Genome Editing the Plant and Animal Genomes conference series

It’s now nearly mid-way between Plant and Animal Genome Conferences held each January in San Diego. This is an annual conference where you can pick up on trends in genomic research with an emphasis on crops and to a lesser extent farmed animals. For me, far more interesting than the headline topics of the Workshops and Symposia, are the subjects of the little huddles that form, recombine and reform like Dictyostelium colonies around the sessions! This year, they were present not only around circulation areas but permeated into the large commercial exhibition. And the hot topic? Genome editing: CRISPRs, TALENs and the like, using designed nucleases to alter specific genes or regulatory sequences within the genome. I started to write about #PAGXXIII during the meeting, but one thing and another made me hold of posting – not least uncertainty where genome editing was going. Now it is clear I should have posted much earlier.

Over the years, PAG meetings have charted the course of discovery of every gene and type of regulatory sequence, all of which become targets for genome editing when they are of agronomic interest. One kit and reagent company exhibiting this year, said to me that the genome editing ‘customer base was different’ from their regular molecular biology products, with a nod in the direction of recruitment-oriented stands of the major plant biotech seed companies. So it looks as though the young technology might be coming to a field near you in short order. This year has already seen the commercial launch of the first genome-edited crops: sulfonylurea herbicide-resistant Brassicas in the US and Canada by San Diego-based Cibus (www.cibus.com, with other pipeline products including phytate-modified maize following, and 12 Cibus delegates, not giving talks, at #PAGXXIII). I expect we will now see a flood of crops with edits of the many key target genes to improve weaknesses in existing genes: notably, many of the relevant agronomic genes were identified and published around the late 1990s so will no longer have any IP protection and provide immediate targets. Quite what the European regulators will make of this tide, and whether the farmers will be able to grow them, is unknown. I do note that the Board of Cibus includes Alain Pompidou, formerly Professor of Histology, Embryology and Cytogenetics in Paris, with stints as a European Parliament member and as President of the European Patent office. This sounds to me like qualifications to tackle any EU blockages! There are, of course, lots of guides to genome editing technology now appearing: http://www.nature.com/articles/nplants201411 gives a useful view in the new journal Nature Plants.

The study of the avalanche of genome sequence data was pervasive in the talks at PAGXXIII. My title for my blog about the 2011 iteration of the meeting offered the alternatives of “Drowning in the data or the calm before the genome sequence storm?”  History shows now it was clearly the latter. We can get the genomic DNA sequence of most species for a few thousands to tens-of-thousands of dollars in the context of a three-year project – whether walnut, duckweed, dandelion or Utricularia, although wheat and pine with genomes in excess of 3Gb of so still prove a formidable challenge, especially when sorted chromosomes are not available to partition the genome. For another few thousand dollars, we can get a picture of the diversity present in a crop or wild species – the breeders are genotyping hundreds to tens of thousands of accessions with a range of platforms and analyses. It will be interesting when these capabilities permeate down through international and national agricultural research programmes to individual University labs where many fundamental questions about genecology will be addressed with unprecedented detail – nearly 100 years after they were asked.

What was unexpected to me even a couple of years ago was a clear winner in the genome sequencing market: the domination of @Illumina was quite astonishing. Illumina were announcing new sequencing machines that overtake their own already stunning offerings. Sorry, but 454, Ion Torrent, ABI Solid, Licor: all dead or seriously moribund. PacBio with their long-read single-molecule system was at PAG, offering chemistry promising longer reads than ever, and perhaps complementing some of the Illumina capabilities. BioNano (another San Diego company) was also there using optical mapping looked interesting for stretching DNA.

Others developments were perhaps evolutionary rather than revolutionary. After being to many sessions over the years pushing the view that species-X ‘is the reference genome’, we still have exhortations to produce a ‘reference genome’, and even a ‘pan genome’. One genome may only represent two-thirds of all the genes that are possible within a species, and certainly nothing like the genetic or allelic diversity that is out there – so let’s not just genotype with existing markers, but check all genes are represented. Clearly much to do here still – and assembly software has a very long way to go!

Any word-cloud of plant and animals genomics would surely highlight ‘epigenetic’. Sometime near the end of last year, I said to someone on Twitter to not worry about explaining their results, just shout loudly “IT’S EPIGENETICS”. Well, conferences in 2015 are certainly the places to follow that exhortation! At the beginning of ‘epigenetics’, a lab asked us to look at meiosis in some material: unknown to them, it was a diploid x tetraploid hybrid. I’m afraid much of what I see and hear this year are just as far from ‘real’ epigenetics as that, and there seems to be a slew of presentations (manuscripts, posters and talks) which seemed to redefine straightforward developmental control as the big-E.

It is interesting to revisit my PAG notes after five busy months. Genome Editing becomes ever more exciting. Cheap sequence data continues to amass and be useful for the questions being asked, but only a fraction of its real value is being used. Epigenetics extends its role as the catch-all explanation (“Daddy, why’s that man floating in the air?” “Son, that’s called levitation”). Maybe next year…