Category: Breeding

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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.

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Parasites push promiscuity

Many hermaphrodite plants (and some animals) — including many crops — have what is called a mixed mating reproductive strategy. That means they reproduce by both self- and cross-fertilization, with important consequences for the amount and structure of their genetic variation. The prevalence of mixed mating systems is surprising because inbreeding depression should work to get rid of self-fertilization, resulting in “pure strategies of either outcrossing or selfing.” Now a new study suggests that its natural enemies — pests, parasites, herbivores, etc. — may have a strong effect on the evolution of a plant’s mating systems:

For example, enemies may alter the availability of mates in a population, which may have direct consequences for victim mating system evolution. Enemies may also influence the expression of traits that are important for mating system evolution, thereby improving the evolutionary stability of mixed mating as a reproductive system.

Thus the dynamics of the interactions between a species and the biodiversity that surrounds it can counter the effects of inbreeding depression and lead to the stability of an otherwise doomed evolutionary strategy. I wonder how important this has been in the evolution of agrobiodiversity. After all, concentrating plants in dense near-monocultures like agriculture does is a boon to natural enemies.

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Agriculture important, World Bank discovers

The World Bank is suddenly all concerned about agriculture. Within a few days there’s the result of an independent evaluation of its assistance to sub-Saharan Africa, and the latest World Development Report, which focuses on agriculture for development. The NY Times has an article on the African report:

At a time of growing debate about how to combat hunger in Africa, the evaluation team recommended that the bank, the single largest donor for African agriculture, concentrate on helping farmers get the basics they need to grow and market more food: fertilizer, seeds, water, credit, roads.

Ah, seeds. If only it were that easy. The World Development Report 2008 actually refers to the spread of improved varieties as “slow magic” (p. 159, chapter 7), pointing out that crop improvement “has been enormously successful, but not everywhere.” Then, on page 259, in a discussion of the “global agenda for the 21st century,” the money quote:

Conserving genetic resources for future food security. Genetic resources and seeds have been the basis for some of the most successful agricultural interventions to promote growth and reduce poverty (chapter 7). Conserving the world’s rich heritage of crop and animal genetic diversity is essential to future global food security. Gene banks and in situ resources that provide fair access to all countries and equitably share the benefits are a global public good that requires global collective action.

Chapter 8, on Making Agricultural Systems more Environmentally Sustainable, should also make for interesting reading.

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Mutant teff

Sometimes a crop just doesn’t have the genes for it, as a good friend of mine who dabbled in taro breeding used to say. So then you have to try something else. “Zerihun Tadele is using the latest biotechnological methods to produce dwarf tef lines in order to prevent lodging, which causes significant yield losses.” The technique involved is TILLING (Targeting Induced Local Lesions IN Genomes), an automated methods for inducing, and then detecting, potentially useful point mutations. But is there really no short(ish) teff variety among the 4743 accessions in the genebank of Ethiopia’s Institute of Biodiversity Conservation? By the way, IBC has just won the Sultan Qaboos Environmental Preservation Prize. Congratulations!