Genetic Determinism Exists for the Global DNA Methylation Rate in Sheep

Abstract

Recent studies showed that epigenetic marks, including DNA methylation, influence production and adaptive traits in plants and animals. So far, most studies dealing with genetics and epigenetics considered DNA methylation sites independently. However, the genetic basis of the global DNA methylation rate (GDMR) remains unknown. The main objective of the present study was to investigate genetic determinism of GDMR in sheep. The experiment was conducted on 1,047 Romane sheep allocated into 10 half-sib families. After weaning, all the lambs were phenotyped for global GDMR in blood as well as for production and adaptive traits. GDMR was measured by LUminometric Methylation Analysis (LUMA) using a pyrosequencing approach. Association analyses were conducted on some of the lambs (n = 775) genotyped by using the Illumina OvineSNP50 BeadChip. Blood GDMR varied among the animals (average 70.7 ± 6.0%). Female lambs had significantly higher GDMR than male lambs. Inter-individual variability of blood GDMR had an additive genetic component and heritability was moderate (h ² = 0.20 ± 0.05). No significant genetic correlation was found between GDMR and growth or carcass traits, birthcoat, or social behaviors. Association analyses revealed 28 QTLs associated with blood GDMR. Seven genomic regions on chromosomes 1, 5, 11, 17, 24, and 26 were of most interest due to either high significant associations with GDMR or to the relevance of genes located close to the QTLs. QTL effects were moderate. Genomic regions associated with GDMR harbored several genes not yet described as being involved in DNA methylation, but some are already known to play an active role in gene expression. In addition, some candidate genes, CHD1, NCO3A, KDM8, KAT7, and KAT6A have previously been described to be involved in epigenetic modifications. In conclusion, the results of the present study indicate that blood GDMR in domestic sheep is under polygenic influence and provide new insights into DNA methylation genetic determinism.

Keywords: QTL; blood; epigenetics; genetic correlation; heritability.

FIGURE 1

Chromosome plots of the likelihood ratio test values obtained for global DNA methylation rate by LDLA analysis. The likelihood ratio test (LRT) is plotted against SNP haplotype positions (four consecutive SNPs) for chromosomes 1, 2, 3, 5, 11, 13, 14, 16, 17, 18, 21, 23, 24, and 26. The horizontal lines indicate the 5, 1, and 0.1% genome wide thresholds. One percent chromosome wide thresholds were OAR3, 47.6; OAR5, 37.4; OAR13, 42.6; OAR14, 35.9; OAR16, 38.7; OAR17, 42.3; OAR18, 40.6; OAR21, 37.3; OAR23, 45.7; OAR24, 42.8, and OAR26, 47.1. 5% chromosome wide thresholds were OAR1, 45.5; OAR2, 45.0; OAR11, 41.3; OAR13, 38.3; OAR24, 38.4.