Understanding morphological and genetic variability in the segregating citrus populations is essential for effective selection and genetic improvement. In current study, 120 F₁ hybrids derived from ‘Daisy’ tangerine (♀) × Carrizo citrange (♂) were evaluated using integrated morphological characterization (qualitative 47 and quantitative 18 traits) and microsatellite (SSR) marker-based molecular analyses. Morphological diversity was recorded nearly in all vegetative traits, such as growth habit, branching pattern, leaf morphology, stem, and spine characteristics. Quantitative traits such as plant height, branch size, spine length, leaf chlorophyll content, and leaf biomass exhibited wide variation, high genotypic and phenotypic coefficients of variation, and exceptionally high broad-sense heritability (94.62–99.91%) coupled with high genetic advance, indicating strong additive genetic control and suitability for phenotypic selection. Correlation analysis between genotypic and phenotypic data revealed strong positive associations among leaf size, branching traits, internodal length, stem girth, and plant height, suggesting coordinated genetic regulation of plant vigour. Multivariate analyses showed that principal components associated with vegetative vigour and leaf traits accounted for a major proportion of total morphological variation, while hierarchical clustering clearly distinguished parental groups and hybrid classes. Molecular analysis using 153 polymorphic SSR markers confirmed high genetic diversity and heterozygosity within the population. UPGMA, AMOVA, principal coordinate and STRUCTURE analyses consistently indicated extensive recombination among the hybrids and predominant genetic variation within the individuals. Overall, integrated morphological and molecular data highlight, this F₁ hybrid population as a valuable genetic resource for marker-assisted selection and QTL mapping aimed towards developing resilient citrus rootstocks.

Huanglongbing (HLB) is a major constraint to citrus production, but the genetic basis of physiological responses to Candidatus Liberibacter asiaticus (CLas) 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 CLas exposure. Fifteen physiological and environmental traits were measured and CLas 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 CO₂ flux, accompanied by increased intercellular CO₂ 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 CO₂ 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.