Comparative epigenetics: relevance to the regulation of production and health traits in cattle

Doherty, Rachael; Farrelly, Cliona O'; Meade, Kieran G.

doi:10.1111/age.12140

Cited by 23 publications

(16 citation statements)

References 113 publications

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“…The variants identified by GWAS usually account for only a fraction of the total trait heritability. The ‘missing heritability’ can be explained in part by the epigenetic effects on gene regulation through EWAS studies ( Doherty et al, 2014 ). Furthermore, advances in RNA sequencing technologies are enabling miRNA discovery in livestock species and the role of miRNA regulation of livestock phenotypes is beginning to emerge.…”

Section: Potential Application Of Epigenetics Information In Livestocmentioning

confidence: 99%

Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

Ibeagha‐Awemu

Zhao

2015

Front. Genet.

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Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.

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Section: Potential Application Of Epigenetics Information In Livestocmentioning

confidence: 99%

Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

Ibeagha‐Awemu

Zhao

2015

Front. Genet.

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“…In vertebrates, the CpG island is distinct owing to their lack of DNA methylation and absences of CpG deficiency (Deaton et al, 2011). Mutation in CpG island of MSTN gene could change the regulation of expression via the generated CpG island and/or changed target sites for transcriptional regulator (Doherty et al, 2014). Mutation in MSTN gene in cattle showed different characteristics such as increasing of birth weight, higher muscling, faster growing, hyperplasia and hypertrophy in muscle (Kambadur et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Polymorphism of Myostatin (MSTN) Promoter Gene and its Association with Growth and Muscling Traits in Bali Cattle

Khasanah

Gunawan

Priyanto

et al. 2016

Med Pet

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Myostatin (MSTN) gene plays a key role in skletal muscle homeostasis such as inducing muscle athrophy, poliferation of myoblast, increasing ubiquitin-proteasomal, downregulating IGF pathway, and glucolysis. Myostatin gene expression is controled by CpG island located in promoter region. The objectives of this research were to identify polymorphism of MSTN promoter gene and to associate the polymorphism of SNP with growth and muscling traits in Bali cattle. A total of 48 Bali cattle from BPTU-HMT Bali island was screened to identify genetic polymorphisms in MSTN promoter region using sequencing method. The growth and muscling traits were measured at 12 months of age. The muscling traits were evaluated using ultrasound console with linear transducer having frequency 6.5 Hz and scaning we conducted at 130 mm in deep. Analysis of polymorphism was conducted by using PopGen 1.32 software. The association of MSTN with growth and muscling traits were analyzed by using General Linear Model (GLM) procedure. This result showed that a total of 20 polymorphic SNPs (seven SNPs in CpG island) were detected in this region. Although, only 3 SNPs (g.-8078C>T, g.-7996G>C, and g.-7930A>G) had equilibrium condition in Hardy-Weinberg analysis. The association result showed that 2 SNPs (g.-7799T>C and g.-7941C>T) were significantly associated with intramuscular fat percentage (P≤0.05) in Bali cattle. Although the 2 SNPs were nominally significant at nominal P≤0.05 threshold, they were not significant after Bonferroni correction for multiple testing. It could be concluded that MSTN promoter gene was polymorphic in Bali cattle and there were 2 SNPs associated with carcass quality.

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“…These epigenetic changes are induced by environmental condition and are potentially heritable. Epigenetics research holds the key to understanding how environmental factors contribute to phenotypic variation in traits of economic importance in cattle including development, nutrition, behaviour and health (Doherty et al 2014). …”

Section: Introductionmentioning

confidence: 99%

A data filtering to utilizing Human Methylation arrays in genome-wide study of bovine DNA methylation

Kobayashi

Takeda

2016

The Journal of Animal Genetics

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DNA methylation is important for regulating gene expression during many biological processes. There are two popular techniques for detecting genome-wide DNA methylation profiles: next-generation sequencing and DNA arrays. We conducted a pilot study for data filtering using Human Methylation arrays to evaluate the genome-wide methylation profiles using bovine DNA samples. Five tissues of two female Japanese Black cattle were analyzed in this study. We focused on the detection P-value as an indicator of the reliability of data. Here, detection P-values were used for examining array performance, which indicate the proportion of 600 negative control probes with higher signal intensity than measured for each probe. We first investigated the distribution of detection P-values using bovine DNA, and next evaluated bovine sequences with high similarity to human sequences on the probes by a BLAST search. A total of 75,207 CpG sites had a detection P-value of 0 in all examined samples (15.5%). The detection P-values for bovine DNA were markedly worse than for humans and monkeys, but better than for mice. The CpG sites with low signal intensity apparently had low quality. The total signal intensity level at each CpG site was also shown to be very important to improve array performance, similarly to the detection P-value. Among the CpG sites that fulfilled the thresholds of both detection P-value and mean total signal intensity, it was determined that approximately 70% had been evaluated properly. Therefore, it was expected that useful methylation data with good quality were obtained for approximately 50,000 CpG sites (about 10% of all probes). These results show that the Human Methylation arrays have potential for evaluating a few tens of thousands of CpG sites in cattle by appropriate filtering to ensure the quality of the data.

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Comparative epigenetics: relevance to the regulation of production and health traits in cattle

Cited by 23 publications

References 113 publications

Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

Polymorphism of Myostatin (MSTN) Promoter Gene and its Association with Growth and Muscling Traits in Bali Cattle

A data filtering to utilizing Human Methylation arrays in genome-wide study of bovine DNA methylation

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