Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep

Abstract

ObjectiveThe objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production.MethodsSix samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups.Results23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups.ConclusionIn the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.

Combined approaches to identify genomic regions involved in phenotypic differentiation between low divergent breeds: Application in Sardinian sheep populations

“…Anyway, the genome‐wide scan performed here by comparing relatively close populations, such as Sardinian breeds, is unlikely to be confounded by demographic history and ascertainment bias. Among the most significant SNPs identified in the GWAS analysis, the first one, rs161255946 (at position 42,854,458 bp on OAR19) was located within ACOX2 gene involved in growth (Cao, Jin, Ma, & Zhao, ) and lipid metabolism pathway (Lim et al, ). This marker was also identified as significant by the bayescan approach.…”

Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca

“…Repeat sequences were inferred to comprised 33.1% of the genome in L. guanicoe, 32.7% in V. vicugna, and 27.02% in L. glama, lower values than in most mammals [11], although such sequences were difficult to assemble most likely due to the limitations of short-read sequencing. Resequencing of seven individuals per species (Additional file 1: Figure S2; Table S8) yielded an average sequence depth of 16-fold after filtering (31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45) Gb, Additional file 1: Table S9). Resequencing uncovered 21.3 million SNPs and a heterozygous SNP rate of 0.0030 for alpaca, 25.2 million and 0.0023 for vicuña, 16.7 million and 0.0018 for guanaco, and 16.1 million and 0.0020 for llama, indicating a higher overall SNP rate for the Vicugna lineage.…”

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes

“…Epigenetic research has permeated several fields of biological research, from molecular to evolutionary biology ( Richard and Stein, 2012 ). However, despite the importance of epigenetic mechanisms in biology in general, epigenetic studies in production animals are incipient, with some studies performed in chickens ( Pértille et al, 2017a , 2019 ; Bélteky et al, 2018 ; Guerrero-Bosagna et al, 2020 ), in cattle ( Su et al, 2014 ; Fang et al, 2017 ; Zhou et al, 2018 ; Sevane et al, 2019 ), in sheep ( Cao et al, 2017 ; Capra et al, 2017 ; Zhang X. et al, 2017 ; Zhang Y. et al, 2017 ), and pigs ( Gao et al, 2014 ; Choi et al, 2015 ; Yuan et al, 2017 ; Wang and Kadarmideen, 2019 , 2020 ). Among production animals, chickens have recently emerged as a promising model for epigenetic studies ( Frésard et al, 2013 ) following their historical use as a model for translational research with implications for human health and physiology ( Kain et al, 2014 ).…”