TABLE 2.
Alteration of epigenetic markers in relation to livestock production traits.
| Parameter | Breed | Organ | Epigenetic alteration | Production trait | Model and references |
| Milk | |||||
| High and low milk yield | Holstein cows | Peripheral blood mononuclear cells | 72 DMRs between high and low milk yield, 252 DMRs across herd environments | Milk yield | Dechow and Liu, 2018 |
| High and low milk yield | Holstein cows | Jugular venous blood | DNA methylation rates in the lower-yield cows were significantly higher than those in the higher-yield animals | Milk and protein yield | Wang L. et al., 2019 |
| Experimentally induced mastitis by E. coli and S. aureus | Holstein cows | Liver and mammary gland tissues | Remethylation of upstream promoter of CSN1S1 gene in response to E. coli infection | αS1-casein synthesis | Vanselow et al., 2006 |
| Once/twice daily milking | Holstein cows | Liver and mammary gland tissue | Altered methylation of four CpG within the distal upstream regulatory region of the CSN1S1 gene | Milk production (yield and milking frequency) | Nguyen et al., 2014 |
| Different lactation stages | Holstein cows | Blood | DNA methylation of EEF1D was lower in the dry period than the early stage of lactation | Milk production | Liu X. et al., 2017 |
| Different lactation stages | Xinong Saanen goats | Mammary gland tissue | Methylation levels of 95 and 54 genes in the lactation period were up- or downregulated, respectively, relative to the dry period | Milk production | Zhang X. et al., 2017 |
| Different lactation stages | Xinong Saanen goats | Mammary gland tissue | Inhibition of miR−145 increased methylation levels of FASN, SCD1, PPARG, and SREBF1 | Milk fat synthesis | Wang et al., 2017b |
| High- and low-concentrate diet feeding | Guanzhong goats | Mammary gland tissue | Increased DNA methylation level in the promoter regions of the ACACA and SCD genes | Milk fat production and composition | Tian et al., 2017 |
| Meat | |||||
| Two sheep breeds differing in meat production ability | Small-tailed Han and Dorper × small-tailed Han crossbred sheep | Longissimus dorsi muscles | 808 DMRs and global loss of DNA methylation in the DMRs in the crossbred sheep, 12 potential DMGs | Meat production | Cao et al., 2017 |
| Two cattle breeds exhibiting different meat production ability | Japanese black and Chinese Red Steppes cattle | Longissimus dorsi muscles | 23,150 DMRs identified, 331 DMRs correlated negatively with expression of DE genes, 21 DMRs located in promoter regions | Muscle development and related meat quality traits | Fang et al., 2017 |
| Divergent beef tenderness | Angus beef | Longissimus dorsi muscles | DNA methylation profiles related to beef tenderness, and 7215 DMRs between tender and tough beef | Beef tenderness | Zhao et al., 2020 |
| Three cattle breeds differing in meat production abilities | Simmental, Yunling, and Wenshan cattle | Longissimus dorsi muscles | 18 DM and DE genes between Simmental and Wenshan cattle, 14 DM and DE genes between Simmental and Yunling cattle, 28 DM genes between Wenshan and Yunling cattle | Meat quality | Chen Z. et al., 2019 |
| Three growth stages | Polled yak | Longissimus dorsi muscles | 1,344, 822, and 420 genes with DM CCGG sites and 2,282, 3,056, and 537 genes with DM CCWGG sites between 6-month-old vs 90-day-old, 6-month-old vs 3-year-old, and 3-year-old vs 90-day-old fetuses, respectively | Muscle development and growth | Ma et al., 2019 |
| Feed restriction | Angus–Simmental crossbred cows | Longissimus dorsi and semitendinosus muscle | One DMR in IGF2 | Muscle function | Paradis et al., 2017 |
| Fetal and adult cattle | Qinchuan cattle | Longissimus dorsi muscles | Three DMCs in the core promoter region of SIX1, histone H4 and E2F2 bind to SLX1 | Muscle development | Wei et al., 2018 |
| Obese, lean, and miniature pig breeds | Tongcheng, Landrace, and Wuzhishan pigs | Blood leukocytes | 2,807, 2,969, and 5,547 DMGs in the Tongcheng vs Landrace, Tongcheng vs Wuzhishan, and Landrace vs Wuzhishan comparisons, respectively | Fat-related phenotype variance | Yang et al., 2016b |
| Obese and lean type pig breeds | Landrace pigs and Rongchang pigs | Backfat | 483 DMRs in the promoter regions | Fat deposition and fatty acid composition | Zhang S. et al., 2016 |
| Castrated and non-castrated pigs | Male Huainan pigs | Liver and adipose tissues | GHR methylation rate in the liver of castrated and non-castrated pigs were 93.33% and 0, respectively | Castration-induced fat deposition | Wang et al., 2017e |
| Pig breeds differing in metabolic characters | Duroc and Pietrain | Longissimus dorsi muscles | More than 2,000 DMCs | Muscle metabolism | Ponsuksili et al., 2019 |
| Three pig breeds differing in fatness traits | Polish Large White, Duroc and Pietrain | Subcutaneous fat, visceral fat, and longissimus dorsi muscle | H3K9ac and H3K4me3 correlated to the expression level of selected genes | Adipose tissue accumulation | Kociucka et al., 2017 |
| Highest and lowest pH among littermates | Duroc | Longissimus dorsi muscle | 3,468 DMRs, including 44 and 21 protein-coding genes with hyper- and hypomethylation regions in their gene bodies | Postmortem energy metabolism and pH | Park et al., 2019 |
| High and low boar taint | Pigs | Testis | 32 DE genes with DMCs | Boar taint | Wang and Kadarmideen, 2019a,c |
| Different growth stages | Gushi hens | Breast muscle | 2,714 DMRs and 378 DMGs | Intramuscular fat deposition and water-holding capacity | Zhang M. et al., 2017 |
| Different feed conditions and breeds | Daninghe and Qingjiaoma chickens | Breast muscle | 46 CpG sites and 3 CpG islands in UCP3, different methylation levels of UCP and FATP1 between groups | Breast muscle (intramuscular fat content) | Gao et al., 2015, 2017 |
| Egg | |||||
| Before and after reproductive maturation | Hy-Line Brown commercial female chickens | Ovaries | Increased methylation of two CpG sites in ERα; increased H3K27ac and decreased H3K36me3 related to increased ERα mRNA transcript | Reproductively mature, egg production | Guo M. et al., 2020 |
| Betaine supplementation | Laying hens | Liver | Hypomethylation of promoter in GR | Egg production | Omer et al., 2018, 2020 |
| Wool | |||||
| Different generations of cashmere goats | Cashmere goats | Skin | 336 hyper- and 753 hypomethylated 5mC, corresponding to 214 hyper- and 560 hypomethylated genes | Cashmere traits | Dai et al., 2019 |
| Anagen and telogen stages | Cashmere goats | Skin | 1,311 DMRs corresponding to 493 DMGs (269 hyper- and 224 hypomethylated DMGs) | Hair cycling and cashmere growth | Li et al., 2018 |
| Coarse type and fine type cashmere | Cashmere goats | Skin | 9,085 DM N6-methyladenosine sites | Cashmere fiber growth | Wang et al., 2020f |
| Cashmere goats and other goat species | Cashmere goats | Skin | Altered methylation degree of HOXC8 exon 1 | Cashmere fiber growth | Bai et al., 2017 |
| Anagen and telogen stages | Cashmere goats | Skin | Altered promoter methylation of HOTAIR gene | Cashmere fiber growth | Jiao et al., 2019 |
DM, differentially methylated; DE, differentially expressed; DMR, differential methylated region; DMG, differential methylated gene; DMC, differential methylated CpG; H3K9ac, histone H3 lysine 9 acetylation; H3K4me3, trimethylation at the fourth lysine residue of histone H3 protein; H3K27ac, acetylation at the 27th lysine residue of histone H3 protein; H3K36me3, trimethylation at the 36th lysine residue of histone H3 protein.