The position of the major QTL for Citrus tristeza virus resistance is conserved among Citrus grandis, C. aurantium and Poncirus trifoliata

Citrus tristeza virus, CTV, is one of the most important citrus pathogens. Although CTV-resistant citrus rootstocks derived from Poncirus trifoliata are common, useful genetic resistance within the genus Citrus for scion improvement is very limited and no CTV-resistant sweet orange cultivar is yet available. Quantitative trait locus (QTL) analysis of the accumulation and distribution of CTV was carried out in a segregating population of 201 C. grandis × C. clementina hybrids derived from a reciprocal cross between two commercial varieties, Chandler (Ch) and Fortune (F), to genetically study the CTV resistance response. Chandler and 13 of its hybrids were found resistant to T-346 CTV isolate. The mortality of C. grandis × C. clementina hybrids, as well as CTV-challenged C. aurantium × P. trifoliata hybrids, was found to be related to the CTV resistance response. The type of cytoplasm (F or Ch) was not associated with the CTV resistance. A major QTL contributing around 24% of the total variance for CTV accumulation and spatial distribution was detected on linkage group 4b. Its position is conserved among C. grandis, C. aurantium and P. trifoliata. Seventy candidate genes of the CTV resistance response were obtained by transcriptomic bulk segregant analysis of resistant versus susceptible CTV-inoculated hybrids. Thirteen out of 28 of those candidates could be mapped on the C. grandis and/or C. clementina linkage maps. None was located on linkage group 4b, but four of them were found to be associated with CTV resistance through a minor QTL (CTVCh14) or epistatic interactions (CTVCh15, CTVCh17 and VIC).