Genetic diversity and population structure of citrus rootstocks revealed by morphological traits and Start Codon Targeted (SCoT) polymorphism

The identification and utilization of genetically diverse citrus rootstocks are essential for sustainable citrus production. However, integrated studies combining phenotypic descriptors and functional molecular markers for comprehensive characterization of diverse citrus rootstocks remain largely unexplored under Indian agro-climatic conditions. In the present study, seventeen commercially important, indigenous, and hybrid citrus rootstock genotypes were evaluated using 27 fruit and seed morphological traits and 19 Start Codon Targeted (SCoT) primers to assess phenotypic diversity, genetic relationships, and population structure. Considerable phenotypic variability was observed, with coefficients of variation exceeding 20% for 21 traits, while fruit weight (68.24%) and fruit shape (70.32%) exhibited the highest variability. Principal Component Analysis identified seven components with eigenvalues > 1, cumulatively explaining 86.9% of the total variation. Molecular analysis generated 63 bands, of which 83.41% were polymorphic, with an average polymorphism information content (PIC) of 0.324, demonstrating the effectiveness of SCoT markers in discriminating citrus rootstocks. Principal Coordinate Analysis and UPGMA clustering resolved the germplasm into four major groups largely corresponding to pedigree relationships. Population structure analysis identified two major genetic pools (K = 2), while Analysis of Molecular Variance revealed moderate but significant genetic differentiation among clusters (PhiST = 0.2159). Mantel analysis revealed a weak and non-significant association between morphological and molecular diversity ( r = 0.071, P = 0.259), whereas Procrustes analysis indicated moderate congruence between the two datasets ( r = 0.435, P = 0.086), suggesting that the two approaches capture complementary patterns of diversity. The integrated use of morphological descriptors and SCoT markers provided a comprehensive assessment of genetic diversity and relationships among citrus rootstocks. The genetically distinct rootstocks identified in this study constitute valuable genetic resources for germplasm conservation and may serve as potential parental materials for future citrus rootstock breeding and improvement programmes under Indian conditions.