Category: Breeding

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Ethiopia goes for decaf

Reuters reports that Ethiopian coffee farmers will soon be able to grow a variety which is naturally low in caffeine. Details are sketchy. The whole thing seems to be based on the following statement by Mr Abera Deressa, State Minister of Agriculture and Rural Development, at an unnamed coffee research conference:

“Coffee research centres are in the process of planting seedlings of natural coffee with low caffeine varieties, to enable Ethiopia to supply the world market within the shortest possible time.”

The article mentions the 2004 controversy between the Ethiopian government and Brazilian researcher Paulo Mazzafera, who

declared he had discovered a variety of naturally decaffeinated coffee from 6,000 specimens collected in Ethiopia in the 1980s. The find sparked a dispute with Ethiopian authorities who accused him of taking the bushes without permission.

However, it is not clear whether the low-caffeine variety now being planted in research centres has anything to do with the one Mazzafera identified.

Decaffeinated coffee accounts for 10 percent of total coffee sales in the world, a multibillion-dollar industry. Natural decaf brews could dominate over the current chemically caffeine-reduced options in today’s health-conscious market.

The story has been picked up all over the place. It should run and run. Hopefully we’ll get some more details soon.

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Wheats and gluten

Sometimes it takes some personal connection to get me motivated enough to try and understand something a little more fully. Laziness, I guess. Anyway, for example, I vaguely knew about the gluten seed storage proteins of wheat and the coeliac disease they cause in about 1% of the population. But I decided to delve a little deeper only when an old friend I hadn’t seen for a while visited today and told me that she was a sufferer, and that she needed to know how to describe the condition in italian so she wouldn’t get into trouble eating in restaurants here in Rome.

Having sorted that out, I was interested to know whether there are differences among wheat species in the “toxicity” of their glutens. You’ll remember that wheat comes in a polyploid series: diploid, tetraploids and hexaploids. And that three distinct genomes are involved: AA, BB and DD. Diploid einkorn (AA) and BB genome species got together to form tetraploid emmer and durum wheat (AABB). And these hybridized with wild diploid Triticum tauschii to make hexaploid (AABBDD) bread wheat.

It turns out that differences in gluten toxicity do exist. An analysis of the ancestral A, B and D genomes of wheat found that DNA sequences associated with 4 peptides that have been identified as triggering a response in coeliac patients are not distributed at random. For example, the B genome sequences analyzed did not reveal any of the “guilty” sequences.

On the basis of such insight, breeding strategies can be designed to generate less toxic varieties of wheat which may be tolerated by at least part of the [coelic disease] patient population.

Oh, and coeliac disease is called celiachia in italian.

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Fido decoded

An article by Elaine Ostrander in the latest American Scientist summarizes recent advances in canine genomics, which have been considerable:

The dog genome has been mapped and sequenced. A host of disease loci have been mapped, and in many cases the underlying mutations identified. Our understanding of how dog breeds relate to one another is beginning to develop, and we have a fundamental understanding of the organization of the canine genome. The issue of complex traits is no longer off-limits. We have begun to understand the genetic portfolio that leads to variation in body size and shape, and even some performance-associated behaviors.

Some snippets:

  1. Between-breed genetic variation is about 27.5% of the total, compared to about 5% between human populations.
  2. Dog breeds fall into 4 main groups: Asian and African dogs, plus grey wolves; mastiffs; herding dogs and sight hounds; and modern huntings dogs.
  3. 75% of the 19,000 genes that have been identified in the dog genome show close similarities with their human counterparts.
  4. Variation in a single gene (IGF1) explains a lot of the size differences among and within breeds.

What to do with all this information?

It is certainly hoped that the disease-gene mapping will lead to the production of genetic tests and more thoughtful breeding programs associated with healthier, more long-lived dogs. It will be easier to select for particular physical traits such as body size or coat color… Finally, canine geneticists will have a chance to develop an understanding of the genes that cause breed-specific behaviors (why do pointers point and herders herd?).

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Fungal agricultural biodiversity

More today about fungi as important constituents of agricultural biodiversity. Following the recent post on the microsymbiotic Frankia, I ran across a couple of papers on other fungi and their interactions with crop plants in agricultural systems. 

First, there’s Trichoderma. According to a recent review in Soil Biology and Biochemistry ((Francesco Vinale, Krishnapillai Sivasithamparam, Emilio L. Ghisalberti, Roberta Marra, Sheridan L. Woo and Matteo Lorito, Trichoderma-plant-pathogen interactions. Soil Biology and Biochemistry. In Press, Uncorrected Proof.)):

Trichoderma spp. are among the most frequently isolated soil fungi and present in plant root ecosystems. These fungi are opportunistic, avirulent plant symbionts, and function as parasites and antagonists of many phytopathogenic fungi, thus protecting plants from disease. So far, Trichoderma spp. are among the most studied fungal BCAs [bio-control agents] and commercially marketed as biopesticides, biofertilizers and soil amendments. Depending upon the strain, the use of Trichoderma in agriculture can provide numerous advantages: (i) colonization of the rhizosphere by the BCA (“rhizosphere competence”) allowing rapid establishment within the stable microbial communities in the rhizosphere; (ii) control of pathogenic and competitive/deleterious microflora by using a variety of mechanisms; (iii) improvement of the plant health and (iv) stimulation of root growth.

Then there’s arbuscular mycorrhizal fungi (AMF). Another paper ((Christine Picard, Elisa Baruffa and Marco Bosco, Enrichment and diversity of plant-probiotic microorganisms in the rhizosphere of hybrid maize during four growth cycles. Soil Biology and Biochemistry. In Press, Uncorrected Proof.)) in the same journal suggests that different maize genotypes had quite different effects on the AMF population in the soil in which they were grown, stimulating “their own adapted phylogenetic AMF subgroups.” According to the authors:

Several new sets of data obtained in this way would be necessary to have a significant view of the actual beneficial interactions between rhizospheric microorganisms and plant roots; but we are confident that such an effort will lead to the definition of new criteria for the rapid breeding of sustainable varieties.

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Genotyping Support Service

The CGIAR’s Generation Challenge Programme‘s mission is

To use advanced genomics science and plant genetic diversity to overcome complex agricultural bottlenecks that condemn millions of the world’s neediest people to a future of poverty and hunger

They’ve just announced a new service: the Genotyping Support Service. What will GSS do?

Here’s a sample of what our latest service offers: assessing proposals, hiring genotyping services from the best providers, taking care of the administrative hassles, ensuring the generation of high-quality data and training participating researchers to interpret and work with the data to optimise outputs. In this way, researchers get to use the technology right away, while also learning how to get the greatest mileage out of the technology, thus creating local capacity. As such, GSS contributes to GCP’s effort to support and motivate plant breeding ‘champions’ in developing regions.