STSM - Genomic evaluation of multi-country methane emissions in Dairy cattle

Hi, I’m Gareth Difford, a PhD student at Aarhus University in Denmark working with genetics and methane emissions in Dairy Cattle and this is my blog about my METHAGENE COST Action STSM to Wageningen, The Netherlands. My goal was to work on a multi-country dataset of methane emission records from multiple instruments/techniques on lactating Holstein cattle in multiple production systems, what could be more Methagene than that?

First week
My Methagene STSM was grated for two weeks (09 May 2016 – 20 May 2016). Starting fresh and early Monday morning I had a coffee meeting with Yvette and we formulated a game plan. I was expecting a steep learning curve adapting to the ways of the Wageningen research group, but being a DMU man myself and finding out I had to learn some ASReml was like crashing head on into Everest. Combining data from Ireland and Australia (SF6), UK (LMD), The Netherlands and Denmark (Sniffer with CO2 tracer) towards predicting breeding values for methane emission was always going to be a tall challenge, but a step that is sorely needed towards combatting climate change. What I was not fully prepared for was the complexities that can be found in datasets from multiple countries, nesting interaction terms, evaluating over parameterisation and really conceptualising the models we build, luckily I had a good teacher. After the first day of running my brain at full steam, it was time to recover and I did this by enjoying the Dutch beer culture and the chiming of bells at the Wageningen Market square.

The second day kicked off with some minor breakthroughs in modelling nested effects within contemporary groups before the first cup of coffee. In between learning a ‘few tricks’ in ASReml 3, the Dutch weather was spectacular by northern European standards and this leant itself to eating lunch outside and getting acquainted with the Wageningen Livestock research group and getting reacquainted with some of our Dutch Methagene counterparts. Methagene STSM’s are also about networking outside of your normal collaborators and I hope this will lead to some new collaborations and research initiatives. In that spirit I accepted the offer of joining the Animal Breeding and Genomics team in ‘the battle’ lead by team leader Coralia. In short, many mixed teams of staff complete on human sized hamster obstacle courses for points. An extremely athletic but unifying experience, all in all, a great way to get to know people.

The day of the defence started off with an informative discussion with both chairs of Methagene cost action, Yvette de Haas and Jan Lassen (who was in Wageningen as an opponent for the Phd defence of another Methagene member Liansun Wu). Discussion focussed on reducing the inherent within country parameters while still achieving accurate predictions, not an easy task. In the defence we heard about Linasun’s ‘artificial reference cow’, an extremely useful tool in validating on-farm methane recording devices and definitely something to look out for in further Methagene work. Liansun also developed a methane hood for generating flux measures of methane and carbon dioxide in barns which he validated with the artificial reference cow. Hopefully further development will follow for commercial application. Congratulations to Liansun on his successful defence! You can stream the recording of the defence here: https://wurtv.wur.nl/p2gplayer/Player.aspx?id=cXpzf1

Second Week
In the second week, work shifted to modelling with an H^-1 matrix instead of exclusively using pedigree or genotype information. This in itself is likely to remain a key step in collaboration efforts using new or difficult to measure phenotypes on limited numbers of cows, as linking international pedigrees can be challenging and thus decrease the accuracy of expected genetic relationships in the A^-1 matrix and since not all cows are genotyped the usefulness of accurate realized genetic relationships with lower numbers of observations can be called into question. With the help of Bernt Guldbransen and Donagh Berry we achieved a mixture of both matrices which resulted in the need to re-run all our models with the H-1 matrix. Luckily in the hours after work there were many beautiful sites to visit and quiet walkways in Wageningen to reflect on results and the next steps (beware of bicycles).

As my final days in Wageningen drew to an end, the number of models running and results generated grew at a furious pace. It was a pleasant surprise to be invited to afternoon cake and coffee celebrating Yvette’s career at Wageningen. Congratulations on 12.5 years at the department Yvette, we wish you many more! On the second-to-last day I leap at the kind offer of Johan Ploegaert to view the methane hood from Liansun’s PhD research. Johan demonstrated the methane hood and how it achieves a mass flux from a few hours of records a day, a very interesting tool for comparing mass flux methane emissions on-farm in barn conditions with those of respiration chambers where natural cow behaviour is altered.

I thoroughly enjoyed my time spent in Wageningen and appreciate the STSM initiatives offered by Ecost Methagene for young researchers, I highly recommend an STSM to Wageningen to the rest of the Methagene network. Not only did I make new acquaintances, learn loads about combining data from multiple countries and collaboration but I also got to add a new genetic software to my CV and enjoyed the entire process. A big thank you to Yvette de Haas, Marcin Pszcola and Jan Lassen for making it possible, I look forward to the ongoing research collaborations and doing our share in combatting global climate change.