猪ZP4基因的SNP鉴定、选择压及其与产仔数的关联分析

doi:10.11843/j.issn.0366-6964.2017.05.002

Abstract

Abstract:

In this study, we investigated the single nucleotide polymorphisms (SNP) of ZP4 gene, its selective pressure and association with litter size in pigs. Totally, 328 sows and their litter size records were collected from Large White, Landrace and Landrace×Large White hybridization pig populations. Direct sequencing method was used to clone and identify the nucleotide mutation in ZP4. The generalized linear regression model was applied to investigate the correlation between ZP4 SNP and litter size.The lositan software, Tajima's testing and Fu and Li's D testing were used to detect the selective pressure of ZP4. Our results demonstrated that 27 SNPs were detected in ZP4, and A268T was significantly correlated with number of total litter size in the 3 populations (P< 0.05). A268T was only significantly associated with number of born alive in Landrace and Large White pig populations (P<0.05). We also detected that T2950C was under positive selection and this mutation was linked with A268T. Our results suggested that A268T was a direct selection marker that could be used in pig marker assistant selection.

CLC Number:

S828
S813.1

LIANG Guo-ming, CHEN Feng-jian, ZHAO Qin-tao, LIU Chen-hui, TANG Zhong-lin. Study on SNP Identification, Selective Pressure and Association Analysis with Litter Size for ZP4 Gene in Pigs[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(5): 793-801.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.xmsyxb.com/EN/10.11843/j.issn.0366-6964.2017.05.002

https://www.xmsyxb.com/EN/Y2017/V48/I5/793

References

[1] ROTHSCHILD M F, JACOBSON C, VASKE D A, et al. The estrogen receptor locus is associated with a major gene influencing litter size in pigs.[J]. Proc Natl Acad Sci USA, 1996, 93: 201-205.
[2] BERGFELDER-DRüING S, GROSSE-BRINKHAUS C, LIND B, et al. A genome-wide association study in Large White and Landrace pig populations for number piglets born alive[J]. PLoS One, 2015, 10(3): e0117468.
[3] SELL-KUBIAK E, DUIJVESTEIJN N, LOPES M S, et al. Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population[J]. BMC Genomics, 2015, 16: 1049.
[4] GUO X, SU G, CHRISTENSEN O F, et al. Genome-wide association analyses using a Bayesian approach for litter size and piglet mortality in Danish Landrace and Yorkshire pigs[J]. BMC Genomics, 2016, 17: 468.
[5] SATO S, KIKUCHI T, UEMOTO Y, et al. Effect of candidate gene polymorphisms on reproductive traits in a Large White pig population[J]. Anim Sci J, 2016, 87(12): 1455-1463.
[6] MARANTIDIS A, LALIOTIS G P, AVDI M. Association of RBP4 genotype with phenotypic reproductive traits of sows[J]. Genet Res Int, 2016, 2016: 4940532.
[7] OKABE M. Sperm Acrosome Biogenesis and Function During Fertilization[M]. Cham: Springer International Publishing, 2016: 1-13.
[8] KANAI S, KITAYAMA T, YONEZAWA N, et al. Disulfide linkage patterns of pig zona pellucida glycoproteins ZP3 and ZP4[J]. Mol Reprod Dev, 2008, 75(5): 847-856.
[9] YONEZAWA N, KANAI-KITAYAMA S, KITAYAMA T, et al. Porcine zona pellucida glycoprotein ZP4 is responsible for the sperm-binding activity of the ZP3/ZP4 complex[J]. Zygote, 2012, 20: 389-397.
[10] CONNER S J, LEFIÈVRE L, HUGHES D C, et al. Cracking the egg: increased complexity in the zona pellucida[J]. Human Reprod, 2005, 20(5): 1148-1152.
[11] SUZUKI K, TATEBE N, KOJIMA S, et al. The hinge region of bovine zona pellucida glycoprotein ZP3 is involved in the formation of the sperm-binding active ZP3/ZP4 complex[J]. Biomolecules, 2015, 5(4): 3339-3353.
[12] MONNÉ M, JOVINE L. A structural view of egg coat architecture and function in fertilization[J]. Biol Reprod, 2011, 85(4): 661-669.
[13] GUPTA S K, BHANDARI B, SHRESTHA A, et al. Mammalian zona pellucida glycoproteins: structure and function during fertilization[J]. Cell Tissue Res, 2012, 349: 665-678.
[14] PRASAD SV S S, CARINO C, WANG N, et al. Structure and function of the proteins of the mammalian Zona pellucida.[J]. Cells Tissues Organs, 2000, 166: 148.
[15] YUAN J F, JAFER O, AFFARA N A, et al. Association of four new single-nucleotide polymorphisms in follicle-stimulating hormone receptor and zona pellucida glycoprotein with reproductive traits in pigs[J]. Animal, 2007: 1249-1253.
[16] YUAN J F, MOAEEN-UD-DIN M, GONG Y Z, et al. Identification of mutations of zona pellucida glycoprotein (ZP3) and its association with pig reproductive traits[J]. J Anim Breed Genet, 2007, 124(3): 144-149.
[17] BARRETT J C, FRY B, MALLER J, et al. Haploview: analysis and visualization of LD and haplotype maps[J]. Bioinformatics, 2005, 21(2): 263-265.
[18] TAJIMA F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3): 585-595.
[19] FU Y X, LI W H. Statistical tests of neutrality of mutations[J]. Genetics, 1993, 133(3): 693-709.
[20] GOUDET G, MUGNIER S, CALLEBAUT I, et al. Phylogenetic analysis and identification of pseudogenes reveal a progressive loss of zona pellucida genes during evolution of vertebrates[J]. Biol Reprod, 2008, 78(5): 796-806.
[21] GUPTA S K, BHANDARI B. Acrosome reaction: relevance of zona pellucida glycoproteins[J]. Asian J Androl, 2011, 13(1): 97-105.
[22] NAKANO M, IKEDA Y, TANIGUCHI T, et al. Three susceptible loci associated with primary open-angle glaucoma identified by genome-wide association study in a Japanese population[J]. Proc Natl Acad Sci U S A, 2009, 106(31): 12838-12842.
[23] KONDKAR A A, EDWARD N B, KALANTAN H, et al. Lack of association between polymorphism rs540782 and primary open angle glaucoma in Saudi patients[J]. J Neg Res BioMed, 2017, 16(1): 3.
[24] 袁敏敏, 李大金, 周雷, 等. 猪ZP4B细胞表位人源化定点突变[J]. 中国免疫学杂志, 2004, 20: 184-186.
YUAN M M, LI D J, ZHOU L, et al. Porcine ZP4B cell epitope humanized site - directed mutagenesis[J]. Chinese Journal of Immunology, 2004, 20:184-186. (in Chinese)
[25] 袁敏敏, 李大金, 周雷,等. B细胞表位人源化的猪ZP4在大肠杆菌中的表达与鉴定[J]. 中国免疫学杂志, 2005, 21: 826-827.
YUAN M M, LI D J, ZHOU L, et al. Expression and identification of human ZP4 in B cell epitopes in Escherichia[J]. Chinese Journal of Immunology, 2005, 21:826-827.(in Chinese)
[26] BUKOWSKA D, KEMPISTY B, ZIÓKOWSKA A, et al. Expression and distribution of zona pellucida proteins 3 and 4 in morphologically abnormal canine oocytes: a confocal microscopic observation-based study[J]. Medycyna Weterynaryjna, 2016, 72: 68-74.
[27] MECZEKALSKI B, NAWROT R, NOWAK W, et al. Study on the zona pellucida 4 (ZP4) gene sequence and its expression in the ovaries of patients with polycystic ovary syndrome[J]. J Endocrinol Invest, 2015, 38(7): 791-797.
[28] 陈芳芳, 张玲. 女性免疫避孕的研究进展[J]. 生殖与避孕, 2016, 36(7): 585-588.
CHEN F F, ZHANG L. Advance of female contraceptive vaccine[J]. Reproduction & Contraception, 2016, 36(7):585-588.(in Chinese)
[29] AMARAL A R, MOLLER L M, BEHEREGARAY L B, et al. Evolution of 2 reproductive proteins, ZP3 and PKDREJ, in cetaceans[J]. J Hered, 2011, 102(3): 275-282.
[30] CHEN S, COSTA V, BEJA-PEREIRA A. Evolutionary patterns of two major reproduction candidate genes (Zp2 and Zp3) reveal no contribution to reproductive isolation between bovine species[J]. BMC Evol Biol, 2011, 11: 24.
[31] KIM Y, STEPHAN W. Joint effects of genetic hitchhiking and background selection on neutral variation[J]. Genetics, 2000, 155(3): 1415-1427.
[32] RENZETTE N, KOWALIK T F, JENSEN J D. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity[J]. Mol Ecol, 2016, 25(1): 403-413.
[33] 赵谦, 浦亚斌, 关伟军, 等. 猪重要性状全基因组关联分析的研究进展[J]. 畜牧兽医学报, 2015, 46(6): 873-881.
ZHAO Q, PU Y B, GUAN W J, et al. Research progress of genome-wide association studies for important traits in pig[J]. Acta Veterinaria et Zootechnica Sinica, 2015, 46(6):873-881.(in Chinese)
[34] 郝兴杰, 胡林, 张淑君. 全基因组关联分析方法的研究进展[J]. 畜牧兽医学报, 2016, 47(2):213-217.
HAO X J, HU L, ZHANG S J. Progresses in research of genome-wide association study methods[J]. Acta Veterinaria et Zootechnica Sinica, 2016, 47(2):213-217.(in Chinese)

Study on SNP Identification, Selective Pressure and Association Analysis with Litter Size for ZP4 Gene in Pigs

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	NIU Naiqi, ZHAO Runze, ZONG Wencheng, LIU Xiance, LIU Hai, SHI Guohua, JING Xitao, ZHANG Longchao. Association of Polymorphisms of GREB1L and MIB1 Genes with Rib Number and Carcass Traits in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 79-86.
[2]	ZHU Xueli, ZHANG Longchao, WANG Lixian, PU Lei, LIU Xin. Association Analysis of AQP9 and RPS10 Gene Polymorphisms with Backfat Thickness in Beijing Black Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 87-98.
[3]	SHI Shengjie, WANG Liguang, GAO Lei, CAI Chuanjiang, HE Weixian, CHU Guiyan. Effect of miR-24-3p on Estradiol Synthesis in Porcine Granulosa Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 169-178.
[4]	YANG Kai, LU Zhuoda, HE Jian, ZHANG Ruiqi, WANG Suqing, LI Kebiao, ZHAO Yunxiang, ZHU Xiaoping, GUO Jinbiao. The Population Effect of Commercial Pigs on the Accuracy of Genomic Selection for Carcass Traits in Duroc Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4943-4951.
[5]	LI Chao, ZHAO Xueyan, WANG Yongjun, WANG Yanping, REN Yifan, LI Jingxuan, WANG Huaizhong, WANG Jiying, SONG Qinye. Analysis on the Structural Composition and Function of Bacterial Microbiota of Caecum and Colon in Laiwu and DLY pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5033-5045.
[6]	XU Tingting, QI Fenfang, HUANG Shihui, NIU Xi, LI Sheng, RAN Xueqin, WANG Jiafu, XIE Jian. Study of the Polymorphisms of Structural Variation and the Expression of MAP3K4 gene in Xiang Pig [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5046-5055.
[7]	XUE Hongyan, YANG Mengyu, YANG Huan, DONG Lijun, CAI Xiaqing, ZHAO Zemin, WANG Xianzhong. The Role of ALOX15B-JNK in Heat Stress-induced Oxidative Stress and Apoptosis of Sertoli Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5056-5065.
[8]	HU Ziping, WANG Ligang, ZONG Wencheng, HOU Renda, SU Yanfang, NIU Naiqi, WANG Lixian, WANG Yuan, ZHNAG Longchao. Genetic Structure Analysis of Jianbai Xiang Pig Population Based on Genomic SNP and ROH [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4117-4125.
[9]	JI Zhengyu, NI Mengru, ZHANG Zhaobo, ZHAO Gan, HUANG Zan, LI Pinghua, HUANG Ruihua, HOU Liming. Research on Adipogenic Capacity and Gene Expression Pattern of in Vitro FAPs Cells Derived from Longissimus Dorsi Muscle of Suhuai Pig [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4126-4142.
[10]	BI Huan, QIN Hai, YUAN Wei, ZHANG Yudan, ZHANG Yiyu, CHEN Wei. Effect of Knocking down TYRP1 Gene on Melanin Production in the Xiang Pig Epidermal Melanocytes [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4143-4153.
[11]	LIU Pan, LI Ruiqi, TAN Zhankun, WANG Yifei, CHEN Xiaochen, HE Weixian, DU Renrang, MA Jian, CHU Guiyan, CAI Chuanjiang. Effects of High Fiber Diet on Growth Performance, Meat Quality and Intestinal Microbiome of Growing-finishing Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4247-4259.
[12]	LI Pinghui, PU Guang, WANG Zhongyu, ZHOU Wuduo, NIU Peipei, WU Chengwu, HOU Liming, HUANG Ruihua, LI Pinghua. Effect of Dietary Fiber Level on Blood and Intestinal Immune Indexes of Meishan Pigs and Preliminary Analysis of Its Mechanism [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4260-4277.
[13]	WANG Hui, FENG Baoliang, WU Dan, XIANG Guangming, WANG Nan, MU Yulian, LI Kui, LIU Zhiguo. Research Progress of CD163 Gene and Disease-Resistant Breeding on Porcine Reproductive and Respiratory Syndrome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3127-3138.
[14]	ZHANG Wanfeng, ZHAO Tianzhi, LI Jiao, YOU Ziwei, YANG Yang, CAI Chunbo, GAO Pengfei, CAO Guoqing, GUO Xiaohong, LI Bugao. Study on NR2F2 Gene Regulating Proliferation and Apoptosis of Porcine PK15 Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3242-3251.
[15]	LIAN Yuju, ZHANG Zhiyuan, LIAO Xiaobo, WEI Hongjiang, YIN Yulong, LIU Mei. Breeding Methods and Application Progress of Medical Miniature Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2667-2682.