QTL Mapping of Citrus Tolerance to Huanglongbing Based on Genotyping-By-Sequencing Approach

Little resistance to Huanglongbing (HLB), associated with infection by Candidatus Liberibacter asiaticus (CLas), is found within commercial citrus varieties, though Poncirus trifoliata has been described as resistant or tolerant. An intergeneric F1 population of 170 individuals was developed from the crossing of Citrus sinensis and P. trifoliata. Utilizing the Genotyping-by-Sequencing approach, a SNP-based genetic map was constructed separately for the two parents using pseudo-testcross. Finally 654 high-quality SNP markers were mapped into nine linkage groups for P. trifoliata, constituting a total genetic length of 1027.8 cM with mean inter-marker distance of 1.57 cM. For C. sinensis, 787 high-quality SNP markers were mapped into nine linkage groups, constituting a total genetic length of 755.3 cM and with mean inter-marker distance of 0.96 cM. Genetic maps of both parents showed high linear correlation with the sweet orange genome. After being exposed to intense HLB pressure for two years in a field trial, a collection of 113 individuals with 8 clonal replicates, including 688 F1 progenies, 40 P. trifoliata and 16 C. sinensis, were phenotyped for CLas titer by qPCR from 2013 to 2015 three times per year. Some related traits were also investigated, e.g. visual rating of HLB symptom, circumference of trunk, and size of canopy. Combining the QTLs from different traits, generally six QTLs were found in P. trifoliata, on chromosome 2, 6, 7, 8 and 9, explaining 10-24% of variance; while four QTLs were found in C. sinensis, respectively mapped on chromosome 2, 3, 8 and 9, explaining 10-16% of variance. The final identified QTLs could be good targets for breeding to support long-term control of this devastating disease.