W193
The Genome Of Coffee Leaf Rust, The Most Devastating Pathogen Of Coffee, and Development Of Molecular Markers For Marker-Assisted Selection In Coffee Breeding Programs

Date: Sunday, January 13, 2013
Time: 5:30 PM
Room: Sunset
Marco A. Cristancho , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchina, Caldas, Colombia
Huver Posada , Colombian National Coffee Research Center (CENICAFE), Chinchina, Caldas, Colombia
Alvaro Gaitan , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchina, Caldas, Colombia
William Giraldo , Colombian National Coffee Research Center (CENICAFE), Chinchina, Caldas, Colombia
David Botero , Colombian National Coffee Research Center (CENICAFE), Chinchina, Caldas, Colombia
Javier Tabima , Colombian National Coffee Research Center (CENICAFE), Chinchina, Caldas, Colombia
Diana Ortiz , Colombian National Coffee Research Center (CENICAFE), Chinchina, Caldas, Colombia
Alejandro Peralta , Colombian National Coffee Research Center (CENICAFE), Chinchina, Caldas, Colombia
Silvia Restrepo , Universidad de los Andes, Bogota, Colombia
Diego Riaņo , Universidad de los Andes, Bogota, Colombia
Fernando Garcia , Colombian National Coffee Research Center (CENICAFE), Chinchina, Caldas, Colombia
Camilo Lopez , Universidad Nacional de Colombia, Bogota, Colombia
Marcela Yepes , Cornell University, Geneva, NY
Herb Aldwinckle , Cornell University, Geneva, NY
Coffee leaf rust, caused by the fungus Hemileia vastatrix, is the most damaging disease of coffee worldwide. The pathogen has caused yield reductions of up to 30% in susceptible varieties of Coffea arabica in recent epidemics associated with climate change in Colombia and several Central American countries. We have sequenced de novo the genome and transcriptome of H. vastatrix race II using next-generation sequencing platforms: 454 Roche and Illumina. The H. vastatrix genome is over 250 Mb, one of the largest fungal genomes to date. The assembled genome has 92% coverage, a GC content of 32%, and a very large proportion of repeated sequences; over 74% of the H. vastatrix genome is composed of repeats, with prevalence of LTR retro-transposons. We predicted a set of 14,445 proteins encoded by the coffee rust genome, and 44 secreted proteins that might be involved in pathogenesis. Three transcriptome assemblies from different isolates/races were obtained with 44,297, 55,791 and 64,752 contigs with average contig size of 675, 716 and 828 bp. Most H. vastatrix race II transcripts (84%) were mapped to the assembled genome. H. vastatrix isolate/race diversity at the transcriptome level is significant, since they only share 76-78% of expressed sequences. 
Only 36% to 44% H. vastatrix transcriptome sequences had homology with Puccinia or Melampsora proteins showing the high level of genetic diversity present in rust fungi. We have also developed molecular markers for H. vastatrix that are being used for genetic diversity studies. 

In addition, we have developed molecular markers for host derived resistance against this pathogen that are linked to the introgression of C. canephora (rust resistant genotype) in breeding F5 lines of C. arabica, particularly in the resistant components of the Castillo variety of Colombia. These markers have high potential to accelerate development of rust resistant varieties through marker-assisted selection in coffee breeding programs.

Note:  This abstract will have two presenters Marco Cristancho and Huver Posada