Current Challenges and Genomic Advances Toward the Development of Coffee Genotypes Resistant to Biotic Stress

Abstract

Coffee (Coffea spp.) is an important agricultural world commodity. Biotic stresses caused by pests or phytopathogens can affect not only the coffee production, but also the grain quality. They interfere with physiological processes affecting plant growth and development, and damaging different plant organs and tissues, such as leaves, roots, and fruits. The use of chemicals to control diseases and pests directly affects coffee cultivation sustainability and are often inefficient. This scenario could worsen with the rapid insurgence of new and/or more aggressive pathogens and pests as a result of the world climate change. Thus, coffee breeding with a focus on the development of resistant cultivars is the best strategy to control these biotic stresses. In this context, biotechnological tools can help the coffee breeding in a persuasive way. Advances in genomic editing techniques, such as CRISPR, are capable of introducing punctual modifications in the plant genome. As an alternative to the use of chemicals, the sequence-specific gene silencing via RNA interference (RNAi) holds a great promise for effective management of agricultural pests. The emergence of high-throughput sequencing technology has allowed unprecedented advances in genomic and transcriptomic data. The genomic and transcriptomic coffee data can now be used to identify a large number of genes and molecular markers that determine coffee resistance to pathogens and pests. The identification of these genes helps to elucidate plant pathogen interactions, as well as can be targets for genome editing. The implementation of molecular markers, through assisted selection, can help accelerate breeding programs and pyrimidize resistance genes. In addition, the genomic and transcriptomic data of pathogens and pests are useful to identified targets for RNAi approaches. In this review, we address the research in modern genetics and molecular biology related to the main biotic stresses of coffee plants and its implications for coffee breeding.