John Jacobs is an Expert Scientist in the Genomics group of the Trait Research organization of Bayer Crop Science . Located in Ghent, Belgium, John has been with Bayer and predecessor companies since 1999. During his career at Bayer, John has been involved in the development of genomic tools, hybrid systems, and yield traits for cotton, rice, and oilseeds and, more recently, wheat.
Soon after reinitiating the wheat R&D program at Bayer Crop Science in 2010, John became the company representative in the IWGSC Coordinating Committee in 2011 and the lead representative of the company in two IWGSC projects sponsored by Bayer Crop Science for a total amount of €1.4 million. The first project in 2015 was aimed at completing physical maps for 6 chromosome arms and the second project in 2016 generated whole genome profiling tags for all minimal tiling paths to fine-tune the physical maps, anchor sequence maps, and remove inconsistencies between and within either of them.
We met John, recently, at the Bayer Innovation Center in Ghent for a discussion about his work with the IWGSC and his views about the future of agriculture.
What are the benefits of being part of an International Consortium?
I see at least three benefits: it is a networking tool to stay in touch with the scientific community; it ensures early awareness and access to information; and, it allows us to help shape the public sequencing efforts. Moreover, some of our internal sequencing efforts were inspired by the interactions in the Consortium.
The IWGSC announced in January 2016 that a reference sequence would be available as early as 2017. What is your definition of a high quality reference sequence?
While it is difficult to define absolute standards, a reference sequence should be as complete as possible, with as few gaps and ambiguity as reasonably possible. The entire gene space and low-copy sequence space should be accurately covered and annotated. In plants, the Arabidopsis genome sequence is still the best benchmark.
According to you, how should the annotation be done?
Structural annotation will require a combination of automated and manual approaches, validated with experimental evidence. This should result in a clear understanding of the boundaries of expressed and regulatory sequences, including alternative transcripts, small and long non-coding RNAs, etc. Annotation is a continuous process, as new layers of evidence (e.g. epigenetics) are being added. Dependent on how it is defined, functional annotation is yet a completely different and challenging playground…
Growing up on a dairy farm in the Netherlands (living in a 250 year-old farmhouse), John has always been interested in biology and especially intrigued by the workings of living cells.
At the age of 18, he left the farmhouse – for good, but with pain in the heart – to study Molecular Sciences at Wageningen University, followed by a PhD at Radboud University in Nijmegen, focusing on secondary metabolism in Marigolds.
He then moved to Belgium for two post-docs, first at the University of Ghent and subsequently at Plant Genetic System (PGS, now part of Bayer Crop Science), both on post-transcriptional gene silencing.
Since 1999, John has been working for Bayer Crop Science and predecessor companies on genome platform technologies, mutant populations, hybridization systems, and yield programs for cotton, oilseed rape, rice and wheat.
John is married and has three children. He enjoys returning to the family farm, now bravely run by his youngest brother.
Why is it so important to have a reference sequence of high quality?
The reference sequence is the starting point for the development of genetic markers and for gene discovery. Gaps and inaccuracies in the reference genome in any regions of interest lead to costly delays and unproductive detours in these projects.
How is Bayer Crop Science using the reference sequence for breeding applications?
As said, the reference sequence is the basis for many of our marker and gene discovery projects. In our Breeding projects, we focus mostly on disease resistance, quality and hybrid enabling traits, while in Trait Research, we focus on yield (Crop efficiency). We approach yield via key phenotypic traits and biological processes by trying to understand the underlying genes and molecular processes. We either start from candidate genes or follow an open-ended genetic discovery approach. In both cases, the reference sequence is crucial in bridging from genes to genetics and vice versa.
Once the first version of the IWGSC reference sequence is completed, what do you think should be the role of the IWGSC in the future?
Projects don’t end by delivering a sequence. The IWGSC can remain a “guardian” and coordinator of anything that happens to the reference sequence. Annotation would be the first and most important task. The IWGSC could also play a role in data sharing, education, training and promotion of the use of the reference sequence and advanced marker platforms in the broader wheat breeding community. Especially wheat breeders in the developing countries or small companies may benefit from such activities. The Chinese Spring reference sequence clearly does not represent all diversity in the wheat germplasm pool and therefore it is important to create additional public sequences for lines that are of general interest to the wheat community. While the sequencing effort itself has become much more straight forward, coordination is still required to attract funding, avoid duplication, and ensure high standards of data quality and data sharing.
In the effort to double wheat productivity, a high quality, manually annotated wheat genome is only one component. What other research or technology gaps need to be addressed to double wheat productivity by 2050?
The reference sequence is indeed just one component in the quest for higher yield and it will mainly support genetic improvement by breeding and gene editing. Much of this is about incremental improvements, balancing trade-offs and delicate fine-tuning of biological functions. To do this effectively we will need to gain much more understanding about all the (molecular) interactions and control mechanisms within plants and between plants and their environment. We should also think about completely novel and disruptive trait concepts, such as herbicide tolerance and Bt toxins have been in the past. Perhaps hybrids will be disruptive in wheat. Finally, we should think beyond genetics, towards digital farming and high-precision crop management.
How do you see the farm of the future?
We move towards integration of product offerings, data-based guidance of decision making and automation of farm management. I recently read that a modern tractor is already technologically more sophisticated than the first space shuttle that went to the moon. Farmers will become like pilots in a cockpit or traffic controllers in an airport control tower, monitoring sensors and pushing buttons to activate autonomous machinery. The germplasm will be just one component in that game, but one that is close to my heart.