Posts

Posted on

Tracking down those sodium exclusion genes in wheat: Part 2

The story thus far: Our plucky heroes have traced Triticum monococcum C68-101, the wild parent of a tetraploid wheat (Line 149) with interesting salinity tolerance genes, to the University of Sydney. Maybe. Kinda. Sort of. But they keep digging, and their perseverance is not long in being rewarded. We hear again from Ray Hare.

You may remember that you asked me back in March to track down the source details of the T. monococcum used as the donor of the sodium exclusion genes Nax1 and 2. At last after some detective work I have a fairly good set of identifiers that match up.

The original seed, that was obtained by the University of Sydney, came as part of a collection of monococcums from Dr Ralph Riley of the Plant Breeding Institute, Cambridge. Prof. Eldrid Baker assembled this collection of Triticum species back in the 1960’s. C68-101 is an accession identifier in the University of Sydney Wheat register with the accession number NS 3637. It is also known as “Triticum aegilopoides – 3″. All of the entries in the University species collection have now been lodged with the Australian Winter Cereals Collection where this monococcum accession has the AUS number 98382.

I have not been able to trace the original collection location. It is likely to be Israel or a neighbouring country. PBI Cambridge had links with the Hebrew University. I have seen no shortage of all manner of Triticum species in Syria, Lebanon, Jordan and Israel.

I would be fairly confident that other monococcums have these Nax genes. We checked out two others from this set and each one showed Na exclusion activity. We simply had to select one accession to conduct our studies.

As I said before, the A genome diploids remain rather under researched. Who knows what may come from this ploidy level. It is quite possible that few diploids were involved in the original formation of the progenitor tetraploids and some of this A genome variation has been lost in the formation of the hexaploids. The total variation in the A genome in hexaploids is likely to be small when referenced back to that in the monococcums. I have seen good isozyme variation evidence that clearly supports this belief, in the order of a few orders of magnitude.

I am happy to be of additional assistance.

Posted on

Featured: Old Tanzanian sorghum

Mark Nesbitt knows who the Director of Agriculture is Tanzania was in 1934:

The sorghum collection – all 956 accessions – was acquired by J.D. Snowden while working on his 1936 book (still in print!) “Cultivated Races of Sorghum”. It’s a perfect example of a collection that 20 years ago would have seemed useless (old seeds, mostly dead) but thanks to new techniques (DNA analysis) suddenly looks very interesting as a record of landrace distribution before the Green Revolution.

So, any gene jockeys out there interested in extracting DNA from old seeds? Just for information, there are 1058 sorghum accessions from Tanzania in Genesys. How much can it cost to run a bunch of microsatellites on 2,000 samples?

Posted on

Kew doesn’t store seed only at the Millennium Seed Bank

The Livingstone Online website coming up pretty much out of the blue on my Facebook timeline a couple of days back reminded me that I had wanted to point to the online database of the Kew Economic Botany Collection, if for no other reason than that we haven’t done it before, and that the collection includes seed samples, not least a few collected on the good doctor’s expeditions. Then of course they went and posted something about the database on their blog yesterday. Anyway, we’ve talked about the potential value of museum seed specimens before. In particular, if you search for “sorghum seed” in this case you get (among other things) what is clearly a rather remarkable collection of material from Tanzania, sent to Kew in 1934 by the “Director of Agriculture.” Each seed sample is labelled with a local name. Wouldn’t it be great to go back and see if landraces with those names can still be found, and maybe even compare their DNA with anything that can be extracted from these old seeds?

Posted on

D Landreth not so important to seed diversity

Thanks to the very good offices of our friends at Seed Savers Exchange, I now have a copy of the most recent (6th) edition of the Garden Seed Inventory. I wanted this in order to see whether the loss of The D. Landreth Seed Company, America’s oldest, as it happens, while tragic for the business and its customers, would also be a great loss for agricultural biodiversity. Long answer short: not so much.

The Garden Seed Inventory is a catalogue of catalogues, listing all the varieties available from all the catalogues SSE can get its hands on. That makes it a very useful snapshot of what is out there (in the US), how widely available it is, and the ebbs and flows in comercially-available diversity of crops and varieties. The Introduction to the book contains lots of analysis of this type, and I thought I remembered that it listed all the varieties that are available only from a single supplier and each supplier’s “unique” varieties. It doesn’t.

It does, however, list the 27 companies (10% of the total number covered by the inventory) that list the most unique varieties. D. Landreth is not among them. It also lists the companies that had introduced the most “new unique varieties”. Perhaps unexpectedly, there’s quite an overlap with the “most uniques”. and D Landreth isn’t in that list either. All of which suggests to me that while the passing of D Landreth would indeed be sad for its owners and customers, it would not be an immediate disaster for commercially-available agricultural biodiversity in the United States.

Does D Landreth have any varieties not available elsewhere? That one is difficult to answer using the Inventory. More than 450 pages of closely spaced entries is a lot to look through, searching for those with a single source coded La1. It ought to be a doddle from the database that stores the original records, but I’m sure SSE has much else on its mind at the moment. Mind you, if 45 owners of the Inventory were to scan 10 pages each …

Posted on

Finding your way in the agricultural spatial data jungle

The recent announcement of a major rethink for the HarvestChoice website sent me on a voyage of discovery. Remember that HarvestChoice, “a partnership between IFPRI and the University of Minnesota, generates knowledge products that help guide strategic investments to improve the well-being of poor people in Sub-Saharan Africa through more productive and profitable farming.” That classically includes maps. And there are definitely a lot of spatial datasets on the site. And in Mappr there is a potentially useful online tool for combining different layers and summarizing the results. No doubt a valuable site.

But let me focus here on a separate issue, and that is whether the resources available globally to develop and present such data, in such sites, are being used, er, optimally. The question occurred to me when, in exploring the maps available at HarvestChoice, I came across a dataset labelled “Cattle population (head) (2005).” The source for the data is helpfully provided:

HarvestChoice/IFPRI 2010/FAO. 2007. Gridded livestock of the world 2007, by G.R.W. Wint and T.P. Robinson. Rome, pp 131.

The funding agency is given as the Bill and Melinda Gates Foundation, and data availability is described as follows:

Data available for download in CSV format. Spatial data layer may be explored using MAPPR and downloaded in geoTIFF and ASCII raster formats.

Now, the 2007 FAO publication referenced as the source of the data is downloadable as a pdf from FAO. But the data are also available in a variety of formats from the FAO Animal Production and Health Division website. Among the formats FAO (and only FAO) offers is a Google Earth file, which is probably going to be the most useful for the average user.

And then there’s ILRI. Map 4 in their monumental Mapping Poverty and Livestock in the Developing World of 2002 does not look too dissimilar to the above, though it may be based on older data. It’s a pdf, of course, but for all I know the data are also available in a more useable format somewhere on the ILRI website. I can’t be sure because their database of GIS datasets is just too clunky to spend any significant time struggling with, frankly. Which is not to say that I didn’t…

So what exactly has HarvestChoice added to the sum total of human happiness by making “Cattle population (head) (2005)” available on its website, above and beyond FAO’s contribution? I’m really hard put to say. The datasets are easier to use in Google Earth from FAO’s website than in any format provided by IFPRI, in my opinion. And the basic analyses available in Mappr will probably be useful to some, sure, but since sharing the map itself is tricky from there, you still have to got to FAO for that.

So the poor user probably has to navigate at least two separate and quite different websites to get all she needs. One wonders whether the donors behind all of these different efforts to provide data on cattle population numbers around the world (if indeed there were more than one, apart from the aforementioned Gates Foundation) considered that before green-lighting the projects. And, of course, that’s just cattle numbers. Life is just way too short for me to plough through all the other datasets at HarvestChoice looking for overlaps like these, but I’d be willing to bet this is not an isolated example. We know that crop distribution data is also out there in all sorts of different places, forms and formats. And, in fact, there’s some evidence of balkanization in other types of livestock data too. I’m not saying it’s hell out there for spatial data in agriculture, on a par with Genebank Database Hell. But it is definitely a bit of a jungle.

Does it matter? I don’t know. Maybe the users of these types of data really like having multiple websites to visit for downloading and visualization. Maybe the funds involved in developing all these different datasets and websites are minimal anyway. I’d really like to hear from the people involved at HarvestChoice, FAO and ILRI (are there other players?). But is there even a forum in which these guys meet to discuss data issues? Because if there were, and I by some miracle were to be invited to it, what I would say is that what I would prefer is a single place to go for cattle population numbers maps and the like (e.g. crop production data), with lots of options for exporting the raw data for use in my own GIS, the ability to import and combine my own datasets online, and some elegant ways of sharing the results. 1 That, for me, would be value for money. And I can’t believe I’m alone in that.