DArTseq molecular markers associated with water stress tolerance and size reduction in citrandarins rootstocks

In Brazil, most orchards are not irrigated and flowering usually occurs in August/September, the season with the least rainfall, making it necessary to use drought-tolerant rootstocks. Reduced scion vigor, associated with drought tolerance, are essential factors for high-density planting systems in conditions of limited water availability. The identification of molecular markers potentially associated with these characteristics is essential to accelerate the improvement of citrus rootstocks. This study aimed to identify DArTseq molecular markers related to dwarfism and drought tolerance in citrandarin rootstocks (Citrus sunki × Poncirus trifoliata) using an in silico Bulk Segregant Analysis (BSA) approach. Experiments were conducted in Barretos, a municipality in the northern region of the São Paulo state. The bulks were selected based on vegetative development and leaf rolling scores for drought tolerance. The molecular markers were identified through differences in allele frequency between the groups, and the markers putatively associated underwent functional annotation to infer candidate genes for these characteristics using the Blast2GO program with the NCBI nr database. A total of 12 candidate markers were identified and associated with the characteristics of interest, including six related to reduced vigor and six to drought tolerance. The functional annotation enabled the identification for gene sequences associated with biological processes related to plant development, root architecture, hormonal regulation, and response to abiotic stress. The identified markers represent candidate genomic regions potentially involved in vigor regulation and drought response. These results represent valuable resources for future research in citrus rootstock breeding programs.