Genetic Diversity、Phylogeography And Population Demography Of Ziziphus Jujuba Var.Spinosa

Ziziphus jujuba var.spinosa（sour jujube）is widely distributed in temperate regions in Northern China and harbors important ecological and economic values.Accompanied with the development of researches on wild germplasm related to cultivated fruit species,abundant gene resources in Z.jujuba var.spinosa will provide important genetic resource for cultivation and breeding of jujube.However,protection and sustainable utilization of this important germplasm is threatened by various factors.Some basic studies concerning genetic diversity,genetic structure and population dynamic will facilitate future protection and sustainable utilization of sour jujube.In the present study,single-copy nuclear gene markers of Ziziphus were screened and developed with bioinformatic method.Genetic diversity,genetic structure and population dynamic of 21 sour jujube populations distributed in China were investigated with these single-copy nuclear gene markers.Phylogeographic structure and divergence time between main lineage of sour jujube were researched using chloroplast genome data.Furthermore,we collected 498 distribution information of sour jujube through field investigation and literature retrieving.The population dynamic of sour jujube responding to geological,present and future environmental conditions was modeled and predicted in MaxEnt with 10 low-correlated environmental variables and visualized in ArcGis.The main resutles were as follows:1)A number of 13 single-copy nuclear gene markers were developed in the present study.The length of these markers varied between 295-887 bp with a total length of 9806 bp.The value of π and θ_w varied from 0.00073 to 0.01220 and from 0.00105 to 0.01209 with mean value of 0.00513 and0.00531.The mean value of R_m was 3.Result of neutral tests showed that all the single-copy nuclear gene markers were confirmed to the neutral evolution.Phylogenetic and structure analysis indicated that the developed single-copy nuclear gene markers were suitable for genetic study of sour jujube.Inter-chromosome fusions and segmental duplication events occurred frequently in sour jujube genome,which resulted in difficulties in marker development.More markers will be developed and applied in genetic study of sour jujube and Ziziphus.2)5 single-copy nuclear gene markers were randomly selected for genetic study of sour jujube distributed in China.328 individuals from 21 sour jujube populations were sampled.The length of the5 single-copy nuclear gene markers varied between 199 and 846 bp.The number of segregating sites and haplotype diversity ranged from 24 to 82 and from 0.611 to 0.940.The mean value of R_m was 8.Tajima’s D,Fu and Li’s D^* and F^* and multilocus HKA tests showed that all the single-copy nuclear gene markers were under neutral evolution..Sour jujube distributed in China harbored high level of nucleotide diversity（π=0.00720,θ_w=0.0153）,which was resulted from mating system and complex population dynamic of this species.Mismatch and Bayesian skyline plot analysis showed that sour jujube experienced population expansion during evolutionary history.This expansion occurred approximately at 11.57 Ka（95% CI: 9.76-14.07 Ka）,when the global climate became warm during this period.STRUCTURE analysis showed that genetic composition of individuals was similar.AMOVA analysis indicated that populations of sour jujube showed moderately high level of genetic differentiation(F_st=0.197).Variation within populations contributed majority to the total variation（80.30%）.Dispersal abilities of seed and pollen of sour jujube resulted in the low level of gene flow among populations.Mantel test showed high correaltion between genetic distance and geographic distance,indicating gene flow among populations was strongly affected by geographic distance.3)We randomly selected 1 individual from each population to sequence and assemble chloroplast genome of sour jujube.Results showed that the length of chloroplast genome of sour jujuba ranged from 159399 bp to 161279 bp and GC content varied between 36.51% and 37.30%.Chloroplast genome of sour jujuba contained 1 LSC,1 SSC and 2 IRs,and coded 112 genes including 78 protein coding genes,30 tRNA genes and 4 rRNA genes.Phylogenetic analysis of chloroplast haplotype revealed two intraspecific cluster,which was consistent with the STRUCTRUE analysis and medianjoinging network.The chloroplast genome haplotype native to the centran populations was more ancient than other haplotypes and it was speculated that the glacial refugie of sour jujube located at the Loess Plateau.Divergence of the two clusters occurred approximately at 55.86 Ma（95%HPD:31.82-79.37Ma）,which may be driven by climatic and topographical conditions.4)Results of population dynamic modeling with Max Ent showed that the average value of AUC of training data and test data was 0.943 and 0.932,respectively,indicating accurate and reliable modeling and predicting in MaxEnt.Mean temperature of coldest season contributed most to MaxEnt modeling（35.4%）while soil contributed least（0.1%）.The mean temperature of the coldest season（Bio11）,the mean precipitation of the hottest season（Bio18）,annual range of temperature（Bio7）and elevation were four major environmental factors affecting distribution of sour jujuba.Areas with Bio11,Bio18 Bio7 and elevation rangng from-8.5℃-4.9℃,245-550 mm,1.8℃-15.7℃ and approximately1000 m were suitable for sour jujube.Distribution of sour jujube in present environmental conditions was mainly in areas from the Loss Plateau to Shandong Peninsula,which was consistent with the distribution of sour jujube recorded in literatures.In the Last Glacial Maximum,distribution range of sour jujube was shrunk and retreated southward.Distribution range of total suitable and highly suitable area of sour jujube in the Last Interglacial expanded compared with present distribution..This was consistent with the retreat-recolonization model revealed in some temperate plant species responding to glacial-interglacial cycles in Quaternary.It was found that another glacial refugie for sour jujube may locate at the north of the Qinling Mountains.The total suitable distribution range of sour jujube responding to future environmental conditions was smaller than present distribution while highly suitable area increased.The distribution range of sour jujube moved toward high latitude areas in future environmental conditions.Present and future protection strategies of sour jujube should be implemented in regions adjacent to the Loss Plateau and high latitude areas.In the present study,bioinformatic method were used to develop single-copy nuclear gene markers in Ziziphus.Analysis results indicated that application of these single-copy nuclear gene marker in genetic research of sour jujube was suitable.Z.jujuba var.spinosa distributed in China showed relatively high level of genetic diversity and moderate genetic differentiation.Distribution range of sour jujube in different geological periods varied substantially in responding to various environmental conditions.This study put a solid foundation for modeling and predicting population dynamic of plant species corresponding to environmental oscillations,but also for protection and utilization of plant germplasm.