RNA-guided silencing pathways in Coffea spp.: genome-transcriptome-wide analyses

Abstract

Brazil is the major producer and exporter of coffee beans, which are the second most traded commodity worldwide. Coffee is a biannual crop whose phenology is strongly influenced by environmental factors, such as photoperiod, temperature and rainfall distribution. The coffee tree presents sequential flower development and several blossoming events. These events lead to unequal maturation of fruits and, therefore, impair the quality of the beverage and increase the production costs. Within the panorama of climate changes, studies aiming to clarify the regulation of developmental mechanisms for crop breeding are extremely required. microRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs), 21 nt long on average, that regulate mRNA expression in plants inhibiting their translation with or without cleavage of the target. The aim of this dissertation was to provide a wide analysis of coffee miRNAs and to unravel the RNA-guided silencing pathways. To do that, the Coffea canephora genome was surveyed for the identification and characterization of the miRNAs and the components of RNA-silencing pathways. Furthermore, small-RNAseq libraries were constructed from floral buds in different development stages, aiming to identify conserved and genus-specific miRNAs related to floral development in coffee. These two studies represent a pioneering work that offers a significant step towards a better understanding of the transcriptional and post-transcriptional regulation of floral development in this major crop. The identification and characterization of the components in the RNA-guided silencing pathways in this important crop provide not only knowledge of the plant biology, but also basis for further enhancement through biotechnological tools to address its constraints.