Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus.

The excessive accumulation of chloride (Cl) in leaves due to salinity is frequently related to decreased yield in citrus. Two salt tolerance experiments to detect quantitative trait loci (QTLs) for leaf concentrations of Cl, Na, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin () and the disease-resistant donor were performed with the aim to identify repeatable QTLs that regulate leaf Cl (and/or Na) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl was detected in chromosome 6 (), where 23 potential candidate genes coding for transporters were identified using the genome as reference. Transcriptomic analysis revealed two important candidate genes coding for a member of the nitrate transporter 1/peptide transporter family (NPF5.9) and a major facilitator superfamily (MFS) protein. Cell wall biosynthesis- and secondary metabolism-related processes appeared to play a significant role in differential gene expression in . Six likely gene candidates were mapped in showing conserved synteny in In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in to improve salt tolerance in citrus rootstock breeding programs are provided.