基于全基因组差异甲基化分析鉴别影响苏姜猪体重的候选基因

doi:10.16431/j.cnki.1671-7236.2021.08.021

Abstract

Abstract: The study was aimed to analyze the difference of genome-wide DNA differential methylation in Sujiang pigs with different body weight, as to screen the differentially methylated genes (DMGs) that affect the body weight of Sujiang pigs.In the study, three 180-day-old Sujiang pigs with high body weight and three 180-day-old Sujiang pigs with low body weight were detected by the whole genome bisulfite sequencing (WGBS) method.The degree of genome-wide DNA methylation, differentially methylated regions (DMRs) and DMGs were analyzed.The candidate genes affecting the body weight of Sujiang pig were identified by GO and KEGG pathway enrichment analysis of DMGs.The results showed that average 4.1% cytosine (C) were methylated in the whole genome of Sujiang pigs.Average 98.41% methylcytosines occurred on CG sequences.The DNA methylation level of exon, intron and 3'UTR was higher than that of promoter and 5'UTR at CG sequence context.A total of 1 657 DMRs and 575 DMGs were detected in this study.The distribution of DMRs on chromosome 8 was the most, 88.89% of the DMRs were within the length of 500 bp, and 62.78% of the DMRs were distributed in the distal intergenic.98 DMGs were significantly enriched in 53 GO terms and 29 signal pathways, including negative regulation of TOR signaling, carbohydrate derivative catabolic process, adipocytokine signaling pathway and FoxO signaling pathway.Five candidate genes related to body weight of Sujiang pigs were identified:leptin receptor(LEPR), tumor necrosis factor receptor associated factor 6(TRAF6), myogenic factor 6(MYF6), calcium dependent secretion activator 2(CADPS2) and epidermal growth factor(EGF).In this study, the whole genome DNA methylation map of Sujiang pigs with high and low body weight was drawn by WGBS, which laid a foundation for the further study of the molecular mechanism of body weight difference in Sujiang pigs.

Key words: Sujiang pigs; DNA methylation; whole genome bisulfite sequencing; body weight; candidate gene

CLC Number:

S813.1

XU Pan, ZHONG De, MA Zheng, LIU Linyu, WANG Yihui, ZHAO Xuting. Identification of Candidate Genes for Body Weight in Sujiang Pigs Based on Genome-wide Differential Methylation Analysis[J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(8): 2889-2900.

References

[1] JONES P A.Functions of DNA methylation:Islands,start sites,gene bodies and beyond[J].Nature Reviews Genetics,2012,13(7):484-492.
[2] LLUIS F,COSMA M P.Resetting epigenetic signatures to induce somatic cell reprogramming[J].Cellular and Molecular Life Sciences,2013,70(8):1413-1424.
[3] LAENOI W,UDDIN M J,CINAR M U,et al.Molecular characterization and methylation study of matrix gla protein in articular cartilage from pig with osteochondrosis[J].Gene,2010,459(1-2):24-31.
[4] LIU X,YANG J,ZHANG Q,et al.Regulation of DNA methylation on EEF1D and RPL8 expression in cattle[J].Genetica,2017,145(4-5):387-395.
[5] 吴贤锋.山羊STAT3和STAT5A基因SNPs,mRNA表达及甲基化对生产性能的影响[D].杨凌:西北农林科技大学,2015. WU X F.SNPs,mRNA expression and methylation of STAT3 and STAT5A genes and their influences on production traits in goats[D].Yangling:Northwest A&F University,2015.(in Chinese)
[6] XU P,NI L,TAO Y,et al.Genome-wide association study for growth and fatness traits in Chinese Sujiang pigs[J].Animal Genetics,2020,51(2):314-318.
[7] KRUEGER F,ANDREWS S R.Bismark:A flexible aligner and methylation caller for Bisulfite-Seq applications[J].Bioinformatics,2011,27(11):1571-1572.
[8] HAO F,CONNEELY K N,HAO W.A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data[J].Nucleic Acids Research,2014,42(8):e69.
[9] WU H,XU T L,FENG H,et al.Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates[J].Nucleic Acids Research,2015,43(21):e141.
[10] PARK Y,WU H.Differential methylation analysis for BS-seq data under general experimental design[J].Bioinformatics,2016,32(10):1446-1453.
[11] YU G C,WANG L G,HAN Y Y,et al.clusterProfiler:An R package for comparing biological themes among gene clusters[J].OMICS,2012,16(5):284-287.
[12] 蒋曹德,邓昌彦,熊远著.猪个体DNA甲基化百分差异与胴体性状的关系[J].农业生物技术学报,2005,13(2):179-185. JIANG C D,DENG C Y,XIONG Y Z.Relationship between individual DNA methylation percentage difference and carcass traits in pig[J].Journal of Agricultural Biotechnology,2005,13(2):179-185.(in Chinese)
[13] LI M,WU H,LUO Z,et al.An atlas of DNA methylomes in porcine adipose and muscle tissues[J].Nature Communications,2012,3:850.
[14] YANG Y,ZHOU R,MU Y,et al.Genome-wide analysis of DNA methylation in obese,lean,and miniature pig breeds[J].Scientific Reports,2016,6:30160.
[15] 张恬.猪肌内脂肪全基因组甲基化差异分析及候选基因研究[D].北京:中国农业科学院,2016. ZHANG T.Study on genome-wide methylation differential analysis and candidate genes in pig IMF[D].Beijing:Chinese Academy of Agricultural Science,2016.(in Chinese)
[16] 郭添福,张志燕,陈冬,等.不同性别大白猪肌肉全基因组高分辨率单碱基甲基化差异分析[J].畜牧兽医学报,2018,49(11):2326-2339. GUO T F,ZHANG Z Y,CHEN D,et al.High resolution and single base genome-wide methylation variance analysis of muscle of Large White pigs with differnent sexes[J].Acta Veterinaria et Zootechnica Sinica,2018,49(11):2326-2339.(in Chinese)
[17] 刘会敬.中外猪种胚胎不同发育时期骨骼肌转录组和全基因组甲基化分析[D].武汉:华中农业大学,2018. LIU H J.Integration of DNA methylome and transcriptome analysis of prenatal skeletal muscles between Tongcheng and Yorkshire pigs[D].Wuhan:Huazhong Agricultural University,2018.(in Chinese)
[18] 张效川.发情期和间情期奶山羊卵巢全基因组甲基化差异分析[D].杨凌:西北农林科技大学,2020. ZHANG X C.The analysis on methylation differential of ovarian genome between oestrous and dioestrous phases of dairy goats[D].Yangling:Northwest A&F University,2020.(in Chinese)
[19] MEISSNER A,GNIRKE A,BELL G W,et al.Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis[J].Nucleic Acids Research,2005,33(18):5868-5877.
[20] CHOI M,LEE J,LE M T,et al.Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing[J].DNA Research,2015,22(5):343-355.
[21] YUAN X L,GAO N,XING Y,et al.Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing[J].Scientific Reports,2016,6:22138.
[22] JACINTO F V,BALLESTAR E,ESTELLER M.Methyl-DNA immunoprecipitation (MeDIP):Hunting down the DNA methylome[J].Biotechniques,2008,44(1):35,37,39 passim.
[23] 董辉.基于MeDIP-Seq研究皖南花猪和大约克猪背最长肌基因差异甲基化[D].合肥:安徽农业大学,2015. DONG H.Study on differential methylation of genes in longissimus dorsi muscle of Wannanhua pig and Yorkshire pig based on MeDIP-Seq technology[D].Hefei:Anhui Agricultural University,2015.(in Chinese)
[24] CLEMENT K,VAISSE C,LAHLOU N,et al.A mutation in the human leptin receptor gene causes obesity and pituitary dysfunction[J].Nature,1998,392(6674):398-401.
[25] MUNOZ G,OVILO C,SILIO L,et al.Single- and joint-population analyses of two experimental pig crosses to confirm quantitative trait loci on Sus scrofa chromosome 6 and leptin receptor effects on fatness and growth traits[J].Journal of Animal Science,2009,87(2):459-468.
[26] PEREZ-MONTARELO D,FERNANDEZ A,FOLCH J M,et al.Joint effects of porcine leptin and leptin receptor polymorphisms on productivity and quality traits[J].Animal Genetics,2012,43(6):805-809.
[27] ASAGIRI M,TAKAYANAGI H.The molecular understanding of osteoclast differentiation[J].Bone,2007,40(2):251-264.
[28] ZHANG C Y,WANG Z,BRUCE H L,et al.Associations between single nucleotide polymorphisms in 33 candidate genes and meat quality traits in commercial pigs[J].Animal Genetics,2014,45(4):508-516.
[29] DO D N,STRATHE A B,OSTERSEN T,et al.Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping[J].PLoS One,2013,8(8):e71509.
[30] WANG X,ZHENG F,LIU O S,et al.Epidermal growth factor can optimize a serum-free culture system for bone marrow stem cell proliferation in a miniature pig model[J].In Vitro Cellular & Developmental Biology-Animal,2013,49(10):815-825.

Identification of Candidate Genes for Body Weight in Sujiang Pigs Based on Genome-wide Differential Methylation Analysis

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	TANG Bihui, PAN Lu, LI Haiying, ZHAO Xiaoyu, WU Yingping, JIANG Teng, DING Yawen, WU Linan, CAO Yan, MEI Zhiyong. Genome-wide Selection Signal Analysis of Laying Traits in Geese [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 3015-3025.
[2]	ZHOU Di, AO Ye, JIANG Guirong, ZHAO Zhonghai, LI Jun, YANG Rong, GONG Fei, CHEN Changxue, SHEN Yin, LI Hui. Polymorphism of MEF2C Gene Exon and Its Association Analysis with Weight and Body Size Traits in Qiandongnan Xiaoxiang Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(7): 2613-2621.
[3]	SHAO Yandi, JIANG Qiufei, FENG Yuan, WANG Yu, ZHANG Juan, ZHOU Zihang, WANG Weizhen, YU Baojun, FENG Xiaofang, CHEN Yafei, GU Yaling. Research Progress on Candidate Genes of Cattle Reproductive Traits [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(6): 2270-2278.
[4]	YU Simeng, GUO Zhanbao, HU Jian, ZHOU Zhengkui, HOU Shuisheng. Analysis of Genetic Differentiation Between IAS Grassland Ducks and Cherry Valley Ducks [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(3): 801-808.
[5]	XUE Qian, LI Guohui, ZHANG Huiyong, YIN Jianmei, ZHOU Chenghao, ZHU Yunfen, XING Weijie, SU Yijun, ZOU Jianmin, HAN Wei. Genome-wide DNA Methylation Analysis of Hypothalamus and Ovary in Langshan Chicken [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(2): 417-424.
[6]	SUN Lingzhu, RAN Xueqin, LIU Chang, NIU Xi, HUANG Shihui, WANG Jiafu. Detection of Genome Exon SNPs and Analysis of Candidate Genes for Reproduction and Body Type Traits in Xiang Pig [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(2): 537-553.
[7]	LIU Haixia, ZHU Aiwen, WANG Buzhong, GENG Xinzhi, ZHENG Ankang. Research Progress on Mechanism of Melanin Deposition and Related Candidate Genes in Black-bone Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(12): 4588-4596.
[8]	XU Lei, ZHANG Menghua, WANG Dan, ZHANG Xiaoxue, FAN Shoumin, LIU Jianming, LIU Jiangwei, YAN Chengxu, HUANG Xixia, WANG Yachun. Estimation of Genetic Parameters of Body Size and Body Weight in Xinjiang Brown Cattle at Different Growth Stages [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(11): 4105-4114.
[9]	REN Xiaoli, FAN Yuying, HUANGFU Heping, DONG Qing, SHI Dongmei, LIU Yun. Research Progress on Epigenetic Regulation Mechanism in Canine Tumor [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(11): 4319-4326.
[10]	SI Jinglei, HUANG Ye, CHEN Kuirong, LYU Dongling, CHENG Feng, TIAN Weilong, LIU Xiaoxiao, LIANG Liang, LI Yueyue, FENG Lingli, GAO Jiuyu, MO Jiayuan, LIANG Jing, LAN Ganqiu. Evaluating of the Association Between Early-stage Weight and Gut Microbiota in Duroc Pigs Using 16S rRNA Sequencing [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(1): 190-199.
[11]	ZHANG Hui, LI Xiaoyu, DI Ran, LIU Yufang, CHU Mingxing. Analysis on Difference of Transcription and DNA Methylation Level of AANAT Gene in Ovary of Tan Sheep at Different Reproductive Stages [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(1): 226-234.
[12]	LIU Xiangping, ZHU Jing, BAI Hao, KONG Linglin, GU Huabing, DOU Xinhong. Correlation Between Growth Traits and Immune Indexes of Xueshan Chickens [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(5): 1481-1488.
[13]	DU Jianwen, YANG Xuemei, WANG Dan, ZHU Hua, HE Junmin, ABLAT Sulayman, TIAN Yuezhen, ZHAO Bingru, XU Xinming, FU Xuefeng, HANIKEZI Tulafu, WU Weiwei, TIAN Kechuan, HUANG Xixia. Analysis of DNA Methylation and mRNA Expression Levels of ITGB2 Gene in Different Fineness of Subo Merino Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(4): 1009-1017.
[14]	MO Jiayuan, GAO Jiuyu, FENG Lingli, LI Yueyue, TIAN Weilong, LIU Xiaoxiao, CHENG Feng, LIANG Liang, LEI Shuqiao, WEN Wei, LIANG Jing, LAN Ganqiu. Genome-wide Association Study on Alive Litter Size Trait in Bama Xiang Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(12): 3965-3975.
[15]	CAI Chunbo, XU Kai, LI Meng, YANG Yang, ZHAO Yan, GAO Pengfei, GUO Xiaohong, CAO Guoqing, LI Bugao. Correlation Analysis Between Haplotypes of ApoA5 Gene on Body Weight and Meat Quality in Jinfen White Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(11): 3563-3572.