Hot or not? A SNP provides the answer

ResearchBlogging.orgTime was when you tested how hot a chilli pepper was by tasting a teeny bit with your tongue, at least if you were brave. The hotter it tasted, the more capsaicin it contained, and the hotter it was. Then came Wilbur Scoville and his eponymous scale. ((An extract of the pepper is diluted with sugar water until a panel of testers can no longer detect any heat. Thus a mild little pepperoncino scores around 500 SHU (Scoville Heat Units), meaning that the extract has to be diluted 500 times to lose all heat, while a decent African birdseye starts at around 100,000 SHU. And Luigi’s little hottie Naga Jolokia is ten times hotter still, at 1,040,000 SHU.)) Now, all you need is a well-equipped molecular biology laboratory.

Maria Arnedo-Andrés and her crew have identified a single nucleotide polymorphism, or SNP, associated with pungency in chillies. ((Ana Garcés-Claver, Shanna Moore Fellman, Ramiro Gil-Ortega, Molly Jahn and María S. Arnedo-Andrés (2007) Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp. Theoretical and Applied Genetics, 115: 907-916. DOI 10.1007/s00122-007-0617-y.)) A snip is a single letter difference between the DNA of two different organisms. Sometimes a SNP makes a visible and important difference to the organism. The genetic difference that causes sickle cell anemia is one such SNP. More often, the SNP is just a marker. It is associated with some other difference, but does not actually cause it. Breeders like markers because they allow them to quickly see whether some desired gene has been inherited after a breeding experiment. If the marker is there, chances are the nearby gene is there too. There are gazillions of known SNPs out there, mapped to squillions of differences. But, until now, no SNP that could tell you whether a chilli pepper was hot.

There have been markers before, but they were either unreliable, failing to distinguish hot from sweet. Or they were physically a long way away from the actual genes for hotness, meaning that they were not very useful to breeders.

The researchers grew a wide range of peppers, different species and different varieties. Two people tasted five ripe fruits from each type of plant. If all five were not pungent, the plant was considered non-pungent. But if just one fruit (or more) tasted hot, the plant was considered pungent. Then comes the magic, actually detecting the sequence differences among the different samples.

They found one; in all pungent varieties, and only pungent varieties, there is a letter G at position 253 of an identifiable bit of DNA. In all non-pungent varieties, that space is taken by a T.

This result is just a beginning. Breeders will use the SNP to determine very early on, long before ripe fruits have been produced, whether those fruits will be hot or not. Researchers still don’t fully understand how plants make capsaicin. The SNP will help them home in on the genes responsible. And this blog will have taken the opportunity to use that nifty little icon up there on the right to indicate that we are serious and responsible members of the scientific blogosphere, dealing with peer-reviewed research in a serious and responsible manner.

Reinventing the wheel

More evidence of multiple independent domestication events. Previous work has shown such a pattern for rice in Asia and cucurbits in the America. Now it’s the turn of barley in Eurasia. A paper just out ((Saisho, Daisuke, Purugganan, Michael. (2007) Molecular phylogeography of domesticated barley traces expansion of agriculture in the Old World. Genetics.)) looked at both sequences of 5 genes and also morphological traits in a geographically widespread set of 250-odd landraces. ((From a Japanese university genebank.))

The results suggest that the crop was first domesticated 10,000 years ago somewhere in the Fertile Crescent, from whence it spread to Europe, North Africa and Ethiopia (the material from Ethiopia was somewhat distinct, as has already been documented). However, there was apparently also a second domestication, much later. It occurred in the region encompassing southern Central Asia, the eastern Iranian plataeau and the edge of the Indian subcontinent, and it is material from here that spread eastward starting maybe 2,500 years ago, possibly along the Silk Road, to give rise to the barleys of India, the Himalayas and China.

This is not an unusual pattern in Eurasian agricultural biodiversity. Sheep and cattle DNA data also show “two highly divergent lineages that distinguish European and Asian types, indicating a second independent evolution of these livestock species outside the Near East.” Not unusual, but somewhat puzzling. As the barley authors conclude:

It remains unclear why different cultures sought to re-invent these domesticated species several times rather than simply obtain them through diffusion from other farming societies.

The authors of the barley study speculate that the second domestication happened either because of the transmission of knowledge, or as an independent innovation. I find the second option a bit hard to take. Could it be that the results of the first domestication effort were just not adapted to conditions outside the Fertile Crescent, or there was a barrier to their diffusion? Or maybe it was just a matter of pride for the inhabitants of the Iranian plateau to have their own agrobiodiversity?

Another thing CWR can do

Nitrification is the oxidation of ammonia to nitrite. It’s an important part of the nitrogen cycle and all that, but bad news for agriculture, because up to 70% of applied N fertilizer can be lost to plants this way. There are synthetic nitrification inhibitors out there (e.g. dicyandiamide), but now comes news that a wild relative of wheat is also pretty good at slowing down the process. Researchers have identified the bits of the genome involved in biological nitrification inhibition in Leymus racemosus, and have managed to get them to do their stuff in wheat too. ((Subbarao, G. et al. (2007) Can biological nitrification inhibition (BNI) genes from perennial Leymus racemosus (Triticeae) combat nitrification in wheat farming? Plant Soil 299:55-64.)) Is there nothing crop wild relatives can’t do?