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Genomic and epigenomic signatures of climate-mediated selection in cattle

Periodic Reporting for period 1 - AdaptClim (Genomic and epigenomic signatures of climate-mediated selection in cattle)

Reporting period: 2015-05-01 to 2017-04-30

Official assessments of climate change impacts in Europe predict substantial economic losses due to the progressive upward trend in average temperatures over the next century, and the decrease in annual rainfall. Global warming will lead to a decreased forage production and quality, and an increased disease risk, which will significantly change conditions for livestock production.
Increasing climate resilience and enhancing sustainable production for animals in harsh environments are important goals for the livestock sector. The outcomes from this project will help provide strategies for the maintenance of European farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance and efficiency under predicted climatic change models.
This project aimed to address the role of epigenetic regulation of thermal adaptation in cattle by comparing the whole genomes and methylomes of two tropical Creole cattle breeds and their main Iberian ancestors, and to evaluate the genomic and epigenomic components implicated in rapid adaptation to extreme climatic conditions, and as a result to identify biomarkers of resilience. Apart from the inherent advance in knowledge on the interaction between genome and epigenome, this project provided insights into the biology and evolution of a species under drastic climate change. The outcomes from this project will help in designing management systems to improve productivity, thermal and stress tolerance, and disease resistance in cattle.
Whole-genome sequencing (WGS). Blood-extracted DNA from four Creole samples was used for WGS. WGS data was deposited in the NCBI short reads archive (SRA) under accession SRP147280 (Project ID: PRJNA471656). We submitted an article reporting whole-genome sequencing (WGS) results to the journal Data in Brief. The manuscript is now under revision (Sevane N, Martínez R, Bruford MW. 2018 Whole-genome sequencing data on tropically adapted Creole cattle. Data in Brief, under revision).

Epigenomic analyses. DNA from three Creole and three Spanish samples was used for Reduced Representation Bisulphite Sequencing (RRBS) to generate data suitable for analysing genome-wide DNA methylation patterns at single nucleotide resolution. Assessment of differences in methylation in Creole and Spanish samples revealed candidates involved in tropical adaptation processes, including genes implicated in immune responses, nervous system, energy management, heat resistance and skin and coat attributes. Although further work is needed, this first characterization of methylation patterns driven by profound environmental change provides a valuable pointer for the identification of biomarkers of resilience for improved cattle performance and welfare under predicted climatic change models. We submitted an article reporting these results to Animal Genetics on February 6, and has recently received a decision of “Minor Revisions” (Sevane N, Martínez R, Bruford MW. 2018. Genome-wide differential DNA methylation in tropically adapted Creole cattle and their Iberian ancestors. Animal Genetics, minor revision). The data sets supporting the results of this article were deposited in the Gene Expression Omnibus (GEO) with accession GSE101796.

Genomic analyses. We combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic effective population size (Ne) contraction. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future-proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change. The article was published in the journal Evolutionary Applications in May 2018 (Pitt D, Bruford MW, Barbato M, Orozco-terWengel P, Martínez R, Sevane N. 2018. Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics. Evolutionary Applications, https://doi.org/10.1111/eva.12641). The data sets supporting the results of this article were deposited in the Dryad Digital Repository with accession https://doi.org/10.5061/dryad.g4f4790.
With the SNP array data generated within this project, we have participated in another study on cattle domestication and the results have also been published in the journal Evolutionary Applications (Pitt D, Sevane N, Nicolazzi EL, MacHugh DE, Park SDE, Colli L, Martinez R, Bruford MW, Orozco-terWengel P (2018) Domestication of cattle: two or three events? Evolutionary Applications, https://doi.org/10.1111/eva.12674).
Derived also from the body of knowledge on the state-of-the-art in genomics and epigenomics gained during this research period and with the FACCE-JPI ERA-NET Climate Smart Agriculture project ClimGen project, we plan to write a review on livestock epigenomics approaches, focusing on the challenges faced by this novel research field when applied to non-model organisms, which I will lead. We also plan to publish dissemination articles mirroring the sci
The increasing importance attributed to epigenetic processes include key mechanisms underlying natural phenotypic variation and the responses of organisms to environmental change, making the combination of epigenomic and genomic information developed in this project a promising and challenging approach, and one of the first studies to our knowledge comparing epigenetic processes in livestock. Thus, AdaptClim has broadened and diversified my experience, providing a major step-change in the knowledge of evolutionary genetics and epigenetics and opening an entirely new research field. This has gained me my next postdoctoral contract (Juan de la Cierva – Incorporación) and the opportunity for integrating effectively into a research group and leading a new one in the short term.
The results from the project are being presented to the livestock sector, since our main purpose is the implementation of the knowledge generated. The collaboration between AdaptClim and the FACCE-JPI ERA-NET Climate Smart Agriculture project ClimGen, led by Mike Bruford, the host researcher, has broadened the impacts of AdaptClim, reaching a wider scientific and dissemination network interested in directly addressing the expected impacts of environmental change.
We hope that the new lines of research in adaptation to climate change and epigenetics developed here may be attractive not only for the EU countries, but also for third-party countries that will face similar climate damage effects.
Romosinuano cattle breed exhibiting the slick hair coat
Selection signatures in the BTA20 genomic region shared by the Colombian cluster and Senepol breed
Differentially methylated genes between Creole and Spanish cattle samples