTAGT) diplotype had significantly (P<0.05) higher number of piglets born alive, primary litter weight, number of weaned piglets, and weaning litter weight compared to individuals with the H1H2 (TCTAGT) diplotype and H2H2 (CCAATT) diplotype. The H2H2 (CCAATT) individuals had significantly (P<0.05) higher average birth weight than individuals of other diplotypes except for H4H4 (CCTTGG), and its average weaning weight was significantly (P<0.05) higher than that of other diplotypes. The three mutation sites in intron 4 of CRISP3 gene were significantly associated with 6 reproductive traits of Kole pigs, which could be used as candidate molecular markers for selection of reproductive traits in Kole pigs.

Key words: Kela pig, CRISP3 gene, single nucleotide polymorphism, reproductive trait

CLC Number:

S828

XIANG Jin, WANG Chunyuan, WU Yan, TAN Yuancheng, YANG Suan, ZHANG Yiyu. CRISP3 gene SNP identification and its impact on reproductive traits in Kela pigs[J]. Acta Agriculturae Zhejiangensis, 2024, 36(6): 1270-1278.

Figures/Tables 7

References 28

[1]	陈琼, 王济民. 我国肉类消费现状与未来发展趋势[J]. 中国食物与营养, 2013, 19(6): 43-47.
	CHEN Q, WANG J M. Current situation and future trends of meat consumption in China[J]. Food and Nutrition in China, 2013, 19(6): 43-47. (in Chinese with English abstract)
[2]	贾梦雨, 李尚, 刘刁, 等. 母猪繁殖性状分子遗传标记研究进展[J]. 黑龙江畜牧兽医, 2022(1): 38-43.
	JIA M Y, LI S, LIU D, et al. Advances in molecular genetic markers for reproductive traits in sows[J]. Heilongjiang Animal Science and Veterinary Medicine, 2022(1): 38-43. (in Chinese with English abstract)
[3]	颜华, 王立贤, 王立刚, 等. 六个候选基因多态性与母猪繁殖性状关联分析[J]. 农业生物技术学报, 2009, 17(2): 249-255.
	YAN H, WANG L X, WANG L G, et al. Genetic polymorphism of six genetic loci and their correlation with reproductive traits[J]. Journal of Agricultural Biotechnology, 2009, 17(2): 249-255. (in Chinese with English abstract)
[4]	卢世豪, 崔浩, 闫耀晖, 等. VRTN基因型对猪生长和繁殖性能的影响[J]. 石河子大学学报(自然科学版), 2022, 40(4): 460-465.
	LU S H, CUI H, YAN Y H, et al. Association of VRTN gene polymorphisms with growth and reproductive trait in pig[J]. Journal of Shihezi University(Natural Science), 2022, 40(4): 460-465. (in Chinese with English abstract)
[5]	李若岚, 代宇星, 温作晨, 等. FSHR、LHβ基因多态性和法系长白猪繁殖性状的联合关联分析[J]. 中国畜牧杂志, 2021, 57(S1): 92-97.
	LI R L, DAI Y X, WEN Z C, et al. Joint association analysis of FSHR, LHβ gene polymorphism and reproductive traits of Landrace in legal system[J]. Chinese Journal of Animal Science, 2021, 57(S1): 92-97. (in Chinese)
[6]	周礼渝. 多群体全基因组关联性分析鉴别母猪繁殖性状的遗传位点[D]. 南昌: 江西农业大学, 2016.
	ZHOU L Y. Genome-wide association studies for female reproductive traits on three populations[D]. Nanchang: Jiangxi Agricultural University, 2016. (in Chinese with English abstract)
[7]	张宇, 周佳伟, 吴俊静, 等. 大白猪繁殖性状全基因组关联分析[J]. 中国畜牧杂志, 2022, 58(8): 94-99.
	ZHANG Y, ZHOU J W, WU J J, et al. Reproductive traits of Large White pig genome-wide association study[J]. Chinese Journal of Animal Science, 2022, 58(8): 94-99. (in Chinese)
[8]	DOTY A, BUHI W C, BENSON S, et al. Equine CRISP3 modulates interaction between spermatozoa and polymorphonuclear Neutrophils1[J]. Biology of Reproduction, 2011, 85(1): 157-164.
[9]	GONZALEZ S N, SULZYK V, WEIGEL MUÑOZ M, et al. Cysteine-rich secretory proteins (CRISP) are key players in mammalian fertilization and fertility[J]. Frontiers in Cell and Developmental Biology, 2021, 9: 800351.
[10]	KRÄTZSCHMAR J, HAENDLER B, EBERSPAECHER U, et al. The human cysteine-rich secretory protein (CRISP) family[J]. European Journal of Biochemistry, 1996, 236(3): 827-836.
[11]	UDBY L, COWLAND J B, JOHNSEN A H, et al. An ELISA for SGP28/CRISP-3, a cysteine-rich secretory protein in human neutrophils, plasma, and exocrine secretions[J]. Journal of Immunological Methods, 2002, 263(1/2): 43-55.
[12]	GIBBS G M, ROELANTS K, O’BRYAN M K. The CAP superfamily: cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins: roles in reproduction, cancer, and immune defense[J]. Endocrine Reviews, 2008, 29(7): 865-897.
[13]	BJARTELL A, JOHANSSON R, BJÖRK T, et al. Immunohistochemical detection of cysteine-rich secretory protein 3 in tissue and in serum from men with cancer or benign enlargement of the prostate gland[J]. The Prostate, 2006, 66(6): 591-603.
[14]	LIAO Q, KLEEFF J, XIAO Y, et al. Preferential expression of cystein-rich secretory protein-3 (CRISP-3) in chronic pancreatitis[J]. Histology and Histopathology, 2003, 18(2): 425-433.
[15]	EVANS J, D’SYLVA R, VOLPERT M, et al. Endometrial CRISP3 is regulated throughout the mouse estrous and human menstrual cycle and facilitates adhesion and proliferation of endometrial epithelial cells1[J]. Biology of Reproduction, 2015, 92(4): 99.
[16]	崔世泉, 李剑虹, 崔卫国, 等. 母猪哺乳初期的母性行为与催乳素受体基因多态性关系的初探[J]. 遗传, 2007, 29(1): 47-51.
	CUI S Q, LI J H, CUI W G, et al. Preliminary study on the relationship between sow maternal behaviour during early lactation and polymorphism of PRLR gene[J]. Hereditas, 2007, 29(1): 47-51. (in Chinese with English abstract)
[17]	杨酸, 郭小江, 杨红文, 等. 柯乐猪PRLR基因多态性与繁殖性状的关联性[J]. 浙江农业学报, 2023, 35(3): 556-564.
	YANG S, GUO X J, YANG H W, et al. Correlation of PRLR gene polymorphisms and reproductive traits in Kele pig[J]. Acta Agriculturae Zhejiangensis, 2023, 35(3): 556-564. (in Chinese with English abstract)
[18]	赵春萍, 张雄, 张静, 等. 不同屠宰体重对柯乐猪胴体性状、肉品质及风味的影响[J]. 黑龙江畜牧兽医, 2022(6): 36-41.
	ZHAO C P, ZHANG X, ZHANG J, et al. Effect of different slaughter weight on meat quality and flavor of Kele pigs[J]. Heilongjiang Animal Science and Veterinary Medicine, 2022(6): 36-41. (in Chinese with English abstract)
[19]	REDDY T, GIBBS G M, MERRINER D J, et al. Cysteine-rich secretory proteins are not exclusively expressed in the male reproductive tract[J]. Developmental Dynamics, 2008, 237(11): 3313-3323.
[20]	UPADHAYA S D, YUN H M, HUANG S Q, et al. Efficacy of dietary supplementation of fatty acid compound on performance and production in finishing pigs[J]. Tropical Animal Health and Production, 2017, 49(6): 1281-1288.
[21]	DA ROS V, BUSSO D, COHEN D J, et al. Molecular mechanisms involved in gamete interaction: evidence for the participation of cysteine-rich secretory proteins (CRISP) in sperm-egg fusion[J]. Society of Reproduction and Fertility Supplement, 2007, 65: 353-356.
[22]	ACHACHE H, REVEL A. Endometrial receptivity markers, the journey to successful embryo implantation[J]. Human Reproduction Update, 2006, 12(6): 731-746.
[23]	DUNCAN W C, SHAW J L V, BURGESS S, et al. Ectopic pregnancy as a model to identify endometrial genes and signaling pathways important in decidualization and regulated by local trophoblast[J]. PLoS One, 2011, 6(8): e23595.
[24]	SERROTE C M L, REINIGER L R S, SILVA K B, et al. Determining the polymorphism information content of a molecular marker[J]. Gene, 2020, 726: 144175.
[25]	WIGGINTON J E, CUTLER D J, ABECASIS G R. A note on exact tests of Hardy-Weinberg equilibrium[J]. The American Journal of Human Genetics, 2005, 76(5): 887-893.
[26]	SHAUL O. How introns enhance gene expression[J]. The International Journal of Biochemistry & Cell Biology, 2017, 91: 145-155.
[27]	NOTT A, MEISLIN S H, MOORE M J. A quantitative analysis of intron effects on mammalian gene expression[J]. RNA, 2003, 9(5): 607-617.
[28]	LE HIR H, NOTT A, MOORE M J. How introns influence and enhance eukaryotic gene expression[J]. Trends In Biochemical Sciences, 2003, 28(4): 215-220.

引物名称 Primer name	引物序列(5'→3') Primer sequence (5'→3')	片段长度 Product length/bp	位置 Loci	退火温度 Annealing temperature/℃
CRISP3-F1 CRISP3-R1	TGATGGAACACGATGGAGGAT ATGGCAAACTCCGAAAAGGG	732	外显子3 Exon-3	60
CRISP3-F2	TTAAGGATCTGGTCTTGCCG	664	外显子5 Exon-5	60
CRISP3-R2	AGGCTAGTGCTCAAACATGA
CRISP3-F3	CCCATTGACATTTTGTGCCT	639	外显子6 Exon-6	60
CRISP3-R3	ATTGCTGTGAGCTGTAGTGT
CRISP3-F4	TCAGAGAACTTTTGGGTCCCT	524	外显子8 Exon-8	60
CRISP3-R4	CGGGTATCAAAAGCCAAGGT

引物名称 Primer name	引物序列(5'→3') Primer sequence (5'→3')	片段长度 Product length/bp	位置 Loci	退火温度 Annealing temperature/℃
CRISP3-F1 CRISP3-R1	TGATGGAACACGATGGAGGAT ATGGCAAACTCCGAAAAGGG	732	外显子3 Exon-3	60
CRISP3-F2	TTAAGGATCTGGTCTTGCCG	664	外显子5 Exon-5	60
CRISP3-R2	AGGCTAGTGCTCAAACATGA
CRISP3-F3	CCCATTGACATTTTGTGCCT	639	外显子6 Exon-6	60
CRISP3-R3	ATTGCTGTGAGCTGTAGTGT
CRISP3-F4	TCAGAGAACTTTTGGGTCCCT	524	外显子8 Exon-8	60
CRISP3-R4	CGGGTATCAAAAGCCAAGGT

品种 Breed	SNP位点 SNP loci	基因型频率 Genotype frequency			等位基因频率 Allele frequency		He	Ne	PIC	χ²-HWE
柯乐猪 KeLe pig	g.43796318T>C	TT (143) 0.572	TC (76) 0.304	CC (31) 0.124	T 0.724	C 0.276	0.400	1.666	0.320	14.320
	g.43796424T>A	TT(127) 0.508	TA (104) 0.416	AA (19) 0.076	T 0.716	A 0.284	0.407	1.685	0.324	0.131
	g.43796425G>T	GG(127) 0.508	GT (104) 0.416	TT (19) 0.076	G 0.716	C 0.284	0.407	1.685	0.324	0.131
大白猪 Large White pig	g.43796318T>C	TT (7) 0.35	TC (9) 0.45	CC(4) 0.2	T 0.575	C 0.425	0.489	1.956	0.369	0.126
	g.43796424T>A	TT(6) 0.3	TA (9) 0.45	AA (5) 0.25	T 0.525	A 0.475	0.499	1.995	0.374	0.191
	g.43796425G>T	GG(5) 0.25	GT (11) 0.55	TT (4) 0.2	G 0.525	C 0.475	0.499	1.995	0.374	0.211

品种 Breed	SNP位点 SNP loci	基因型频率 Genotype frequency			等位基因频率 Allele frequency		He	Ne	PIC	χ²-HWE
柯乐猪 KeLe pig	g.43796318T>C	TT (143) 0.572	TC (76) 0.304	CC (31) 0.124	T 0.724	C 0.276	0.400	1.666	0.320	14.320
	g.43796424T>A	TT(127) 0.508	TA (104) 0.416	AA (19) 0.076	T 0.716	A 0.284	0.407	1.685	0.324	0.131
	g.43796425G>T	GG(127) 0.508	GT (104) 0.416	TT (19) 0.076	G 0.716	C 0.284	0.407	1.685	0.324	0.131
大白猪 Large White pig	g.43796318T>C	TT (7) 0.35	TC (9) 0.45	CC(4) 0.2	T 0.575	C 0.425	0.489	1.956	0.369	0.126
	g.43796424T>A	TT(6) 0.3	TA (9) 0.45	AA (5) 0.25	T 0.525	A 0.475	0.499	1.995	0.374	0.191
	g.43796425G>T	GG(5) 0.25	GT (11) 0.55	TT (4) 0.2	G 0.525	C 0.475	0.499	1.995	0.374	0.211

SNP位点SNP loci	g.43796318T>C	g.43796424T>A	g.43796425G>T
g.43796318T>C		0.370	0.370
g.43796424T>A	0.132		1.000
g.43796425G>T	0.132	1.000

CRISP3 gene SNP identification and its impact on reproductive traits in Kela pigs

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类型Type	基因型Genotype	g.43796318T>C	g.43796424T>A	g.43796425G>T	频率Frequency
单倍型	H1(302)	T	T	G	0.604
Haplotype	H2(80)	C	A	T	0.160
	H3(62)	T	A	T	0.124
	H4(56)	C	T	G	0.112
双倍型	H1H1(94)	TT	TT	GG	0.376
Diplotype	H1H2(40)	TC	TA	GT	0.160
	H1H3(46)	TT	TA	GT	0.184
	H1H4(28)	TC	TT	GG	0.112
	H2H2(7)	CC	AA	TT	0.028
	H2H3(8)	TC	AA	TT	0.032
	H2H4(18)	CC	TA	GT	0.072
	H3H3(4)	TT	AA	TT	0.016
	H4H4(5)	CC	TT	GG	0.020

SNP位置 SNP loci	基因型 Genotype	产活仔猪数 Number of piglets born alive	初生窝重 Primary litter weight/kg	初生均重 Average birth weight/kg	断奶仔猪数 Number of weaned piglets	断奶窝重 Weaning litter weight/kg	断奶均重 Average weaning weight/kg
g.43796318T>C	TT(143)	8.923±2.885	8.671±3.312 a	1.086±0.186 a	6.895±2.729	38.703±16.667 ab	5.682±1.209
	TC(76)	8.579±2.041	7.418±2.342 b	0.975±0.226 b	6.553±2.187	35.659±11.298 b	5.501±0.780
	CC(31)	9.258±3.596	9.213±3.312 a	1.131±0.243 a	7.452±3.107	42.108±17.808 a	5.769±1.986
g.43796424T>A	TT(127)	8.583±2.464 b	8.078±2.77 b	1.066±0.195	6.575±2.574 b	37.501±15.548	5.770±0.862 a
	TA(104)	9.539±2.982 a	9.030±3.441 a	1.048±0.227	7.519±2.603 a	40.034±15.125	5.352±1.265 b
	AA(19)	7.000±2.236 c	6.537±2.301 c	1.060±0.256	5.158±2.115 c	32.834±15.904	6.316±2.305 a
g.43796425G>T	GG(127)	8.583±2.464 b	8.078±2.77 b	1.066±0.195	6.575±2.574 b	37.501±15.548	5.770±0.862 a
	GT(104)	9.539±2.982 a	9.030±3.441 a	1.048±0.227	7.519±2.603 a	40.034±15.125	5.352±1.265 b
	TT(19)	7.000±2.236 c	6.537±2.301 c	1.060±0.256	5.158±2.115 c	32.834±15.904	6.316±2.305 a

双倍型 Diplotype	产活仔猪数 Number of piglets born alive	初生窝重 Primary litter weight/kg	初生均重 Average birth weight/kg	断奶仔猪数 Number of weaned piglets	断奶窝重 Weaning litter weight/kg	断奶均重 Average weaning weight/kg
H1H1(94)	8.596±2.665 bc	8.035±2.943 ab	1.077±0.188 bc	6.457±2.781 cd	37.687±17.013 ab	5.918±0.920 b
H1H2(40)	8.450±2.342 bc	7.025±2.497 b	0.970±0.237 c	6.250±2.457 d	33.935±12.475 b	5.514±0.988 b
H1H3(46)	9.848±3.077 ab	10.235±3.500 a	1.114±0.181 b	7.978±2.314 b	41.944±15.629 ab	5.229±1.588 b
H1H4(28)	8.750±1.691 b	8.154±2.214 ab	1.009±0.209 bc	6.964±1.875 c	37.711±10.316 ab	5.426±0.456 b
H2H2(7)	6.143±2.268 c	6.964±3.415 b	1.303±0.119 a	4.143±2.268 d	34.114±24.283 b	7.474±3.608 a
H2H3(8)	8.625±1.685 bc	6.806±1.296 b	0.881±0.224 c	6.625±1.685 cd	37.094±7.339 ab	5.701±0.458 b
H2H4(18)	11.167±3.222 a	10.408±3.101 a	1.053±0.267 bc	9.167±2.407 a	48.708±14.331 a	5.307±0.827 b
H3H3(4)	5.250±0.500 d	5.250±1.300 c	0.990±0.140 c	4.000±0.011 d	22.075±2.450 c	5.518±0.615 b
H4H4(5)	7.400±2.191 bc	8.460±2.630 ab	1.158±0.191 ab	6.6±1.949 cd	32.810±11.763 b	4.914±0.255 b

[1]	YUAN Ye, LIU Rui, WANG Lingyun, SHEN Meng, YE Xuelian, QUAN Xinhua, WANG Ruisen, YAO Xiangtan. Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq [J]. Acta Agriculturae Zhejiangensis, 2023, 35(8): 1773-1781.
[2]	YANG Suan, GUO Xiaojiang, YANG Hongwen, XIONG Li, LI Chen, TAN Yuancheng, WANG Chunyuan, ZHANG Yiyu. Correlation of PRLR gene polymorphisms and reproductive traits in Kele pig [J]. Acta Agriculturae Zhejiangensis, 2023, 35(3): 556-564.
[3]	LIU Pengcheng, ZHANG Ji, QIU Ganyuan, GONG Yu, LI Xuesong, LI Wei, ZHANG Yiyu, LIU Ruoyu. Single nucleotide polymorphism screening and bioinformatics analysis of TBC1D7 gene in Guanling cattle [J]. Acta Agriculturae Zhejiangensis, 2022, 34(7): 1402-1411.
[4]	TAO Peng, YUE Zhichen, ZHAO Yanting, LEI Juanli, LI Biyuan. Variation of acceptor splicing site of BrSPS1Fb of Chinese cabbage and its effect on splicing [J]. Acta Agriculturae Zhejiangensis, 2021, 33(11): 2068-2074.
[5]	REN Weihe, REN Wenwen, MA Boyan, GAO Chenghong, LI Hongxu, LIU Lixia, CAO Xin, ZHANG Li. SNP screening and bioinformatics analysis of MSTN in Japanese White Rabbit [J]. , 2018, 30(12): 2018-2023.
[6]	CHEN Li， LI Guoqin， TIAN Yong， SHEN Junda， TAO Zhengrong， XU Jian， ZENG Tao， LU Lizhi*. Transcriptome analysis of abdominal fats from Peking ducks by RNAseq [J]. , 2016, 28(5): 743-.
[7]	ZHANG Tao, LIU He-he, LUO Jun, LI Liang, HUANG Hui-lan, HE Hua. Cloning of duck IL-2 gene promoter and correlation analysis about polymorphism in the promoter region with its expression levels [J]. , 2016, 28(12): 1985-1991.
[8]	YAO Zhu\\|ping， YE Qing\\|jing， WANG Rong\\|qing， ZHOU Guo\\|zhi， RUAN Mei\\|ying， LI Zhi\\|miao， WAN Hong\\|jian， YANG Yue\\|jian*. SNP marker development of Tomato yellow leaf curl virus resistance gene Ty\\|5 CAPS in tomato [J]. , 2015, 27(5): 787-.
[9]	DAI Li-he;HU Jin-ping;CHU Xiao-hong;XYU Ru-hai;LU Fu-zeng;WENG Jing-qiang;HUANG Shao-zhen. Polymorphism of FSHβ gene and its association with the reproductive traits in different breeds of pigs [J]. , 2013, 25(3): 0-466.
[10]	ZENG Tao;LI Guo-qin;WANG De-qian;LI Jin-jun;TIAN Yong;CHEN Li;HUANG Ai-xia;SHI Fang-xiong;;SHEN Jun-da;TAO Zheng-rong;LU Li-zhi;. Single nucleotide polymorphisms （SNPs） of HSP70 gene segments and their association with laying performance of domestic duck [J]. , 2013, 25(2): 0-234.