Category: Breeding

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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.

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Wild relatives to the rescue (again)

You may remember the recent warnings about a new strain of wheat stem rust called Ug99 making its way from the Rift Valley of Africa across the Red Sea to Yemen, thus threatening the very home of wheat in the Middle East. Jeremy blogged about it a couple of months back. Well, resistance to the disease has now been found in about 70% of the 100-odd samples of a wild wheat (Aegilops sharonensis) collected in southern Lebanon and Israel, according to a paper in Plant Disease. Four of the samples actually have resistance to a whole range of fungal diseases:

Co-author of the paper, Yehoshua Aniksterat, of the Israel-based Institute for Cereal Crops Improvement at Tel Aviv University, told SciDev.Net that although it could be difficult — and take up to five years or more — they may be able to transfer genes from wild to cultivated wheat.

The map below is what GBIF knows about the geographic distribution of A. sharonensis ((Israel Nature and Parks Authority, Israel Nature and Parks Authority (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/1431, 2007-08-14) US National Plant Germplasm System, United States National Plant Germplasm System Collection (accessed through GBIF data portal, http://data.gbif.org/datasets/resource/1429, 2007-08-14).)).

sharonensis.jpg

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A second helping of rice

More today to satisfy your hunger for rice information, hot on the heels of the recent paper trying to explain the pattern of genetic variation across and within two subspecies of cultivated rice, discussed by Jeremy a couple of days ago.

First there’s a paper ((Global Dissemination of a Single Mutation Conferring White Pericarp in Rice. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, et al. PLoS Genetics Vol. 3, No. 8.)) looking at how the red pericarp of wild rice became the white pericarp of cultivated rice. The answer is that a mutation arose in the japonica subspecies, crossed to the indica and became fixed in both under very strong selection pressure by ancient rice farmers. They must have really liked those funny mutant white grains when they first noticed them! Oh to have been a fly on the wall — or a brown plant hopper on the rice stalk — when the white pericarp mutation was first noticed in some ancient paddy…

Then comes news that the three CGIAR centres with an interest in rice — IRRI, WARDA and CIAT — are to boost their collaboration to solve the pressing production problems of Africa. There’s talk of forming a consortium. More flags being prepared.