Molecular Markers Assisted Identification of Intraspecific Hybrids in Ziziphus mauritiana

Abstract

Breeding in Ziziphus mauritiana through hybridization is limited by its small sized flowers, cross incompatibility, low fruit set and poor retention. Correct identification of a hybrid is often difficult when it resembles more with one parent or when new morphological combination of characters arise from recombination of distinct genotypes. Under present study three varieties of Z. mauritiana viz., Tikadi, Seb and Katha were found cross compatible and resulted in improved hybrids viz., F1 (Seb 9 Tikadi), F1 9 Seb and Seb 9 Katha. Ten RAPD primers revealed a total of 108 bands in the range of 150 bp to 3 kb. Among these, 69 bands were polymorphic and exhibited 33.33–90.9 % polymorphism in the banding patterns. The dendrogram clearly delineated variety Tikadi and Katha from Seb. All the three hybrids formed a single cluster with the variety Seb. The 5.8S gene region was found to be highly conserved (99.39 %) followed by ITS-2 (97.77 %). and ITS-1 (90.6–90.8 %). Heterozygous positions in ITS sequences clearly show their hybrid nature and could perform as highly polymorphic molecular markers. Despite SNPs, INDELS and total length polymorphism among parents and their hybrids, all were molecularly identified as Z. mauritiana and did not cause any phylogenetic error. The nucleotide polymorphism in ITS-1 region can serve as a bar code to detect and address genetic diversity within Z. mauritiana.