Biotechnology – Page 16 – Agricultural Biodiversity Weblog

November 26, 2020December 1, 2020

The pangenome is the new genome – Part Deux

1) Today's been a hell of a day for plant #pangenomes.
In https://t.co/FSxNthxoG9 Walkowiak et al analyze up to 16 wheat cultivars to report on the global variation pool accessible to modern breeding pic.twitter.com/xPTtIvEZyC

— BContrerasMoreira (@BrunoContrerasM) November 25, 2020

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

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.
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.
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.
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Some transposable elements affect gene expression.
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:

November 18, 2020

Nibbles: F2F, Jute, IITA, ICARDA, ILRI, Grazing

USDA throws shade on EU’s Farm to Fork strategy. I see trouble in its future.
Turns out jute has a future.
Is CRISPR the banana’s future?
How Svalbard gave ICARDA’s genebank a future.
Ensuring the future of Ethiopia’s livestock through forage seeds.
The future of Europe’s meadows is livestock. No word on forage seed or Farm to Fork.

October 26, 2020October 26, 2020

Brainfood: CGIAR genebanks, Sweet potato heat, Rice breeding, CWR gap trifecta, PES, Wild potatoes, Wild olives, Rare olives, Cryo veggies, Broccoli diversity, Crop switching, Cattle diversity, IK

Germplasm Acquisition and Distribution by CGIAR Genebanks. A lot of stuff going in, a lot of stuff coming out, to everyone’s benefit. 35 years of data, with special focus on the last 10.
Intraspecific diversity as a reservoir for heat-stress tolerance in sweet potato. 132 out of 1973 accessions tolerant of heat, though in different ways. A prime example of the above benefits.
Identification and characterization of high‐yielding, short‐duration rice genotypes for tropical Asia. Short-duration varieties will need to be a bit taller and leafier to yield more. Another example of the above benefits.
Modelled distributions and conservation priorities of wild sorghums (Sorghum Moench). More stuff needs to go into the above genebanks, though, for example from N. Australia.
Ex situ and in situ conservation gap analysis of crop wild relative diversity in the Fertile Crescent of the Middle East. Same from the Fertile Crescent.
In situ and ex situ conservation gap analyses of crop wild relatives from Malawi. And not just the above genebanks either.
The Potential of Payment for Ecosystem Services for Crop Wild Relative Conservation. Ok, we have the gaps (see above), and now here we have the method. What’s stopping us?
Assessing under-Estimation of Genetic Diversity within Wild Potato (Solanum) Species Populations. Wild diploid species more diverse than previously thought. So providing more ecosystem services?
Genetic diversity and differentiation of Olea europaea subsp. cuspidata (Wall. & G.Don) Cif. in the Hajar Mountains of Oman. No word on the ecosystem services being provided.
The investigation of minor and rare Tunisian olive cultivars to enrich and diversify the olive genetic resources of the country. Rare + minor doesn’t mean bad. But maybe an influx of Omani genes would help?
Biobanking of vegetable genetic resources by in vitro conservation and cryopreservation. Yes, even for vegetables.
From landrace to modern hybrid broccoli: the genomic and morphological domestication syndrome within a diverse B. oleracea collection. Four subpopulations: Calabrese broccoli landraces, hybrids, sprouting broccoli, and violet cauliflower. Diversity in modern varieties decreasing with time.
Crop switching reduces agricultural losses from climate change in the United States by half under RCP 8.5. But it will have to be a lot of switching. Hopefully out of broccoli.
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism. An influx of zebu genes about a thousand years ago is responsible for the success of African pastoralism.
Protection of traditional agricultural knowledge and rethinking agricultural research from farmers’ perspective: A case from Turkey. Against power imbalances the gods themselves contend in vain.

October 12, 2020October 12, 2020

Brainfood: Dietary diversity, Farm diversity double, Neolithic dairy, Exotic breeds, Yam viruses, Cassava GWAS, Satellite phenotyping, Forest restoration & disturbance, Genetic rescue, Budwood cryo, SP cryo, Dry grasslands, Botanical gardens, Remote sensing

Agricultural Food Production Diversity and Dietary Diversity among Female Small Holder Farmers in a Region of the Ecuadorian Andes Experiencing Nutrition Transition. Higher diversity of crops on family farms is only weakly associated with greater dietary diversity and lower household food insecurity among female caretakers. Better than nothing, though, right?
Productive Capacity of Biodiversity: Crop Diversity and Permanent Grasslands in Northwestern France. Having a bigger percentage of permanent grassland on your French farm, or a greater diversity of crops, can increase cereal and milk yields. No word on diets.
The influence of landscape composition and configuration on crop yield resilience. No effect on yield per se (see above), but proximity to semi-natural habitat does increase yield stability in UK farms.
Living off the land: Terrestrial-based diet and dairying in the farming communities of the Neolithic Balkans. Ancient farmers had a varied diet, but possibly not involving consumption of raw milk, at least by adults.
Food securers or invasive aliens? Trends and consequences of non-native livestock introgression in developing countries. In 40 countries, the proportion of livestock populations belonging to local breeds has been decreasing by about 1% a year for the past 20 years. Hey, but milk yield per cow has been going up, so there’s that.
Potentials of Cultivated Varieties and Wild Yam Seeds as Efficient Alternative Plant Genetic Resources for Resistant Genotypes against Yam Mosaic Virus (YMV) in Togo. Work with seeds! But were they properly inoculated? Hopefully a virologist will tell us.
Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava. Lots of interesting markers for cassava breeders, or at least those working with material from W Africa. Do it for yams next?
High-resolution satellite imagery applications in crop phenotyping: An overview. Clouds, you say? Not a problem any more. But can it distinguish landraces from modern varieties? What’s needed is a sort of mutant algorithm, I guess.
Crop type identification and spatial mapping using Sentinel-2 satellite data with focus on field-level information. Still some way from being able to distinguish landraces from modern varieties, I see.
Global forest restoration and the importance of prioritizing local communities. I’m shocked I tell you, shocked.
Protection gaps and restoration opportunities for primary forests in Europe. A lot of restoration could usefully be done in currently protected areas, though it would be better if these were expanded. No word on local communities.
Mapping the forest disturbance regimes of Europe. I guess this means that restoration, when it happens, will be monitored from space.
Genetic rescue: A critique of the evidence supports maximizing genetic diversity rather than minimizing the introduction of putatively harmful genetic variation. When you do do restoration, don’t worry about genetic pollution, just go for as much diversity as possible. Well, for small relict populations. Of animals.
Considerations for large-scale implementation of dormant budwood cryopreservation. It’s about the logistics.
Development of a fast and user-friendly cryopreservation protocol for sweet potato genetic resources. It’s the axillary meristems. Among other things.
The human–environment nexus and vegetation–rainfall sensitivity in tropical drylands. Dryland grasslands in Africa and Asia less able to respond to water availability overall, more able in Australia and S America, evens stevens in N America. Would be interesting to mash up particularly hard-hit areas with CWR and forage germplasm collecting localities.
Botanic garden solutions to the plant extinction crisis. Expertise, tools, facilities, and networks are there. You know what’s missing, right?

September 21, 2020September 16, 2020

Brainfood: Bending the curve edition

Bending the curve of terrestrial biodiversity needs an integrated strategy. Meaning: (i) sustainable agricultural intensification, (ii) trade, (iii) less food waste, (iv) more plant-based human diets, and (v) more and better protected areas.
The carbon opportunity cost of animal-sourced food production on land. See (iv) above.
Just ten percent of the global terrestrial protected area network is structurally connected via intact land. See (v) above.
Cropland expansion in the United States produces marginal yields at high costs to wildlife. See (i) above.
A cultivated planet in 2010 – Part 1: The global synergy cropland map. Gotta know where the cropland is before you can do (i) above.
Advances in plant phenomics: From data and algorithms to biological insights. Fancy maths can really help with (i) above.
Retrospective Quantitative Genetic Analysis and Genomic Prediction of Global Wheat Yields. Different fancy maths shows that CIMMYT’s Obregon wheat testing site can really help with (i) above.
Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Here’s some stuff that wheat breeders can use to develop new materials to test at Obregon using phenomics, genomics and fancy maths.
First report on cryopreservation of mature shoot tips of two avocado (Persea americana Mill.) rootstocks. This should help with (iv) above. Eventually, work with me here.
Bread and porridge at Early Neolithic Göbekli Tepe: A new method to recognize products of cereal processing using quantitative functional analyses on grinding stones. Ahem. Well… No, sorry, I got nothing.