Peering at pea data

by Luigi Guarino on February 28, 2017

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!

Footnotes:
  1. For some reason, his passing seems to have gone unmentioned on this blog, for which we sincerely apologize. []

{ 5 comments… read them below or add one }

Dave Wood February 28, 2017 at 7:32 pm

`DOIs are coming’: About time. Twenty-five years ago I wrote “There would be much less confusion and duplication of effort in future if IARCs and national programmes were to adopt a uniform international numbering system for germplasm samples, with each sample receiving a unique number.” (This was in my 1991 review of CGIAR plant genetic resource work with lots of mentions of `agrobiodiversity’ – possibly a first).

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Bob Jarret March 13, 2017 at 4:41 pm

How’s it going Dave?

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Dave Wood March 14, 2017 at 8:13 pm

Bob, Great to hear from you. I’m still stirring things – just finishing a major review on the origins of cereal agriculture that has turned up some surprises.

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Dirk Enneking March 1, 2017 at 2:02 am

The widely distributed Pisum material (L =WBH numbers) could be better documented. The corresponding NGB numbers 10+numeric of L, WBH are not recognisable as such.

To compound the problem, any of this material which passed through the John Innes collection may have acquired JI or JIC numbers, while John Innes material is listed in genesys without a prefix.

Similar issues are likely with material that has passed through the Vavilov Institute and any other collection.

DOIs assigned to the most original accession ie. the material that first entered the genebank system may help to solve this problem, but there is also the issue of split accessions to obtain morphologically homogeneous material as practiced at the IPK, Gatersleben and elsewhere in Eastern Europe.

The beauty of these split accessions is that with the help of their botanical variety characters, any admixture or mishandling is detectable by looking at visible characteristics eg. if the botanical variety name means that the seed is yellow, then it would be odd if that particular accession has red seeds in it. Unfortunately, the taxonomic key to these varieties was published in German, based on earlier Russian work by Govorov (Das morphologische System der Saaterbsen (Pisum sativum L. sensu lato Gov. subsp. sativum). Der Züchter 24:316–337)

Perhaps the ultimate solution is get genetic fingerprints and an estimate of genetic diversity for each accession and DOIs for individual genotypes.

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

Any material collected by collecting missions should receive a DOI or a simple unique and intelligible code for the collection site which can then be linked to documentation about these missions and FIGS.

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May Dominique Mata March 12, 2017 at 3:43 pm

Biodiversity really is important because it is an indicator of a healthy ecosystem.

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