SRAP and SSR marker-assisted genetic diversity, population structure analysis and sex identification in Jojoba (Simmondsia chinensis)

Abstract Simmondsia chinensis (Link) Schneider, commonly known as Jojoba is a woody, dioecious shrub, cultivated all over the globe mainly for its commercially important seed oil (liquid wax ester). Investigations were carried out to analyze genetic diversity and population structure of 57 Jojoba genotypes belonging to 3 different eco-geographical regions of India (Gujarat, Jodhpur, and Jaipur) employing sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers. SRAP markers produced higher mean values of polymorphic bands (6.22), polymorphism information content (PIC: 0.47), effective multiplex ration (EMR: 5.36) and marker index (MI: 2.59) compared to SSR markers (5.87, 0.38, 5.26 and 2.23 respectively). Higher % polymorphism (86.30%) and resolving power (RP: 8.76) were detected by SSR markers than SRAP markers (82.30% and 8.71 respectively). Total genetic diversity (Ht) and genetic diversity within populations (Hs) in Jojoba genotypes were found to be very high (0.47 and 0.45 respectively). AMOVA analysis also revealed higher genetic variation within populations (77%) than among populations (23%). Very low genetic differentiation (Gst: 0.04) and high gene flow (Nm: 10.57) among different populations were observed. The Jojoba population of Gujarat region was observed to be highly diverse (h: 0.48), and that of Jaipur was least polymorphic (h: 0.40). Jojoba male genotypes were found to be more polymorphic (h: 0.46) compared to females (h: 0.44). UPGMA, Neighbor-Joining tree, and population structure analysis divided Jojoba populations into two main clusters, first comprising of Gujarat and Jodhpur populations and second including Jaipur population. Genetic diversity in different Jojoba populations was found to be strongly negatively and significantly correlated with the longitude factor. For sex identification in Jojoba, one SRAP primer combination, 'Em14/Me10' amplified a DNA fragment of 396 bp specific to male genotypes of Jaipur population. This male-specific marker was further positively validated on different genotypes growing in Jodhpur and Gujarat regions and sequenced.