Genetic diversity and phylogenetic relationships in Citrus rootstocks using PCR-based RAPD markers

Citrus is an important group of fruit crops due to high nutritional and cash value. Its limited production and fruit loss due to biotic and abiotic damages necessitate genetic improvement through estimation of phylogenetic relationships among the existing Citrus germplasm. In this study, randomly amplified polymorphic DNA (RAPD) markers were used for the germplasm characterization and genetic diversity estimation of 21 Citrus rootstocks (exotic and local species) grown in Pakistan. In total, 145 RAPD amplicons were generated by the selected five decamer primers, of which 98 were polymorphic that revealed 67.5% polymorphism. The number of alleles amplified by each marker ranged from 22 to 42 with an average of 29 alleles per marker. The pairwise Nei and Li genetic similarity coefficients ranged from 0.45 to 0.97, indicating limited genetic diversity within the tested genotypes. The unweighted pair group method with arithmetic average (UPGMA) dendrogram based on the cluster analysis grouped all of the 21 rootstocks into 4 clusters. Cluster I included 2 local, i.e. Mithi and Gada Dehi and 1 exotic, i.e. C-35 citrange. Cluster II was the largest that included 7 locals, i.e. Jallundri Khatti, Mesero lemon, Lima, Galgal, Kharna Khatta, Sour orange, Khatti, and 5 exotics, i.e. Flying Dragon, Chinese Lime, Cleopatra, Wild orange and Sweet Lime. Cluster III included 2 exotic root-stocks, i.e Persian Lime and Pomelo and 1 local, i.e. Kaghzi lime. One genotype namely Rangpur Lime was divergent and occupied a separate position in the dendrogram and joined the cluster II. Cluster IV comprised the remaining 2 rootstocks and both were exotic, i.e. Red Rough Lemon and Grape fruit. The observed genetic structure might be the result of selection biases in the former breeding patterns or due to hybrid rootstocks which ultimately narrowed the gene pool of the Citrus germplasm in the country. These findings may be effective in improving the integrity of this genus in Southeast Asia.