Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus
2023
Maria J. Asins | Amanda Bullones | Veronica Raga | Maria R. Romero-Aranda | Jesus Espinosa | Juan C. Triviño | Guillermo P. Bernet | Jose A. Traverso | Emilio A. Carbonell | M. Gonzalo Claros | Andres Belver
The excessive accumulation of chloride (Cl<sup>−</sup>) 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<sup>−</sup>, Na<sup>+</sup>, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin (<i>Citrus reshni</i>) and the disease-resistant donor <i>Poncirus trifoliata</i> were performed with the aim to identify repeatable QTLs that regulate leaf Cl<sup>−</sup> (and/or Na<sup>+</sup>) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl<sup>−</sup> was detected in chromosome 6 (<i>LCl-6</i>), where 23 potential candidate genes coding for transporters were identified using the <i>C. clementina</i> 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 <i>LCl-6</i>. Six likely gene candidates were mapped in <i>LCl-6,</i> showing conserved synteny in <i>C. reshni.</i> In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in <i>LCl-6</i> to improve salt tolerance in citrus rootstock breeding programs are provided.
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