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Transcriptomics studies of banana for candidate gene identification in a genetic improvement program framework in Ecuador

Abstract:

Modern breeding techniques including genetic transformation and genome editing need the identification of genes relevant for the improved character. In Ecuador, routinely banana tissue culture and Agrobacterium-mediated transformation are established. Several methods could be used for gene identification and function elucidation. Gene expression analysis were performed in different banana cultivars including 'Williams' (AAA) and the black sigatoka resistant accessions 'Calcutta 4' and 'Tuu Gia'. Two techniques have been applied for gene identification including Suppression Subtractive Hybridization (SSH) and RNA sequencing (RNA-seq). Tissues used for transcriptomic analysis were leaves from grown banana plants in pots with at least three fully developed leaves and 15 cm in height, derived from in vitro culture. For identification of candidate gene resistance to black sigatoka disease, two different bioassays were performed after inoculation of Pseudocercospora fijiensis conidia including: i) a SSH technique on 'Calcutta 4', ii) and a RNA-seq with Illumina® in 'Williams' and 'Tuu Gia' after inoculation of P. fijiensis conidia. Furthermore, SSH was performed after application of a bio-fertilizer in banana plants. Several genes were identified and evaluated for differential expression in banana. In silico functional annotation revealed that different pathways in banana plants are affected including plant growth processes and related to biotic and abiotic stresses. Candidate genes involved in relevant pathways could be used in a genetic improvement program in banana through Agrobacterium-mediated transformation or could be targets for genome editing, for the generation of bananas resistant to black sigatoka, the main constraint in banana production in Ecuador.