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United States Department of Agriculture

Agricultural Research Service

Research Project: CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES

Location: Corn Insects and Crop Genetics Research

Title: A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

Authors
item David, Perrine -
item Chen, Nicolas -
item Pedrosa-Harand, Andrea -
item Sevignac, Mireille -
item Thareau, Vincent -
item Cannon, Steven
item Debouck, Daniel -
item Langin, Thierry -
item Geffroy, Valerie -

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 17, 2009
Publication Date: September 23, 2009
Citation: David, P., Chen, N., Pedrosa-Harand, A., Sevignac, M., Thareau, V., Cannon, S.B., Debouck, D., Langin, T., Geffroy, V. 2009. A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean. Plant Physiology. 151:1048-1065.

Interpretive Summary: One of the ways that plants defend themselves against pathogens is with a type of plant-specific immune system, using a class of "resistance proteins" (R-proteins) that serve roles similar to those of antibodies in mammalian cells. However, plant R-proteins can't recombine in a single individual to form variants to recognize many pathogens. This raises the question of how plants can respond to evolving pathogens. This research describes 26 R-proteins that occur in a large R-gene cluster on a chromosome in common bean, and corresponding regions in soybean. The region is responsible to resistance against several important diseases in common bean and soybean, including bean anthracnose, bean rust, and bean stem and root rot. The main findings are that genes in this bean cluster have both recombined with others in the cluster, and with genes from other chromosomes. In short, this cluster is a recombination hotspot. Two factors appear to contribute to the "recombination hotness": one is a newly-discovered bit of repetitive DNA associated with these R-genes, and the other is the location at the end of a chromosome; similar hotspots have also been found at the ends of human chromosomes. These results are important because they help explain how a group of genes that are critical for plant disease resistance change and keep themselves up to date in response to evolving pathogens. This knowledge is important for plant breeders, who need to keep ahead of pathogens by introducing R-genes from wild plant varieties into related high-value crops.

Technical Abstract: The B4 resistance (R)-gene cluster, located in subtelomeric region of chromosome 4, is one of the largest clusters known in common bean (Phaseolus vulgaris, Pv). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus, in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, in the Pv B4 locus. It was shown to be specific to the Pv genus and present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R genes evolution.

Last Modified: 8/1/2014
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