蓝塘猪与长白猪背最长肌全基因组DNA甲基化分析  

Whole genome-wide DNA methylation of longissimus dorsi muscle in Lantang and Landrace pigs

作　　者：林泽堃 谢芳 罗君谊 陈婷[1] 习欠云[1] 张永亮[1] 孙加节 LIN Zekun;XIE Fang;LUO Junyi;CHEN Ting;XI Qianyun;ZHANG Yongliang;SUN Jiajie(National Engineering Research Center for Breeding Swine Industry,College of Animal Science,South China Agricultural University,Guangzhou,Guangdong 510642,China)

机构地区：[1]华南农业大学、动物科学学院、国家生猪种业工程技术研究中心,广东广州510642

出　　处：《西北农林科技大学学报（自然科学版）》2023年第6期1-10,17,共11页Journal of Northwest A&F University(Natural Science Edition)

基　　金：国家自然科学基金项目(32072714,32072812,31872435,32072814);广东省自然科学基金项目(2020A1515010062);广州市科技项目(202002030037)。

摘　　要：【目的】分析蓝塘猪与长白猪背最长肌组织全基因组DNA甲基化水平,筛选2个猪品种的差异甲基化基因(DMG),为优质肉猪选育提供理论依据。【方法】利用全基因组亚硫酸氢盐测序(WGBS)技术,分析1日龄雄性蓝塘猪与长白猪背最长肌组织全基因组DNA的甲基化水平、差异甲基化区域(DMR)和DMG,并对DMG进行GO注释,揭示蓝塘猪与长白猪差异甲基化基因的功能。【结果】蓝塘猪和长白猪样本测序获得的原始序列数量分别为300005805和300012190条,有效序列数量分别为210334070和210758564条,有效序列与猪参考基因组的比对成功率分别为70.11%和70.25%,Bisulfite转化率分别为98.54%和98.36%。蓝塘猪全基因组范围内胞嘧啶(C)的甲基化率为4.07%,其中CG、CHG和CHH中胞嘧啶的甲基化率分别为74.50%,1.74%和1.51%;长白猪全基因组范围内胞嘧啶的甲基化率为4.44%,其中CG、CHG和CHH中胞嘧啶的甲基化率分别为76.92%,2.13%和1.87%。共检测出13126个差异性甲基化区域,总长度为3357954 bp,含有78234个胞嘧啶。68.50%的差异性甲基化区域分布在基因间区,25.74%分布在内含子,1.89%分布在外显子,1.85%分布在上游2 kb区域,1.78%分布在下游2 kb区域,0.24%分布在CpG岛。甲基化差异基因显著富集于凋亡过程的负调控、细胞迁移的正调控等24个GO条目,其中FAM135B、NR1H2、ID4、ZFPM2、FOXO1等5个基因与蓝塘猪和长白猪的脂肪代谢相关,长白猪FAM135B、NR1H2、ZFPM2和FOXO1的表达水平高于蓝塘猪,而ID4略低于蓝塘猪。【结论】明确了蓝塘猪和长白猪背最长肌组织全基因组DNA的甲基化情况,为深入研究2个猪种肉质差异的分子机制提供了基础数据。【Objective】This study analyzed the genome-wide DNA methylation levels of the longissimus dorsi muscle tissue of Lantang and Landrace pigs and screened out differentially methylated gene(DMG)between the two breeds to provide basis for the selection and breeding of high-quality pork pigs.【Method】Whole genome bisulfite sequencing(WGBS)technology was used to analyze the methylation level,diffe-rentially methylated region(DMR)and DMG of whole genome DNA of longissimus dorsi muscle tissue in 1-day-old male Lantang and Landrace pigs,and the DMG was annotated by GO to reveal the function of di-fferential methylation genes.【Result】The number of original sequences was 300005805 and 300012190 for Lantang and Landrace pigs and the number of effective sequences was 210334070 and 210758564,respectively.Their successful ratios of effective sequence to pig reference genome were 70.11%and 70.25%,and Bisulfite conversion rates were 98.54%and 98.36%,respectively.The genome-wide methylation rate of cytosine(C)in the whole genome of Lantang pigs was 4.07%,and the methylation rates of C in CG,CHG and CHH were 74.50%,1.74%and 1.51%,respectively.The genome-wide methylation rate of C in Landrace pigs was 4.44%,and the methylation rates of C in CG,CHG and CHH were 76.92%,2.13%and 1.87%,respectively.A total of 13126 DMR were detected,with 3357954 bp length and 78234 cytosines.About 68.50%of DMR were distributed in intergenic region,25.74%in introns,1.89%in exons,1.85%in upstream 2 kb region,1.78%in downstream 2 kb region and 0.24%in CpG island.DMGs function was significantly enriched in 24 GO genes,including negative regulation of apoptotic process and positive regulation of cell migration.Among them,FAM135B,NR1H2,ID4,ZFPM2 and FOXO1 genes were related to fat metabolism in Lantang and Landrace pigs.The expression levels of FAM135B,NR1H2,ZFPM2 and FOXO1 in Landrace pigs were higher than those in Lantang pigs,while the expression levels of ID4 in Lantang pigs were slightly higher than that in Landrace pigs.【Conclusion】The gen

关 键 词：蓝塘猪 长白猪 背最长肌 DNA甲基化 肉品质 

分 类 号：S828.2[农业科学—畜牧学]