REALTIME effects of natural selection by pests and pathogens on host tree genome

Funded by French ANR 
January, 1 2008 - September, 30 2012

Participants: UMR1202 BIOGECO (INRA - Univ. Bordeaux, Cestas), UR419 Espèces fruitières (INRA, Villenave d'Ornon), UE0570 (INRA, Cestas), CNG, CEA-IG, Evry

Executive summary

Understanding the relationship between disease, genetic variation and evolution in plants has great importance for both basic and applied sciences. Recent advances in genomics now make it possible to study the adaptive evolution of complex traits, such as disease resistance, from nucleotide sequences to real-world environments. Here, we focused on a major tree species, the European oak Quercus robur with the objective to identify real-time disease-driven changes on the genetic structure of an oak population.

The study was based on a field selection experiment with an oak population exposed to three contrasted levels of powdery mildew. Survival, growth and infection of all individual seedlings (approximately 1500 at the initiation of the study) were monitored during three years. All individuals were genotyped soon after emergence at 828 loci: 9 micro-satellite loci and 819 SNP in 434 candidate resistance genes identified by sequence homology with annotated genes in model species.

Powdery mildew strongly modified growth patterns in oak seedlings, resulting in height growth losses but also changes in the general plant architecture. High heritability values were obtained for variables related to oak receptivity and susceptibility to powdery mildew but not for tolerance to infection. Polymorphisms in 32 different genes were significantly associated with variation in several components of disease resistance. Two SNP co-localized with QTLs for disease. The significance of these genes will be further investigated by studying the evolution of their allelic frequencies during the experiment. Since low mortality rates were observed in the experiment so far even at high disease pressure, relative height will be used as a proxy for fitness in the analyses of disease-driven selection on the genetic structure of the population using the 828 loci.

QTL detection for disease resistance was also performed in Castanea in two inter-specific pedigrees. Micro-satellite markers transferred from Quercus were used to construct the genetic map in order to test if conserved genomic regions in Fagaceae are involved in disease resistance.

Publications and communications

Barreneche T, Richard L, Lalanne-Tisné G, Capdevielle X, Manzano G, Saint Jean G, Lafargue M, Reynet P, Kremer A, Gion J. M, Robin C. 2012. Quantitative trait loci for resistance to Phytophthora cinnamomi in two Fagaceae host species. IUFRO 2012 CONFERENCE “Genetics of Fagaceae and Nothofagaceae”. 9-12 Octobre, Bordeaux, France. (Poster)

Barrès B., Garnier-Géré P., Bérard A., Bodénès C., Boland-Augé A., Burban C., Chancerel E., Fabreguettes O., Lepoittevin C., Plomion C., Robin C., Saint-Jean G., Desprez-Loustau ML. 2012. Identifying the genetic bases of natural variation in resistance to a pathogenic fungus in a population of a perennial plant: the example of Quercus robur and oak powdery mildew. Conférences Jacques Monod, Theoretical and Empirical Advances in Evolutionary Genomics, Roscoff, France, 31 March-04 April 2012 (poster + abstract, public in prep).

Desprez-Loustau ML, Decourcelle T, Delzon S, Dutech C, Feau N, Frigerio JM, Garnier-Géré P, Hamdane-Mougou A, Petit R, Plomion C, Robin C, Vitasse Y and Kremer A. Selective pressures between oaks and their obligate fungal parasite causing powdery mildew (poster) Conference “Forest Ecosystem Genomics and Adaptation”, June 9-11, 2010, San Lorenzo De El Escorial (Madrid) Spain

Desprez-Loustau ML., Saint-Jean G., Barrès B., Cécile Dantec C., Dutech C. 2012. Phenotypic changes in oak seedlings infected by powdery mildew: host tolerance response or host manipulation by the parasite? BSPP Presidential Meeting, Fitness Costs and Trade-offs in Plant-Parasite Interactions, Norwich, United Kingdom, December 16-18 2012 (poster + abstract, publi in prep).

Feau N, Lauron-Moreau A, Piou D, Marçais D, Dutech C, Desprez-Loustau ML. 2012. Niche partitioning of genetic lineages involved in the oak powdery mildew complex. Fungal Ecology 5:154-162

Garnier-Géré P, Lang T, Abadie P, Decourcelle T, Léger V, Frigerio JM, Burban C, Bodénès C, Guichoux E, Robin C, LeProvost G, Reviron MP, Desprez-Loustau ML, Petit R, Plomion C and Kremer A Genome scanning of regions showing divergent evolution between white oaks (Quercus petraea (Matt.) Liebl. and Q. robur L.): new insights from the oak allelic resequencing project. (communication orale) Conference “Forest Ecosystem Genomics and Adaptation”, June 9-11, 2010, San Lorenzo De El Escorial (Madrid) Spain. (communication orale).

Lang T, Abadie P, Decourcelle T, Léger V, Frigerio J-M, Le Provost G, Burban C, Bodénès C, Guichoux E, Reviron M-P, Robin C, Petit R, Desprez-Loustau M-L, Plomion C, Kremer A, Garnier-Géré P 2009. Ecological speciation in oaks : searching for genomic regions showing divergent evolution between Quercus petraea and Q. robur. Genomics of Forest and Ecosystem Health in the Fagaceae (Beech Family)- November 10 - 13, 2009, Research Triangle Park, North Carolina (Poster)

Lang T, Abadie P, Léger V, Decourcelle T, Frigerio J-M, Burban C, Bodénès C, Guichoux E, Robin C, Le Provost G, Tani N, Reviron M-P, Plomion C, Kremer A, Desprez-Loustau M-L, Petit R, Garnier-Géré P. High quality SNP and candidate gene resources development in European oak species from Sanger allelic resequencing and 454 data”.(in prep)

Robin C, Gion J.M, Barreneche T 2012 Quantitative trait loci for resistance to Phytophthora cinnamomi in two host species. 6th Meeting of the IUFRO Working Party 7.02.09 “Phytophthora in Forests and Natural Ecosystems”. 9-14 Septembre Cordoba Espagne (Communication orale)

Robin C, Mougou-Hamdane A, Gion JM, Kremer A, Desprez-Loustau ML. 2011. Quantitative trait loci for resistance to two fungal pathogens in Quercus robur. Fourth International Workshop on the Genetics of Host-Parasite Interactions in Forestry Eugene, Oregon, USA, juillet 2011 (poster).

Contact : Marie-Laure Desprez-Loustau,