| 1. |
- Rezaei, Shiva, et al.
(author)
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GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals
- 2022
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In: STAR Protocols. - : Cell Press. - 2666-1667. ; 3:1
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Journal article (peer-reviewed)abstract
- Summary:The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.
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| 2. |
- Pértille, Fábio, et al.
(author)
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Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes
- 2020
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In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 11
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Journal article (peer-reviewed)abstract
- Production animals are constantly subjected to early adverse environmental conditionsthat influence the adult phenotype and produce epigenetic effects. CpG dinucleotidemethylation in red blood cells (RBC) could be a useful epigenetic biomarker to identifyanimals subjected to chronic stress in the production environment. Here we compareda reduced fraction of the RBC methylome of chickens exposed to social isolation tonon-exposed. These experiments were performed in two different locations: Brazil andSweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposedin each facility and their different lineages. Birds were increasingly exposed to a socialisolation treatment, combined with food and water deprivation, at random periods of theday from weeks 1–4 after hatching. We then collected the RBC DNA from individualsand compared a reduced fraction of their methylome between the experimental groupsusing two bioinformatic approaches to identify differentially methylated regions (DMRs):one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P ≤ 0.05, P ≤ 0.005, and P ≤ 0.0005) to identify DMRs between experimental groups, which were then used for differentanalyses. With both of the approaches more DMRs reached the defined significancethresholds in BR individuals compared to SW. However, more DMRs had higher foldchange values in SW compared to BR individuals. Interestingly, ChrZ was enrichedabove expectancy for the presence of DMRs. Additionally, when analyzing the locationsof these DMRs in relation to the transcription starting site (TSS), we found threepeaks with high DMR presence: 10 kb upstream, the TSS itself, and 20–40 kbdownstream. Interestingly, these peaks had DMRs with a high presence (>50%) ofspecific transcription factor binding sites. Three overlapping DMRs were found betweenthe BR and SW population using the most relaxed p-value (P ≤ 0.05). With the most stringent p-value (P ≤ 0.0005), we found 7 and 4 DMRs between treatmentsin the BR and SW populations, respectively. This study is the first approximation toidentify epigenetic biomarkers of long-term exposure to stress in different lineages ofproduction animals.
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| 3. |
- Sundman, Ann-Sofie, et al.
(author)
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DNA methylation in canine brains is related to domestication and dog-breed formation
- 2020
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 15:10
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Journal article (peer-reviewed)abstract
- Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. During domestication, dogs have evolved an unprecedented between-breed variation in morphology and behavior in an evolutionary short period. In the present study, we explore DNA methylation differences in brain, the most relevant tissue with respect to behavior, between wolf and dog breeds. We optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and three wolves was used. GBS and GBS-MeDIP libraries were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 ± 0.4% of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 ± 4,042,106 unique base pairs. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors may have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding but are also useful to further understanding of epigenetic involvement.
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| 4. |
- Pértille, Fábio, et al.
(author)
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High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
- 2016
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Journal article (peer-reviewed)abstract
- Chicken genotyping is becoming common practice in conventional animal breeding improvement.Despite the power of high-throughput methods for genotyping, their high cost limits large scale use inanimal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and costeffectivegenotyping by sequence approach developed in plants, for its application in chickens. Herewe describe the successful genotyping of a large number of chickens (462) using CornellGBS approach.Genomic DNA was cleaved with the PstI enzyme, ligated to adapters with barcodes identifyingindividual animals, and then sequenced on Illumina platform. After filtering parameters were applied,134,528 SNPs were identified in our experimental population of chickens. Of these SNPs, 67,096 hada minimum taxon call rate of 90% and were considered ‘unique tags’. Interestingly, 20.7% of theseunique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs wereconcordant with a previous Whole Chicken-genome re-sequencing dataset used for validation purposes.The application of CornellGBS in chickens showed high performance to infer SNPs, particularly inexonic regions and microchromosomes. This approach represents a cost-effective (~US$50/sample)and powerful alternative to current genotyping methods, which has the potential to improve wholegenomeselection (WGS), and genome-wide association studies (GWAS) in chicken production.
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