Identification of the Putative Class 3 R Genes in Coffea arabica from CafEST Database

Abstract

Coffee is one of the most important commodities worldwide. For this reason, the sequencing in large scale of expressed sequence tags (ESTs) from different tissues of the coffee tree was performed and resulted in the formation of the Brazilian Coffee Genome EST database (CafEST). There is a raising interest of genetic breeding programs in developing varieties of Coffea arabica with increased resistance to nematodes, pests, and diseases. A high number of plant resistance genes (R genes) have already been isolated and classified into six categories denoted as class 1 to class 6. In this study, we show results of a screening of the coffee transcriptome database for class 3 LLR/NBS/TIR-like R gene related sequences within the C. arabica ESTs from the CafEST database. Based on searches for sequence similarities, we selected a total of 293 ESTs coding for class 3 R proteins, putatively related to disease resistance in C. arabica. Among these reads, 101 ESTs, representing the RPP4 subclass, were grouped into 56 clusters. We found 93 reads representing the RPP5 subclass, which were grouped into 46 clusters. In addition, we also found 99 reads representing the RPS4 subclass, which were grouped into 54 clusters. However, no matches were found with other subclasses of R genes (L, M, N, P, and RPP1) so far. These studies should contribute to the elucidation of the recognition and resistance cascades elicited by R genes. These results may provide relevant information to be applied on coffee breeding programs and on the development of new strategies to obtain genetic durable resistance for plants against pathogens, resulting in positive impacts on the coffee agribusiness.