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 (Citrus reshni) and the disease-resistant donor Poncirus trifoliata 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 (LCl-6), where 23 potential candidate genes coding for transporters were identified using the C. clementina 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 LCl-6. Six likely gene candidates were mapped in LCl-6, showing conserved synteny in C. reshni. In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in LCl-6 to improve salt tolerance in citrus rootstock breeding programs are provided.

The study was co-funded by grants RTA2011-00132-C2 (M.J.A.), AGL2014-56675-R (M.J.A.), AGL2017-82452-C2 (A.Be., M.J.A.), and PID2021-124599OB-I00 (A.Be.) from the Spanish Ministry of Science and Innovation/the Spanish Research Agency, by grant 51917 (M.J.A.) from the Generalitat Valenciana, as well as the European Regional Development Fund (ERDF), MCIN/AEI/10.13039/501100011033, and ERDF “A way of making Europe”. J.E. was supported by a JAE Intro CSIC grant (JAEINT_19_00566).

Peer reviewed