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(s’ouvre dans une nouvelle fenêtre)). 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(s’ouvre dans une nouvelle fenêtre).
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(s’ouvre dans une nouvelle fenêtre)).
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 scientific publications in livestock magazines and the 5th Newsletter of the Climgen FACCE-JPI project, to which my fellowship was allied.
We have disseminated the results of the project among the scientific community and the potential recipients (breeders, breed associations and veterinarians) by attending three scientific specialized meetings and four dissemination conferences.
