Darwin Day 2012: b’lieve I’m fixing to live

I confess to being somewhat peeved this morning, on several counts.

First, I thought it was the 11th, giving me a day to be ready with a post for Darwin Day 2012.

Then, I couldn’t find any evidence of an online celebration of Darwin Day 2012, which seems to have just gone extinct some time around 2010. There are plenty of meatspace celebrations, it is true, including one that is a source of yet more peevishness.

Visible man at the Turin Museum of Human Anatomy Yesterday, Turin University demonstrated huge adaptability in bending Darwin Day to its will. Reasoning, possibly correctly, that nobody would actually come out for an event genuinely about evolution, the University hosted, instead, a seminar on The Evolution of the Blues. I kid you not. And in the Museum of Human Anatomy, no less, where I snapped that revelatory image in November 2008. Don’t get me wrong; I think that The Evolution of the Blues is an admirable subject for a Darwin Day celebration and I can’t think of a better venue than the Museum of Human Anatomy. In fact, I wish I’d been there. But yet another source of peevishness is that the Museum shares a building with a Museum of Fruit & Veg Diversity. Wouldn’t it be nice (hint, hint) if that were the locus and subject for the University of Turin’s celebration of Darwin Day 2013?

But enough whinging. Fortunately, there is something to celebrate for Darwin Day 2012: an excellent explanation by Ford Denison of some of the mysteries of the relationship between nitrogen-fixing bacteria and their plant hosts, based on a recently published paper by Ford and a couple of his ex-students. Such relationships are often called symbiosis, or mutualism, with the clear implication that both sides benefit. The central mystery of such relationships remains: what prevents cheating?

Previous work by Denison’s group had shown that the host plant sanctions rhizobia that don’t fix nitrogen. The nodules formed by non-fixing bacteria are smaller than those of bacteria that do fix nitrogen, consistent with sanctions of some sort. In keeping with the nature of natural selection, they take pains to explain that:

We have called these plant responses “sanctions”, without any implication that plants are self-aware or that sanctions will change the behavior of rhizobia, except via evolutionary decreases in the frequency of rhizobial “cheaters” over generations.

The latest paper takes things further, asking whether partial cheats, which fix a bit of nitrogen but not as much as other strains, also trigger sanctions. As Denison explains it, other researchers have shown that even though nodules of non-fixing bacteria are smaller, they contain similar numbers of rhizobia. Numbers are more important than size for bacterial evolutionary fitness, so the sanctions may not in fact be selecting against non-fixing bacteria. There’s more to the story, which remains inconclusive for now, and I urge you to head to Ford Denison’s blog to read it in full.

Darwin Day and Denison’s post also offer a timely reminder that in agriculture, based as it generally is on artificial selection, fitness, in the evolutionary sense, is seldom straightforward. Dwarf cereals, for example, are a good thing (for us, and for themselves) only if they are growing in a field of other dwarf cereals. As a spontaneous mutation in a stand of normal-height plants, they would be rapidly out-competed. Denison covers this enormous and important subject in his new book Darwinian Agriculture: How Understanding Evolution Can Improve Agriculture, which I was thrilled to learn from Amazon two days ago might be delivered a week earlier than promised.

Are you a graduate student interested in organic plant breeding and seed systems?

This just in from Alex Lyon, a graduate student at the University of Wisconsin-Madison. He She and some friends are planning a symposium for graduate students interested in plant breeding and seed systems for organic agriculture, and he she asked us to help get the word out. Happy to do so.

We are inviting applications from graduate students in plant breeding and related programs for the first Student Organic Seed Symposium. The event will be held at the Lakeview Inn in Greensboro, Vermont, from August 5 – August 8, 2012. Hosted by High Mowing Organic Seeds and organized by students from the University of Wisconsin – Madison, the Student Organic Seed Symposium aspires to build a community of graduate students interested in plant breeding and seed systems for organic agriculture.

For more information, please visit here.

Space is limited — Funding is available — Applications are due February 15, 2012!

We hope to see you in Vermont!

Nibbles: Marker assisted selection, Ecoagriculture, Tomato grafting, Food sovereignty, Rice genomes, Other genomes, Molecular toolkit, Yaks, Evotourism, Sandalwood

Next-generation sequencing and genebanks: a teaser

We’re of course all holding our breath, are we not, over the imminent appearance of the American Journal of Botany Special Issue on what next-generation sequencing (NGS) technologies mean for the plant sciences. A few teasers are already out on the journal’s website, and it looks like the papers will come out in piecemeal fashion over the next weeks, and months for all I know. The paper that’s most relevant to us here is perhaps that of Susan McCouch and others on NGS and genebanks. I saw an early version of it, but am not allowed to share it, so until it comes out officially, here’s a taster from the introduction to the volume as a whole by Ashley N. Egan, Jessica Schlueter and David M. Spooner. I trust the journal will consider it fair use and not come after us with their lawyers.

A total of 1750 national and international gene banks worldwide preserve ~7 million accessions of advanced cultivars, landraces, and wild species relatives of plants that the world depends on for food, fiber, and fuel (FAO, 2010 ). McCouch et al. (2012) present a vision for the potential of large-scale genotyping to help characterize, use, and manage gene bank collections, from their perspectives as scientists working with large-scale rice collections. Genebanks have many pressing challenges due to the large size of their collections and the need to characterize them properly for a wide variety of users. They also face legal constraints (and opportunities) imposed in today’s climate of ownership of genetic resources. The challenges include the need to correctly identify accessions, track seed lots, varieties, and alleles, identify and eliminate duplicate accessions, justify adding new accessions to the collection, identify a small subset of the collection that represents a majority of the variation in the entire collection (a “core collection”), identify geographic areas holding useful sets of diverse alleles, associate genotypes with phenotypes, and motivate innovative collaborations to place useful materials into the hands of plant breeders. McCouch et al. (2012) outline these challenges and show how NGS can vastly improve genetic characterization efforts in genebanks. Initial NGS projects with the rice collections include identification of SNPs and other polymorphisms (http://www.oryzasnp. org/; http://www.ricediversity.org/; http://www.ricesnp.org/) based on large-scale resequencing and genotyping projects.

Back with a full discussion (and a comparison with the paper on the same subject in a recent Brainfood) when the publication is online.

Nibbles: Musa taxonomy kerfuffle, Vouchers, Foodies, Aroid roundup, MAS is ok, Sierra Leone conservation