High-density genetic mapping reveals QTLs associated with Huanglongbing tolerance in citrus

Citrus greening, also known as Huanglongbing (HLB) is a devastating disease in citrus that has severely impacted the global citrus industry. Commercially cultivated varieties, including tangerines ('Daisy' tangerines, C. reticulata), are highly susceptible to HLB, whereas Poncirus trifoliata and its hybrids, such as Carrizo citrange, are widely recognized for their tolerance to HLB disease. While there is no effective control currently available, breeding of HLB-resistant varieties remains the most practical, cost-effective and long-term sustainable strategy. Notably, no reports have been documented linking high coverage, marker density, or quantitative trait loci (QTL) to HLB disease tolerance in the Carrizo citrange × "Daisy" tangerine population.

In current investigation, 120 F₁ hybrids (intergeneric) derived from "Daisy" tangerine × Carrizo citrange was genotyped using Genotyping-by-Sequencing (ddRAD sequencing), leading to construction of high-density SNP based genetic maps for both parents separately. Using an artificial screening approach, F₁ individuals were phenotyped for HLB tolerance under insect-protected cage over two consecutive years.

F₁ hybrids displayed significant variation in HLB disease-related traits, including disease severity, pH difference, and chlorophyll content. QTL analysis using phenotypic variation from both years identified five QTL clusters, located on Ch2 and Ch6 on Carrizo citrange map and Ch1 and Ch6 on 'Daisy' tangerine map. Five regions exhibited co-localization of QTLs associated with two traits. The identified major QTLs explained high phenotypic variation, highlighting significant role in HLB tolerance. This is the high coverage with more marker density were used to identify QTLs associated with HLB tolerance using SNP markers. These findings provide first evidence of quantitative genetic basis of HLB tolerance in Carrizo citrange, while also revealing that 'Daisy' tangerine harbors valuable genetic regions and these regions will used to improve HLB tolerance. This information will be valuable for future efforts in breeding, fine-mapping, genetic engineering, and marker-assisted selection aimed at enhancing disease tolerance.