Molecular detection and variability of jujube witches’-broom phytoplasmas from different cultivars in various regions of China

Abstract:

Abstract：[Objective] Jujube witches’-broom is an important disease in jujube cultivation areas, which causes serious losses in jujube fruit production. To understand the genetic variability and diversity of jujube witches’-broom phytoplasma population from the different cultivars and various regions of China. [Method] We collected 32 samples from 14 cultivars or wild sour jujubes in 7 regions of China and detected them with PCR with the primers R16mF2／R16mR1 for phytoplasma 16S rDNA, SR1/SR for16S-23SrRNA space region (SR) and FD9f/r for secretion proteins (secY). The direct sequencing of PCR products and sequencing by cloned PCR products were used for sequence polymorphism and phylogenetic analyses by comparison to the databases of known conserved gene sequences. [Results] We detected phytoplasmas by PCR amplification of 16SrDNA from all the diseased jujube samples. All the phytoplasma isolates infected various jujube cultivars belonged to subgroup 16SrV-B of elm yellows group and had closer homology with Bischofia polycarpa witches’-broom and cherry lethal yellows phytoplasmas occurred in China than other 16SrV phytoplasmas in other countries. The sequence polymorphism at different extent in 16SrDNA, SR and secY gene and genetic diversity were revealed in phytoplasma strain population related to different habitats, among which the dominant strains were always detected by the direct sequencing of PCR products in all the diseased areas of China. The degree of variability on secY gene of collected phytoplasma strains was greater than that of 16SrDNA and SR sequences, and some base substitutions could not alter encoded amino acid, however certain single base deletions detected in a Shandong and a Beijing strains may have impact on the gene structure or function. [Conclusion] Phytoplasma strains from different cultivars and regions show dramatic genetic diversity. Compared with direct sequencing of PCR products, the sequencing by cloning PCR products was more useful for the displaying of variants and phylogeny in phytoplasma strain population.