I paid tribute to the late great Hans Rosling in my recent post over at the work blog, but CIAT did it better. See also their very enjoyable pean to a bean explorer who is thankfully very much alive, though nearing retirement. And think about joining them.
Brainfood: ABS data, Spanish chestnuts, Norwegian CWR, Bambara genome, AnGR, Jakar sheep decline, Ashanti pig, Bactris biopiracy, Avocado core, Brassicacea phylogeny
- Access and Benefit Sharing under the Convention on Biological Diversity and Its Protocol: What Can Some Numbers Tell Us about the Effectiveness of the Regulatory Regime? That not much has happened. Between 1996 and 2015, out of the 14 countries with ABS legislation in force, 2 agreements for commercial researches per year.
- Genetic monitoring of traditional chestnut orchards reveals a complex genetic structure. The diversity in Spain is in the rootstocks.
- Climate change and national crop wild relative conservation planning. Well, for Norway anyway.
- Integrating genetic maps in bambara groundnut [Vigna subterranea (L) Verdc.] and their syntenic relationships among closely related legumes. Synteny to the rescue.
- Stakeholder involvement and the management of animal genetic resources across the world. Breeders’ associations and cooperatives are the key.
- Decline of Jakar sheep population in pastoral communities of Bhutan: A consequence of diminishing utility, alternate income opportunities and increasing challenges. It’s the fault of the caterpillar fungus.
- Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis. It’s a bit of a mongrel.
- Genetic analysis identifies the region of origin of smuggled peach palm seeds. Genebank confirms biopiracy.
- Genetic Structure and Selection of a Core Collection for Long Term Conservation of Avocado in Mexico. 36 of 318 accessions recover 80% of total alleles, which seems a bit low.
- Genome sequencing supports a multi-vertex model for Brassiceae species. More than just “triangle of U”.
Featured: Pea hell
Dirk has the answer to Pea Genebank Database Hell:
A simple solution would be to agree on a set of prefixes that unequivocally identify each collection preserving those already widely accepted and then to clean up the passport data to link up potential duplicates. The 53674 Pisum accessions in Genesys could possibly be compacted to 1/10
Which is hopefully what DOI will do, though whether it will be possible to apply them retroactively, so to speak, is another question.
Peering at pea data
In Europe, agriculture is highly dependent on imported soybean from South America. Potential alternative sources are protein from peas (Pisum sativum L.) or more local sources like other grain legumes or rapeseed meal (Brassica napus L. subsp. oliefera [sic]). These are also good rotation crops. For farmers, protein and yield are key traits. In this study, a dataset containing 37 descriptors and 1222 accessions from a germplasm collection of P. sativum was analyzed. Scatterplot matrixes and tree regression analysis were used to establish the relationship among descriptors and to identify the most important predictors for seed yield and protein content respectively. Number of flowers per plant was shown to be important for seed yield prediction, followed by number of inflorescences per plant and number of pods per plant. In general, a negative correlation between seed protein content and seed yield was detected, but a few accessions that had both high seed yield and high protein content were identified. The results are discussed in relation to crop improvement and the importance of maintaining germplasm collections.
That’s the abstract from a paper in Genetic Resources and Crop Evolution called “Seed yield and protein content in the Weibullsholm Pisum collection,” by Svein Øivind Solberg, Flemming Yndgaard, Gert Poulsen and Roland von Bothmer. The Weibullsholm pea collection was the brainchild of Stig Blixt, one of the greats plant genetic resources, who died in 2009: 1
Stig Blixt realized early the importance of building and maintaining a base collection of pea germplasm and he must have been one of the early leaders in using the power of a computerised database on the traits and origin of line. The research on peas at Weibullsholm ended in 1986 and by this time Stig Blixt had ensured the pea collection had been safely transferred to the Nordic Gene Bank. In 1988 he was employed as Head of Material Departement at the Nordic Gene Bank and 1989 he became Head of our development projects. He started our engagements in SADC (Southern Africa Development Community). In 1990 he was appointed Director for the gene bank and retired from his post at the end of 1992. He continued as Senior Scientist until his age retirement in 1995.
When I posted a link to the paper on Facebook, Dirk Enneking, who has contributed here in the past, had this to say:
We had three different prefixes in Australia for material from this collection. Peas from Weibullsholm are bound to be in every collection around the globe that keeps peas and my bet is that is highly replicated because of poor documentation in recipient collections, part of the problem being that no prefix was prescribed by the donor. The good news is that a lot of collections now have chance to link to a great set of evaluation data and if these don’t match with local experience to spot errors.
To which I can only say: I wish! Because of the lack of permanent identifiers for genebank accessions, making the link to this set of evaluation data will not always be possible. Ah but fear not, DOIs are coming!
Brainfood: Arabidopsis refugia, Potato diversity, Palm uses, Coffee phylogeny, Traditional harvesting, Buckwheat trends, Maize double haploids, African cattle, Endophenotype
- On the post-glacial spread of human commensal Arabidopsis thaliana. A bit like Neanderthals.
- Exploration of the genetic diversity of cultivated potato and its wild progenitors (Solanum sect. Petota) with insights into potato domestication and genome evolution. Elite cultivars are a pretty diverse lot.
- Fundamental species traits explain provisioning services of tropical American palms. Bigger, more widespread species are more important to local people. Which means some useful things may be being missed.
- Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Origin of the genus could be Africa. Or Asia. Or the Arabian Peninsula. So that narrows it down.
- A quiet harvest: linkage between ritual, seed selection and the historical use of the finger-bladed knife as a traditional plant breeding tool in Ifugao, Philippines. People kept old harvesting technology because it helped them show due reverence to the rice plant, and select seeds.
- Old Crop, New Society: Persistence and Change of Tartary Buckwheat Farming in Yunnan, China. It’s going down, but won’t disappear. No word on what’s happening to diversity though.
- Tapping the genetic diversity of landraces in allogamous crops with doubled haploid lines: a case study from European flint maize. The things people have to do to make use of landraces.
- Conservation of indigenous cattle genetic resources in Southern Africa’s smallholder areas: turning threats into opportunities — A review. We now the breeds, but not all their characteristics, and how to get the most out of them.
- The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype. Oh for pity’s sake, something else to worry about.