MET基因多态性与中国荷斯坦牛繁殖和泌乳性状的关联分析

doi:10.11843/j.issn.0366-6964.2022.11.006

畜牧兽医学报 ›› 2022, Vol. 53 ›› Issue (11): 3769-3785.doi: 10.11843/j.issn.0366-6964.2022.11.006

MET基因多态性与中国荷斯坦牛繁殖和泌乳性状的关联分析

许静漪¹, 徐昊祺¹, 胡丽蓉¹, 张帆², 高清¹, 罗汉鹏¹, 张海亮¹, 师睿¹, 李想¹, 刘林³, 郭刚^4*, 王雅春^1*

1. 中国农业大学动物科学技术学院农业农村部动物遗传育种与繁殖(家畜)重点实验室, 畜禽育种国家工程实验室, 北京 100193;
2. 新疆农业大学动物科学学院, 乌鲁木齐 830052;
3. 北京奶牛中心, 北京 100194;
4. 北京首农畜牧发展有限公司, 北京 100029

收稿日期:2022-04-11 出版日期:2022-11-23 发布日期:2022-11-25
通讯作者: 王雅春,主要从事奶牛分子数量遗传育种研究,E-mail:wangyachun@cau.edu.cn;郭刚,主要从事奶牛分子数量遗传育种研究,E-mail:guogang2180@126.com
作者简介:许静漪(2000-),女,山西晋中人,本科生,主要从事动物科学研究,E-mail:ed-adam@foxmail.com
基金资助:
现代农业产业技术体系（CARS-36）；长江学者和创新团队发展计划（IRT_15R62）；北京三元种业科技股份有限公司自立科研课题（SYZYZ20190005）

Association Analysis of MET Gene Single Nucleotide Polymorphism with Reproduction and Milk Production Traits in Chinese Holstein Cattle

XU Jingyi¹, XU Haoqi¹, HU Lirong¹, ZHANG Fan², GAO Qing¹, LUO Hanpeng¹, ZHANG Hailiang¹, SHI Rui¹, LI Xiang¹, LIU Lin³, GUO Gang^4*, WANG Yachun^1*

1. National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproductive of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
2. College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China;
3. Beijing Dairy Cattle Center, Beijing 100194, China;
4. Beijing Sunlon Livestock Development Company Limited, Beijing 100029, China

Received:2022-04-11 Online:2022-11-23 Published:2022-11-25

摘要/Abstract

摘要： 为筛选与中国荷斯坦牛繁殖和泌乳性状相关的遗传标记，本研究从分子水平探究了MET基因单核苷酸多态（single nucleotide polymorphisms，SNPs）与繁殖和泌乳性状的相关性。通过混池测序法在70头无血缘关系的健康中国荷斯坦公牛中扫描目标基因的SNPs，采用竞争性等位基因特异性PCR （kompetitive allele-specific PCR，KASP）对其后代1 160头中国荷斯坦泌乳牛进行部分SNP的基因分型，基于连锁不平衡分析获得双倍型信息，并采用线性模型对SNP及其双倍型与5个繁殖和6个泌乳性状的估计育种值（estimated breeding values，EBV）进行关联分析。随后，针对位于功能区域的SNPs进行生物信息学分析和基因表达量相关性分析，初步探究其潜在的调控机制。本研究在MET基因中共检测到19个SNPs，说明该基因存在丰富的遗传变异；就其中7个SNPs进行了基因分型，分型结果与目标性状的关联分析结果显示，7个SNPs与多个性状存在显著（P<0.05）或极显著（P<0.01）的关联；位于上游调控区的g.51737889T>C位点GG基因型个体的初产日龄、青年牛首末配种间隔、经产牛首末配种间隔、体细胞评分的EBV最低，说明该基因型个体同时具有较好的繁殖性能和泌乳性能；另一个位于上游调控区的g.51736640A>C位点GG基因型个体的初产日龄、青年牛首末配种间隔、经产牛首末配种间隔、体细胞评分的EBV最低，但乳蛋白率、乳脂率的EBV最低，说明该基因型个体繁殖性能较好，但泌乳性能相对较差；此外，位于第6外显子的g.51660569G>A位点TC基因型个体初产日龄的EBV较低，青年牛首末配种间隔、经产牛首末配种间隔、体细胞评分的EBV最低，说明该基因型个体具有较好的繁殖性能。连锁不平衡分析发现，该基因的7个SNPs形成2个单倍型块，其双倍型与目标性状的关联分析进一步表明，单倍型块1中H1H3个体的繁殖性能较好且泌乳性能中等，单倍型块2中H4H4个体的繁殖性能和泌乳性能均较优秀，为两个优势双倍型；此外，H1H3包含g.51660569G>A位点的TC基因型，H4H4为g.51737889T>C、g.51736640A>C两位点GG基因型的组合，其关联分析结果与单个位点的结果一致。基序分析结果表明，g.51737889T>C与g.51736640A>C位点的优势等位基因G可富集到与基因激活、细胞增殖、分化相关的转录因子，且两位点GG基因型的MET基因表达量均最高，其双倍型H4H4表达量也较高，进一步验证了关联分析结果。综上，本研究获得了中国荷斯坦牛MET基因的多态性图谱，并通过关联分析、生物信息学预测及基因表达量分析发现并验证了MET基因与繁殖、泌乳性状的遗传关联，为中国荷斯坦牛高产高效选育提供了可用的遗传标记。

关键词: MET, 单核苷酸多态性, 单倍型, 基因表达, 奶牛, 关联分析

Abstract: In order to identify genetic markers related to reproduction and milk production traits of Chinese Holstein cattle, the relationships between single nucleotide polymorphisms (SNPs) of MET gene and reproduction and milk production traits was explored. Candidate SNPs of MET were screened through direct sequencing of pooled DNA samples in 70 healthy unrelated Chinese Holstein bulls, and the genotyping of partial SNPs in 1 160 healthy Holstein lactating cattle was performed using kompetitive allele-specific PCR (KASP) method, diplotype information based on linkage disequilibrium analysis was obtained. The linear models were employed to conduct the association analysis between SNPs and their diplotypes and EBVs of 5 reproductive traits and 6 milk production traits. The bioinformatics analysis and the association analysis were conducted on SNPs located in functional areas. In this study, a total of 19 SNPs were detected in MET, indicating rich genetic variations existing within this gene in the population. Among them, 7 SNPs was genotyped, and the association analysis revealed that these SNPs were significantly (P<0.05) or highly significantly (P<0.01) associated with multiple traits. The individuals with GG genotype of g.51737889T>C located in upstream had the lowest EBVs of the age at the first calving (AFC), the interval from the first to last insemination in heifer (IFL_H), the interval from the first to last insemination in cows (IFL_C), and somatic cell score (SCS), which suggested the good reproduction and milk production performance of animals carrying this genotype. The individuals with GG genotype of g.51736640A>C located in upstream had the lowest EBVs of the age at the first calving, the interval from the first to last insemination in heifers, the interval from the first to last insemination in cows, and somatic cell score; however, they had the lowest EBVs of protein percentage (PP), and fat percentage (FP), which suggested animals carrying this genotype had the good performance in reproductive, but with relatively poor performance in milk production. The individuals with the TC genotype at g.51660569G>A in 6^th exon had the lowest EBVs of the interval from the first to last insemination in heifers and the interval from the first to last insemination in cows, which suggested the good reproduction performance of animals carrying this genotype. Linkage disequilibrium analysis revealed that 7 SNPs linked to form 2 haplotype blocks. The association analysis between diplotypes and target traits showed that the individuals with H1H3 diplotype at BLOCK1 had good reproduction performance but medium milk production performance, the individuals with H4H4 diplotype at BLOCK2 had good reproduction and milk production performance, and these two were dominant hiplotypes. In addition, H1H3 diplotype included the TC genotype at g.51660569G>A, H4H4 diplotype was combination of the GG genotype at g.51737889T>C and g.51736640A>C, the results of diplotype association analysis were consistent with that of SNP. The results of motif analysis showed that G allele at g.51737889T>C and g.51736640A>C enriched in transcription factors related to gene activation, cell proliferation and differentiation. The individuals with GG genotype at both SNPs had the highest gene expression, and the individuals with corresponding H4H4 diplotype had higher gene expression, which further verified the results of association analysis. In conclusion, the polymorphism map of MET gene was derived in Chinese Holstein cattle, and the genetic association between MET gene and reproductive and productive traits was identified through association analysis, and verified by bioinformatics prediction and gene expression analysis. The results provided useful genetic markers for genetic selection of Chinese Holstein cattle for higher production as well as higher efficiency.

Key words: MET, single nucleotide polymorphism, haplotype, gene expression, cow, association analysis

中图分类号:

S823.2

许静漪, 徐昊祺, 胡丽蓉, 张帆, 高清, 罗汉鹏, 张海亮, 师睿, 李想, 刘林, 郭刚, 王雅春. MET基因多态性与中国荷斯坦牛繁殖和泌乳性状的关联分析[J]. 畜牧兽医学报, 2022, 53(11): 3769-3785.

XU Jingyi, XU Haoqi, HU Lirong, ZHANG Fan, GAO Qing, LUO Hanpeng, ZHANG Hailiang, SHI Rui, LI Xiang, LIU Lin, GUO Gang, WANG Yachun. Association Analysis of MET Gene Single Nucleotide Polymorphism with Reproduction and Milk Production Traits in Chinese Holstein Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 3769-3785.

参考文献 37

[1]	宋亚东, 李翠霞.中国乳制品进口贸易波动的外溢效应研究[J].农业经济问题, 2022(7):64-80.SONG Y D, LI C X.The research on the spillover effect of China's dairy products import trade[J].Issues in Agricultural Economy, 2022(7):64-80.(in Chinese)
[2]	YAMAJI D, KIMURA K, WATANABE A, et al.Bovine hepatocyte growth factor and its receptor c-Met:cDNA cloning and expression analysis in the mammary gland[J].Domest Anim Endocrinol, 2006, 30(3):239-246.
[3]	BOTTARO D P, RUBIN J S, FALETTO D L, et al.Identification of the hepatocyte growth factor receptor as the c-met proto-oncogene product[J].Science, 1991, 251(4995):802-804.
[4]	GHERARDI E, STOKER M.Hepatocytes and scatter factor[J].Nature, 1990, 346(6281):228.
[5]	STOKER M, GHERARDI E, PERRYMAN M, et al.Scatter factor is a fibroblast-derived modulator of epithelial cell mobility[J].Nature, 1987, 327(6119):239-242.
[6]	ZHAO Y, YE W L, WANG Y D, et al.HGF/c-Met:A key promoter in liver regeneration[J].Front Pharmacol, 2022, 13:808855.
[7]	SANADA F, FUJIKAWA T, SHIBATA K, et al.Therapeutic angiogenesis using HGF plasmid[J].Ann Vasc Dis, 2020, 13(2):109-115.
[8]	KHANDIA R, PATTNAIK B, RAJUKUMAR K, et al.Identification of other cellular receptors for edema factor of bacillus anthracis by independent inhibition of protective antigen evidenced by inhibition of embryo growth and angiogenesis[J].Arch Razi Inst, 2021, 76(4):847-855.
[9]	DE NOLA G, LECLERCQ B, MOUGEL A, et al.Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist[J].Life Sci Alliance, 2022, 5(12):e202201424.
[10]	HAGHANI S, JAMALI-RAEUFY N, ZEINIVAND M, et al.Hepatocyte growth factor attenuates the severity of status epilepticus in kainic acid-induced model of temporal lobe epilepsy by targeting apoptosis and astrogliosis[J].Basic Clin Neurosci, 2021, 12(6):805-816.
[11]	PARROTT J A, SKINNER M K.Developmental and hormonal regulation of hepatocyte growth factor expression and action in the bovine ovarian follicle[J].Biol Reprod, 1998, 59(3):553-560.
[12]	ACCORNERO P, LUVARÀ S, FAVOLE A, et al.Biological role of the HGF/MET ligand/receptor couple in bovine mammary epithelial cells[J].Vet Res Commun, 2007, 31(S1):161-164.
[13]	ACCORNERO P, MARTIGNANI E, MACCHI E, et al.Hepatocyte growth factor exerts multiple biological functions on bovine mammary epithelial cells[J].J Dairy Sci, 2007, 90(9):4289-4296.
[14]	GROISBERG R, ROSZIK J, CONLEY A P, et al.Genomics, morphoproteomics, and treatment patterns of patients with alveolar soft part sarcoma and response to multiple experimental therapies[J].Mol Cancer Ther, 2020, 19(5):1165-1172.
[15]	CHE L, CHI W N, QIAO Y, et al.Cholesterol biosynthesis supports the growth of hepatocarcinoma lesions depleted of fatty acid synthase in mice and humans[J].Gut, 2020, 69(1):177-186.
[16]	徐倩文, 孟迪, 孙秀威.HGF/c-Met在肝细胞癌中作用的研究进展[J].现代肿瘤医学, 2022, 30(8):1504-1507.XU Q W, MENG D, SUN X W.Advances in the study of HGF/c-Met in hepatocellular carcinoma[J].Modern Oncology, 2022, 30(8):1504-1507.(in Chinese)
[17]	MATSUMOTO K, UMITSU M, DE SILVA D M, et al.Hepatocyte growth factor/MET in cancer progression and biomarker discovery[J].Cancer Sci, 2017, 108(3):296-307.
[18]	杨泽民, 罗少洪, 陈耕夫.三种全血基因组DNA提取方法的比较[J].中国实用医药, 2009, 4(12):13-14.YANG Z M, LUO S H, CHEN G F.Comparing the three methods to extract rat genomic DNA from whole blood[J].China Practical Medicine, 2009, 4(12):13-14.(in Chinese)
[19]	SHI R, BRITO L F, LIU A X, et al.Genotype-by-environment interaction in Holstein heifer fertility traits using single-step genomic reaction norm models[J].BMC Genomics, 2021, 22(1):193.
[20]	李想.北京地区中国荷斯坦牛泌乳性能和体型性状遗传评估体系的建立[D].北京:中国农业大学, 2017.LI X.Establishment of genetic evaluation system of lactation performance and type traits for Chinese Holsteins in Beijing[D].Beijing:China Agricultural University, 2017.(in Chinese)
[21]	CABURET S, GEORGES A, L'HÔTE D, et al.The transcription factor FOXL2:At the crossroads of ovarian physiology and pathology[J].Mol Cell Endocrinol, 2012, 356(1-2):55-64.
[22]	LORENZ R, BERNHART S H, ZU SIEDERDISSEN C H, et al.ViennaRNA package 2.0[J].Algorithms Mol Biol, 2011, 6:26.
[23]	GRUBER A R, LORENZ R, BERNHART S H, et al.The Vienna RNA websuite[J].Nucleic Acids Res, 2008, 36(S1):W70-W74.
[24]	宋真, 赵善江, 李来宝, 等.影响荷斯坦奶牛产犊间隔的因素及其研究进展[J].中国畜牧兽医, 2021, 48(3):982-990.SONG Z, ZHAO S J, LI L B, et al.Impact factors and its research progress of calving interval in Holstein dairy cows[J].China Animal Husbandry & Veterinary Medicine, 2021, 48(3):982-990.(in Chinese)
[25]	许艳丽.牛FSHβ基因上游调控区连锁突变对其转录的影响分析[D].长春:吉林大学, 2011.XU Y L.Effect of chain mutation of FSHβ gene upstream regulatory region on transcription in bovine[D].Changchun:Jilin University China, 2011.(in Chinese)
[26]	CAMPBELL D B, SUTCLIFFE J S, EBERT P J, et al.A genetic variant that disrupts MET transcription is associated with autism[J].Proc Natl Acad Sci U S A, 2006, 103(45):16834-16839.
[27]	KOMAR A A, LESNIK T, REISS C.Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation[J].FEBS Lett, 1999, 462(3):387-391.
[28]	WALSH I M, BOWMAN M A, SANTARRIAGA I F S, et al.Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness[J].Proc Natl Acad Sci U S A, 2020, 117(7):3528-3534.
[29]	付鑫.不同毛色山羊皮肤组织MLPH基因差异表达及内含子变异[D].保定:河北农业大学, 2013.FU X.Study on differental expression of MLPH gene and the variations of the intron mutation among different colour Goat skin tissue[D].Baoding:Hebei Agricultural University, 2013.(in Chinese)
[30]	WANG X, DEFRANCES M C, DAI Y, et al.A mechanism of cell survival:sequestration of Fas by the HGF receptor Met[J].Mol Cell, 2002, 9(2):411-421.
[31]	YANG Y, SPITZER E, MEYER D, et al.Sequential requirement of hepatocyte growth factor and neuregulin in the morphogenesis and differentiation of the mammary gland[J].J Cell Biol, 1995, 131(1):215-226.
[32]	NIRANJAN B, BULUWELA L, YANT J, et al.HGF/SF:a potent cytokine for mammary growth, morphogenesis and development[J].Development, 1995, 121(9):2897-2908.
[33]	CHEN R, DAVYDOV E V, SIROTA M, et al.Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association[J].PLoS One, 2010, 5(10):e13574.
[34]	LI Q L, ZHANG Z F, XIA P, et al.A SNP in the 3'-UTR of HSF1 in dairy cattle affects binding of target bta-miR-484[J].Genet Mol Res, 2015, 14(4):12746-12755.
[35]	STATELLO L, GUO C J, CHEN L L, et al.Gene regulation by long non-coding RNAs and its biological functions[J].Nat Rev Mol Cell Biol, 2021, 22(2):96-118.
[36]	文禹粱, 王翔宇, 郭晓飞, 等.不同产羔数小尾寒羊BMP4基因表达及其错义突变与产羔数关联分析[J].农业生物技术学报, 2019, 27(1):80-88.WEN Y L, WANG X Y, GUO X F, et al.BMP4 gene expression in small Tail Han sheep (Ovis aries) with different litter size and association analysis between its missense mutation and litter size[J].Journal of Agricultural Biotechnology, 2019, 27(1):80-88.(in Chinese)
[37]	LIU N J, ZHANG K, ZHAO H Y.Haplotype-association analysis[J].Adv Genet, 2008, 60:335-405.

MET基因多态性与中国荷斯坦牛繁殖和泌乳性状的关联分析

Association Analysis of MET Gene Single Nucleotide Polymorphism with Reproduction and Milk Production Traits in Chinese Holstein Cattle

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