The seventh edition of the Newsletter is here!6/10/2023
The seventh edition of GENE-SWitCH Newsletter is out!
In this issue:
GENE-SWitCH final Conference in Brussels on 6,7 and 8 November11/09/2023
GENE-SWitCH final Conference will take place in Brussels on the 6, 7 and 8 of November 2023.
The first two days will be focused on the project's results and include a panel session dedicated to the 10th anniversary of FAANG. The third day will be joint with the GERONIMO project and focused on stakeholders and policy. Gene-Switch will be present at EAAP 2023 conference02/08/2023
We are glad to announce that the H2020 project Gene-Switch will participated in the EuroFAANG scientific session at the upcoming EAAP conference titled: “Genotype-to-phenotype research across Europe and beyond", on Thursday, 31 August in Lyon, France.
For further details and registration, click here. Latest publication from Gene-Switch project on Functional Annotation26/06/2023
In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle.
More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3′UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5′-GATCCNGYGTTGCYG-3′ and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region. The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes. Click on the button below and read the full paper now! Press release: EuroFAANG research infrastructure is on track22/06/2023
The EuroFAANG cluster addresses challenges in farmed animal production, namely the better use of resources, animal health and welfare, the environment and the climate impact of breeding but also feeding the world with fewer resources.
This is only possible with collaboration with the six partner projects, which tackle a wide range of livestock species, such as farmed fish, ruminants, pigs, and chickens. Set up and led with the joint effort of the six EuroFAANG cluster projects in 2022, a new Horizon Europe project proposal was submitted under the call “Research Infrastructure Concept Development”. Successfully approved by the EU, the new EuroFAANG Research Infrastructure (RI) project now thrives on developing a concept for a formalised infrastructure for farmed animal G2P research in Europe (EuroFAANG). Watch now our third episode of 'Decoding Genome in Monogastrics' webinar series08/06/2023
We are glad to share with you the latest session of our webinar series "Decoding Genome in Monogastrics" which focuses on Epigenetics.
Learn more about animal breeding and animal genetics by watching this last episode! Save the date: Gene-Switch Stakeholder event06/06/2023
Dear Gene-Switch stakeholders,
We are happy to invite you to our next stakeholder event: “GENE-SWitCH meets its stakeholders: new underpinning knowledge on the pig and chicken genomes and how it translates into benefit for the pig and poultry sectors”. The meeting will take place on Thursday 15 June during the Gene-Switch Annual General Meeting! Join us in person or online to discuss the latest advances and achievements in poultry and pig breeding from the Gene-Switch project. Watch now our first two episodes of 'Decoding Genome in Monogastrics' webinar series11/05/2023
Our first two webinars are fully available online on our YouTube Channel!
This webinar series features different topics regarding functional annotation, genomic prediction and epigenetics, which are closely related to the GENE-SWitCH project. You can watch now: 1- What is Annotation and its use? 2- Genomic Prediction Don't forget to register to our third and last episode: Epigenetics! Webinar series: decoding Genome in Monogastrics19/04/2023
GENE-SWitCH project in collaboration with the European Master of Animal Breeding and Genetics by BOKU, are organizing a webinar series focused on decoding genome in monogastrics.
Through this association, the two organizations will share knowledge and resources, ultimately benefiting the field of sustainable animal breeding and genetics. Join us for our third session focusing on Epigenetics on Monday 15 May at 14h (CEST)! AGENDA:
EuroFAANG GENE-SWitCH workshop: applications to attend online are open until 25th January!20/12/2022
This one and a half day workshop will provide detailed training on the utilisation of the wealth of data generated by the EuroFAANG GENE-SWitCH project that is delivering new underpinning knowledge for pig and chicken agriculture.
The workshop will primarily focus on the comprehensive and integrated annotation of the chicken and pig genomes by the Ensembl Genome Browser. The course will also include a deeper dive from the Ensembl analysis teams into gene annotation and regulation, and demonstrations of the specific analyses and genomic prediction models generated by GENE-SWitCH researchers. Applications to attend this now virtual event will be accepted up to 25th January, please contact the FAANG Data Coordination Centre. The sixth edition of the Newsletter is here!22/11/2022
We are happy to share that the sixth edition of the GENE-SWitCH Newsletter is out!
In this issue you can read about the following:
Cooking Up Knowledge From Big Data Using Data Science25/10/2022
Big data keep getting bigger, whether in biology, banking, or marketing, and big data will continue to have a huge impact on our lives. In the coming years, we will need lots of new data scientists who can help make sense of big data with machine-learning methods.
Andrea Rau, researcher of Gene-Switch project at INRAE, explains why Big Data is becoming important in Animal Breeding. We hope you can enjoy reading this interesting article! EuroFAANG GENE-SWitCH workshop: utilisation of GENE-SWitCH data in Ensembl and beyond21/10/2022
This one and a half day workshop will provide detailed training on the utilisation of the wealth of data generated by the EuroFAANG GENE-SWitCH project that is delivering new underpinning knowledge for pig and chicken agriculture.
The workshop will primarily focus on the comprehensive and integrated annotation of the chicken and pig genomes by the Ensembl Genome Browser. The course will also include a deeper dive from the Ensembl analysis teams into gene annotation and regulation, and demonstrations of the specific analyses and genomic prediction models generated by GENE-SWitCH researchers. Applications before Sunday 27th November. WCGALP 2022 – Bitcoin or Genomics: Which brings more?03/08/2022
On the 3rd of July 2022, GENE-SWitCH and GEroNIMO hosted a joint stakeholder event preceding WCGALP titled: “Bitcoins or Genomics: Which brings more?”.
Together with scientists from both projects, we discovered themes like animal breeding, functional annotation, genomics and the challenges in our society. We are delighted to share with you that the recording of this event is now available on our YouTube Channel! WCGALP 2022 – Bitcoin or Genomics: Which brings more?01/06/2022
Every four years, the World Congress on Genetics Applied to Livestock Production (WCGALP) takes place in a different location throughout the world, and this time it is taking place in the harbour city of Rotterdam (The Netherlands).
We are happy to announce that GENE-SWitCH, alongside GEroNIMO project, will bring up to the event very interesting outputs about animal breeding, functional annotation, genomics, and the challenges in our society. Click here to learn more. GENE-SWitCH First Webinar06/04/2022
We are glad to announce our first GENE-SWitCH webinar:
"Feed & Genomics: What's the perfect mix?". During this session, we will dive together into this question with our speakers, on Monday the 9th of May!
Scientific terms for everyone
07/03/2022
In most Horizon 2020 projects, the vocabulary is often very much influenced by scientific terms, specific ways of expressing a situation, impact, or a specific scientific area in general.
For us, it is highly important that people outside the labs and libraries understand what is going on, and what a scientific term means. Scientific terms like “DNA Methylation” are not common for the wider citizens of Europe. We want to change this. We have discovered a series of scientific terms used in our scientific publications, general content, online debates, and discussions. These are words that the European Union also uses when publishing news, legislation, and policy updates from time to time. Over the next 10 weeks, we will explain a series of scientific terms. Explanations will come from a mix of scientists connected to the project with creative animations explaining what the term means and why it is used in relation to EuroFAANG. We hope you will enjoy the videos, share them with your network and learn with us! Newsletter - Issue 403/02/2022
You are invited02/10/2021
We need your inputs and help!
By sharing views on specific needs and concerns, you can help us define the content of the project and thereby maximise the opportunity to benefit from and apply the project’s outcomes! Join our Knowledge Exchange Platform now! EuroFAANG presentation at EAAP24/09/2021Elisabetta Giuffra delivered an excellent presentation about: “Functional Annotation of ANimal Genomes: the European perspective” at the EuroFAANG session, at this year’s Annual Meeting of the European Federation of Animal Sciences, EAAP, in Davos, Switzerland, 2021.
Do you want to know more about the EuroFAANG? Newsletter - Issue 305/07/2021
Interview with Jani de Vos31/05/2021GENE-SWitCH Interview with Jani de Vos, PhD student at Wageningen University.
GENE-SWitCH Fact Sheet18/02/2021
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The GENE-SWitCH project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 817998. This publication reflects the views only of the author, and the European Union cannot be held responsible for any use which may be made of the information contained therein. |