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The pangenome is the new genome – Part Deux

Indeed it was “a hell of a day” (somewhat re-ordered compared to the above tweet thread):

  1. Multiple wheat genomes reveal global variation in modern breeding. Genomes of 10 cultivars from around the world’s breeding programmes and a few other things added to that of Chinese Spring.
  2. A haplotype-led approach to increase the precision of wheat breeding. The above and fancy maths used to spot novel, agronomically significant haplotypes in landrace collections. Here’s a Twitter thread from one of the authors with his insights on why the work is important.
  3. The barley pan-genome reveals the hidden legacy of mutation breeding. Genomes of 20 really diverse barley lines, including a wild relative, used to (among other things) find novel variants in 300 genebank accessions.
  4. Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Some transposable elements affect gene expression.
  5. GreenPhylDB v5: a comparative pangenomic database for plant genomes. Pan-pangenomes, kinda.

LATER: Had completely forgotten I had used that title before :) It’s the zeitgeist for sure. And here’s a nice primer on pangenomes.

LATER STILL: Maybe it’s been a good year for something.

https://twitter.com/PacBio/status/1333429793115803648

Yes, there were lots of pangenomes in 2020:

  1. Soybean
  2. Apple
  3. Maize
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Brainfood: Covid, Tropical trees, Tree GR, Brazil nut, Fair research, ICARDA, FIGS, Landraces, Evolutionary breeding, Range edges, Central Asia, Mixtures, Taro origins, Nigerian abattoirs, Aquaculture policy

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Diversify your landscapes redux

I originally published this post on 29 July, but then Dr Baudron pointed to two additional papers on Twitter, and then later to another one, so I’m re-upping, for the second time, with a sixth bullet point.

There’s a nice series of papers on the benefits of diverse landscapes in Ethiopia from Frédéric Baudron of CIMMYT and others.

Just in case this tweet disappears, or whatever, here are the links:

  1. Wheat yields and zinc content are higher closer to forests because of elevated organic matter in the soil.
  2. Diets are also more diverse nearer forests.
  3. Livestock (but not crop) productivity is higher nearer forests, and smallholder systems generally more sustainable.
  4. Bird diversity benefits from tree cover too, and that provides important ecosystem services to smallholders.
  5. Even limited reforestation in the surrounding landscape is associated with higher wheat yields in simulations, and you can potentially measure it from space.
  6. “More people, more trees.”
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Domesticating the podcast

Want to review the state of knowledge on domestication of chickens, sheep and cattle in less than half an hour? Yes? Well then, Jeremy has a podcast for you. It’s an interview with Olivier Hanotte, who teaches livestock genetics at the University of Nottingham.

The beautiful chicken pic is from a book by photographers Moreno Monti and Matteo Tranchellini.

There’s also a stunning book on the diversity of African cattle from ILRI, where Dr Hanotte also has a position.

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Featured comment: Community seed drying

Denise Costich, who has just retired as head of the CIMMYT genebank, gives us a bit of the back story to a paper we included in a recent Brainfood:

Thanks for the mention of our Dry Chain work… the first time I heard about drying beads was at my very first AGM in Rome in 2012. That was a key introduction to this technology for me. It was there in my “knowledge base” when we first began to tackle the problem of seed storage in remote locations without electricity – the community seed reserves and farmers’ corn cribs of the Western Highlands of Guatemala.

AGM stands for Annual Genebank Meeting. The managers of the CGIAR genebanks have been organizing them since 2012.