High-density SNP mapping reveals genomic hotspots for photosynthetic traits under Huanglongbing disease in citrus

Huanglongbing (HLB) is a major constraint to citrus production, but the genetic basis of physiological responses to Candidatus Liberibacter asiaticus ( C Las) infection remains poorly understood. Here, we characterized photosynthetic and gas-exchange responses and investigated their genetic architecture in 120 F₁ hybrids derived from ‘Daisy’ tangerine × Carrizo citrange. Hybrids were evaluated before HLB infection and across four subsequent assessment periods following artificial C Las exposure. Fifteen physiological and environmental traits were measured and C Las infection was confirmed in all F₁ hybrids by quantitative real-time PCR. HLB-associated physiological responses were characterized by declines in net photosynthetic rate, stomatal conductance, transpiration and intercellular CO 2 flux, accompanied by increased intercellular CO 2 concentration and vapour pressure deficit. Multivariate analysis indicated that gas exchange and water relations constituted the major sources of phenotypic variation, with the first three principal components explaining 81.81% of the total variation. High broad-sense heritability and genetic advance were observed for several key traits, particularly stomatal conductance, intercellular CO 2 flux, net photosynthetic rate, transpiration and vapour pressure deficit, indicating substantial genetic variation for these responses. High-density parental SNP linkage maps were subsequently used for QTL analysis. Twenty-six QTLs were detected on the ‘Daisy’ tangerine map and 28 on the Carrizo citrange map, with individual loci explaining 10.6–17.8% of phenotypic variance. Several QTLs were repeatedly detected across seasons and overlapping loci were identified for physiologically related traits. These stable genomic regions provide useful targets for validation and further dissection of the genetic basis of physiological responses under HLB infection.