Interview: Genome Insights enabling crop innovation using PromethION

Date: Tuesday 20th November

Time: 3pm GMT

Speaker: Alexander Wittenberg, KeyGene

After completing his PhD at the Lab of Plant Breeding in 2007, Alexander Wittenberg joined KeyGene, a leading crop innovation company and the first certified PromethION service provider. Ahead of his webinar on Tuesday 20th November, we spoke to Alexander about the future of crop breeding and the impact long-read technology is having on the generation of plant reference genomes and our understanding of plant biology.

What first ignited your interest in crop breeding and plant biology?

Nature intrigues me as there is so much variation present and it seems there is an exception to any rule that we try to define or describe. Plant breeding makes use of this genetic variation through selection of desired traits, such as yield, biotic and abiotic stresses, and quality traits such as a longer shelf life to reduce food waste. The challenge ahead is to ensure that crop breeding, with all the modern technologies at hand, can keep pace with the increased need for food while at the same time, be more sustainable.

What impact has long-read sequencing technology had on your field?

New genomic tools, like long-read nanopore sequencing on the PromethION platform, provide true genome insight in the crops we are working with. Plant genomes can be very complex and repetitive and long-reads can span these repeats, and so de novo reference genomes become more contiguous, accurate and therefore more valuable. In a recent example, we were able to close a very complex region in a flower genome in which we had fine mapped a resistance trait with long-reads. Other technologies fail to provide a full picture of the organisation of this region, so we are now able to understand the underlying mechanisms and select for this trait in future varieties.

Can you tell us more about how long-read sequencing is benefitting your work?

Long-reads allow us to span large repeats and so results in more complete reference genomes. In addition, many plant genomes are polyploid or heterozygous and long-reads are essential for phasing genomes in haplotypes, and not only single nucleotide polymorphisms, but also structural & epigenetic variation can be extracted from the same dataset. Translation of this variation to biology will significantly reduce the development efforts and time to market for new varieties of crop.

What impact could high-quality reference genomes have on crop breeding and consumers?

A better understanding of the genetic variation present allows for improved and faster breeding. We are developing and implementing technologies that deliver a strong genomic and genetic understanding in crop species, and the genomic insight these approaches provide enable molecular & genomic breeding and trait discovery. As an example, genomics and molecular breeding at KeyGene enabled the development of aphid resistant lettuce varieties, thereby strongly reducing the need for the use of chemicals.

What are the main challenges in your work and how do you overcome them?

Now the generation of data is no longer a bottleneck, the main challenges are in scaling-up the ultra-high molecular weight DNA isolation and sample preparations, as well as drastically accelerate the entire genome analysis process. This is why I am so glad to have a team of bioinformatics experts as direct colleagues within KeyGene

What’s next?

We continue to invest in scaling up DNA isolation and reduce the cost for sample preparation. Bioinformatics developments are drastically accelerating the genome analysis process so that it can keep pace with the speed of data production – we are building a computational toolset that enables real-time genome assembly from noisy long-reads, for whole genome alignment and pan-genome reconstruction at the population-scale. We hope this will accelerate crop innovation, and provide the plant breeder insights to unlock the potential of these natural alleles, improving time to market of new varieties.

Alexander Wittenberg will be talking on ‘Genome Insights enabling crop innovation using PromethION’ in his webinar on Tuesday 20th November at 3pm UK time.