Category: Genetic diversity

Posted on

Goats gnaw on geographic given

This post was chosen as an Editor's Selection for ResearchBlogging.orgWe’re used to thinking — or at least assuming — in agrobiodiversity conservation that genetic distance is a monotonically increasing function of geographic distance. It is, after all, a reflection of the great Waldo Tobler’s First Law of Geography: “Everything is related to everything else, but near things are more related than distant things.” And yet. Why should that necessarily be so for crops and livestock, so willfully and incessantly moved to and fro by people in all kinds of unpredictable ways?

A paper just out in Molecular Ecology in effect tests the First Law of Geography with goat genetic diversity data, microsatellites in fact. ((BERTHOULY, C., DO NGOC, D., THÉVENON, S., BOUCHEL, D., NHU VAN, T., DANES, C., GROSBOIS, V., HOANG THANH, H., VU CHI, C., & MAILLARD, J. (2009). How does farmer connectivity influence livestock genetic structure? A case-study in a Vietnamese goat population Molecular Ecology DOI: 10.1111/j.1365-294X.2009.04342.x)). Goat populations were sampled in 3-8 villages in each of 2-5 communes in each of 10 districts in the remote, mountainous, ethnically mixed Vietnamese province of Hang Giang, for a total of 492 animals. The genetic relationships among the animals were then analyzed.

To the surprise of the authors, the spatial structure of the overall population was poorly explained by simple geographic distance. The ethnicity of their keepers and the husbandry practices to which they were subjected did a much better job of predicting the genetic distance between goats. The most dissimilar goats were not necessarily the ones which lived furthest apart, but rather the ones which were kept in different ways by people of different ethnic groups.

So, if you wanted to maximise the diversity in a Vietnamese goat conservation programme, or your chances of hybrid vigour, you’d pick animals from different ethnic groups or production systems, and not necessarily from different ends of the country. Which is something that I remember sort of almost subconsciously doing when I was collecting crops, but it is nice to see it validated like this. I can’t remember offhand similar work on crops, but no doubt Jacob will set me straight soon enough. In the meantime, I revel in a rule proven.

Posted on

Chinese interdependence

ResearchBlogging.orgA paper just out in Agricultural Science in China reminded me that I wanted to say something about one of the great meta-narratives of plant genetic resources: interdependence — the old no-country-is-self-sufficient-in-PGR mantra. Which, unlike some other meta-narratives, is generally recognized as being true — witness the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). And that despite the fact that measuring interdependence is not by any means easy, and has not often been done.

The paper which caught my eye is not really primarily about interdependence. ((ZHAO, Y., Ofori, A., & LU, C. (2009). Genetic diversity of European and Chinese oilseed Brassica rapa cultivars from different breeding periods. Agricultural Sciences in China 8(8):931-938. DOI: 10.1016/S1671-2927(08)60297-7.)) It just shows that cultivars of winter oilseed rape (canola) from China are very distinct from European ones, on the basis of molecular markers. Which presumably means that yield gains could be had from cross-breeding between the two groups. Which does say something about interdependence, but not very forcefully.

However, that paper reminded me about two others that a colleague had recently sent me, along with the thought that they should be enough, in a perfect world, for China to ratify the ITPGRFA.

The first is about soybean. ((Qin, J., Chen, W., Guan, R., Jiang, C., Li, Y., Fu, Y., Liu, Z., Zhang, M., Chang, R., & Qiu, L. (2006). Genetic contribution of foreign germplasm to elite Chinese soybean (Glycine max) cultivars revealed by SSR markers. Chinese Science Bulletin, 51(9):1078-1084. DOI: 10.1007/s11434-006-1078-4)) It shows, using molecular markers again, that a couple of elite Chinese cultivars benefited greatly, in terms of both specific traits but also their difference from previous Chinese cultivars (that is, the genetic base of the crop as a whole was broadened) from the fact that US and Japanese germplasm was involved in their development, rather than just Chinese stuff.

The second paper makes the interdependence point even more strongly by quantifying the contribution of foreign maize germplasm to production in China, rather than just genetic diversity. ((LI, H., HU, R., & ZHANG, S. (2006). The Impact of US and CGIAR Germplasm on Maize Production in China. Agricultural Sciences in China, 5(8):563-571. DOI: 10.1016/S1671-2927(06)60093-X.)) It turns out that a 1% contribution by US material (based on the coefficient of parentage) translates to an additional 0.01 t/ha (0.2%), and a 1% contribution by CIMMYT germplasm to an additional 0.025 t/ha.

The conclusion: “The extensive utilization of US and CG germplasm improved maize yield potential in China… The government should provide funds to support research on germplasm introduction…” And, we could add, it should ratify the ITPGRFA. No country is self-sufficient in PGRFA. Not even the largest.

Posted on

Upstream blast

ResearchBlogging.org Blast is one of the worst rice diseases. I believe that, thanks to the breeders, most modern varieties have decent levels of resistance. After all, they can be used in varietal mixtures to protect traditional glutinous rice varieties from blast. ((Zhu, Y., Chen, H., Fan, J., Wang, Y., Li, Y., Chen, J., Fan, J., Yang, S., Hu, L., Leung, H., Mew, T., Teng, P., Wang, Z., & Mundt, C. (2000). Genetic diversity and disease control in rice. Nature, 406 (6797), 718-722 DOI: 10.1038/35021046 Also see this post.)) Unfortunately, much of this resistance is not durable, because the pathogen overcomes it with time.

For a long time, durable resistance has been known to exist in some Japanese varieties. But these varieties have not been useful for resistance breeding, as the resistant parent also brought along undesired characteristics: the offspring always had poor eating quality.

Shuichi Fukuoka and colleagues have found out why. They report in Science ((Fukuoka, S., Saka, N., Koga, H., Ono, K., Shimizu, T., Ebana, K., Hayashi, N., Takahashi, A., Hirochika, H., Okuno, K., & Yano, M. (2009). Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice Science, 325 (5943), 998-1001 DOI: 10.1126/science.1175550
see also Normile, D. (2009). New Strategy Promises Lasting Resistance to a Rice Plague Science, 325 (5943), 925-925 DOI: 10.1126/science.325_925)) that it is because of a tight genetic linkage. Resistance is conferred by the Pi21 locus, and:

The eating quality of plants carrying the elite cultivar’s chromosomal sequence from a point less than 2.4 kb downstream of the Pi21 locus was equivalent to that of the elite cultivar, and the plants showed a high level of blast resistance. In contrast, plants carrying the donor chromosomal sequence up to 37 kb downstream of the Pi21 locus showed inferior eating quality.

By crossing in just the right bit of the chromosome, and making sure that the neighboring areas do not tag along, resistance can now be transferred, without spoiling the taste.

Posted on

Wild cassava genetics used to document past changes in vegetation

ResearchBlogging.orgWas southern French Guiana always forested, a refugium for forest species, or was it dominated by more open vegetation during drier, glacial times? A recent paper in Molecular Ecology tries to decide between these competing hypothesis, and the interesting thing for us at the Agricultural Biodiversity Weblog is that it does so through a genetic study of a crop wild relative. ((DUPUTIÉ, A., DELÊTRE, M., DE GRANVILLE, J., & MCKEY, D. (2009). Population genetics of Manihot esculenta ssp. flabellifolia gives insight into past distribution of xeric vegetation in a postulated forest refugium area in northern Amazonia. Molecular Ecology, 18 (13), 2897-2907. DOI: 10.1111/j.1365-294X.2009.04231.x.))

Manihot esculenta ssp. flabellifolia is the closest wild relative of cassava. It is “distributed on an arc partly encircling the Amazon basin, from eastern Bolivia and Peru eastward to northeastern Brazil, northward to the Guianas and then westward to Venezuela.” Its habitat is the transition zone between forest and cerrado in the south, and open environments such as savannas and rocky outcrops in the north. In French Guiana, which was the focus of the study, it is found both in the coastal strip, and on isolated granitic outcrops (inselbergs) in the forested south, with a large gap in between.

Seven microsatellite loci were used to investigate the genetic relationships among 14 populations, 4 from inselbergs and the rest from the coast. The results are pretty easily summarized. First, the inselberg populations were very similar to each other. Second, they were quite different as a group from the coastal populations. Finally, the coastal populations were highly differentiated among themselves.

So, what do these results tell us about the past vegetation history of the region? One conclusion was that the coastal populations (which incidentally, in contrast to the inselberg populations, showed some evidence of introgression from the crop) are relatively recent, and arrived from savannas to the west through a series of bottlenecks, rather than from the south. As for the southern inselberg populations, given the limited range of pollen and seed flow, they seem to be the remnants of a formerly more extensive, fairly homogeneous population. ((Conservation question: Does that mean that seed of the 4 inselberg populations could be bulked and kept as a single accession? Answers on a postcard, please.)) That suggests that southern French Guiana was drier and had a more open vegetation before the Late Glacial Maximum 10,000 years ago. There was probably a forest refugium in the central part of the country, but not in the south.

Assuming, of course, that the adaptation of the species hasn’t changed much along the way. It remains to be seen whether the same pattern will be found in other taxa. Perhaps other species of agrobiodiversity interest will be investigated in the same way.