Information

May 2, 2018

Managing crop breeding data

“It is truly a ‘one-stop-shop’ for the global yam breeding community,” said Ismail Rabbi, a geneticist at IITA and member of the new yam project. “We adopted an ‘open data’ policy and therefore people can access the data from anywhere and help in the improvement of the crop.”

And there are similar resources for cassava, sweet potato and bananas, the common denominator being Lukas Muller at BTI. All these resources are focused very much on the management of material and data within breeding programmes. They have very different, but fairly limited, approaches to the question of linking back whatever the breeder does to accessions in genebanks. For example, it would be good to see DOIs catered for. Open data is all well and good, but open silos are still silos.

April 30, 2018May 2, 2018

More on cassava germplasm from Brazil

You might remember a post from a couple of weeks back comparing the localities of cassava accessions in Genesys (mostly conserved at CIAT) with cultivation of the crop in Brazil. I ended that little piece with the observation that when data from the national genebank system of that country finally makes its way into Genesys, which should not be long now, it will be possible to really figure out where the gaps are in the “global” collection of the crop. Well, as it happens, there was a Tweet just recently which included a photo of a map of where Embrapa’s cassava accessions come from:

Embrapa has collected germplasm from throughout the Amazon region and has characterised this using 20,000 SNPs. Main disease problem is soft rot during heavy rains in this rainforest zone. Working on identifying pathogens & finding genes linked to resistance @IITA_CGIAR @embrapa pic.twitter.com/7go8eipUhn

— James Legg (@jamesplegg) April 28, 2018

So, quick as a flash, I imported it into Google Earth as an image overlay, and after much fiddling to make it fit on top of the background provided by GE (only partially successfully), was able to compare it with the accessions in Genesys:

The two sets of accessions (red for Embrapa, yellow for CIAT) look nicely complementary at a glance. Maybe the gaps in one collection are adequately covered by the other, and vice versa (which of course then brings up the issue of safety duplication, but that’s another post). Or maybe not: this is a really crude way of looking at the data. But it does point to the importance of data sharing and the need for collaboration among genebanks, national and international.

April 30, 2018June 25, 2018

Brainfood: Definitions, Atlantic goats, Sorghum photoperiod, Maize erosion, Dactylis diversity, Chickpea diversity, Social media, TR4, Diet change

‘Genetic resources’, an analysis of a multifaceted concept. You don’t say.
Exploring the genetic diversity and relationships between Spanish and Moroccan goats using microsatellite markers. Different, but connected, except for the ones in the Canary Islands.
Latitudinal Adaptation of Flowering Response to Photoperiod and Temperature in the World Collection of Sorghum Landraces. Out of 20,710: 1697 photoperiod and temperature insensitive, 18,766 photoperiod sensitive and temperature insensitive and 247 photoperiod and temperature sensitive.
Conserving maize in gene banks: Changes in genetic diversity revealed by morphological and SSR markers. Not good ones.
AFLP-based genetic diversity of wild orchardgrass germplasm collections from Central Asia and Western China, and the relation to environmental factors. Strongish ecogeographic structure. Good to see old school markers still in use.
Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea (Cicer arietinum) Landraces from Pakistan. Some differentiation along elevation and temperature gradients despite limited overall diversity.
Capturing genetic variation in crop wild relatives: An evolutionary approach. Environmental data is your friend. But we knew that, right?
New Geographical Insights of the Latest Expansion of Fusarium oxysporum f.sp. cubense Tropical Race 4 Into the Greater Mekong Subregion. Be afraid.
The opportunity cost of animal based diets exceeds all food losses. Never happen.
An Introduction to Social Media for Scientists. It might happen, if you tweet it.
Tweet success? Scientific communication correlates with increased citations in Ecology and Conservation. See what I mean?

April 23, 2018April 28, 2018

Brainfood: Seed libraries, Nepali veggie seeds, Agricultural ES, Zn rice, Sub rice core, SoD, D2N, Root crops knowledge, Horse diversity

Civic seeds: new institutions for seed systems and communities—a 2016 survey of California seed libraries. 6456 seed packets borrowed annually, by 4776 people, from >100 seed libraries, with a 6% return rate.
Vegetables production and marketing: practice and perception of vegetable seed producers and fresh growers in Nepal. Producers like hybrids, consumers prefer open pollinated varieties. Oh, and drying is a problem. No word on whether seed libraries might help.
Exploiting ecosystem services in agriculture for increased food security. Services don’t include crop diversity, apparently.
Molecular Diversity Analysis for Zinc Deficiency Tolerance under Aerobic Rice (Oryza sativa L.) Ecosystem. Two major groups.
Developing Mini Core of Rice Germplasm for Submergence Tolerance. Really mini. Maybe too mini?
CIMMYT’s Seeds of Discovery Initiative: Harnessing Biodiversity for Food Security and Sustainable Development. A “visionary investment.”
Temporal change of Distance to Nature index for anthropogenic influence monitoring in a protected area and its buffer zone. I want a Distance to Genebank index.
Indigenous knowledge and household food security: the role of root and tuber crops among indigenous peoples in the Northern Philippines. The youth are losing it.
Decline of genetic diversity in ancient domestic stallions in Europe. It was artificial selection during the Iron Age.

April 19, 2018April 19, 2018

How to treat those seeds right

The scientific program of this workshop will place seed longevity into a conservation context: ex situ conservation of genetic resources through in situ conservation of wild habitat. The role of seeds in conservation efforts is often marginalized or understated as simply a ‘means to an end.’ Yet, seed longevity is often the basis of successful conservation efforts because it underpins successful stand re-establishment after disturbance, efficient maintenance of crop diversity, and effective management decisions for commercial seed lots. Seed longevity is a complex trait, in which the environment of growth, harvest, processing and storage may interact in unpredictable ways with inherent seed traits. The longevity phenotype itself is difficult to measure as it encompasses both potential and risk, both of which can only be realized in the future.

“This workshop” is the 2nd Seed Longevity Workshop, at Ft Collins, Colorado, 30 July – 1 August 2018. Looks unmissable. I particularly like this bit from the programme:

Time will be reserved in each late afternoon for discussion of current and potentially controversial issues over refreshments:

Using accelerated conditions to forecast longevity; we do it for food and drugs, why not seeds? (led by Olivier Leprince and Julia Buitink, INRA France)

Improving seed banking best practices and standards (led by Fiona Hay, Aarhus Univ, Denmark)

What about seeds that don’t fit the longevity models? – intermediate/recalcitrant and exceptional (sensu Pence) seed paradigms (leaders TBD)

I hadn’t heard of “exceptional” species, but it turns out it just means those which are troublesome to conserve as seeds, because either recalcitrant or just not very prolific.

Anyway, looks like a lot of cool people will be there.