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<p>Jujube/ber (<i>Ziziphus</i> spp.), belonging to the buckthorn family Rhamnaceae, is an important fruit crop, best suited to grow in harsh environmental conditions. Genetic improvement in jujube relies on identification of genetically diverse germplasm, which can be utilized for crop improvement. In the present study, we have compared the relative efficacies of different DNA-based markers to estimate the genetic diversity among twenty-four different accessions of ber. This included the ISSR (Inter-Simple Sequence Repeat), CBDP (CAAT Box Derived Polymorphism), SSR (Simple Sequence Repeat) and the plastidial <i>rpoC1</i> markers. While the highest number of mean polymorphic bands were obtained with ISSRs, the average PIC (Polymorphism Information Content) of the CBDP markers was highest (0.31). The SSR markers on the other hand had the least average PIC (0.25) and resolving power (2.46). Two accessions, IC-0625869 and IC-0625864, both belonging to <i>Z. oenoplia</i>, were consistently clustered separately from the remaining accessions depicting species divergence during evolution. The CBDP markers (CBDP 19 and 22) allowed successful discrimination of the two accessions, which were otherwise non-distinguishable by other markers. The <i>rpoC1</i> marker successfully established the genetic distinctness of the <i>Ziziphus</i> spp., allowing distinct clustering of <i>Z. oenoplia</i> from the other <i>Ziziphus</i> spp. The population structure analysis, based on combined analysis utilizing all the marker data, depicted presence of two distinct populations (K = 2) with an allele frequency divergence and the mean F<sub>ST</sub> (fixation index) of 0.28 and 0.48, respectively, depicting limited gene flow between the two populations. This study provides novel insights into the diversity within ber germplasm and identifies novel markers which can be used to identify different genotypes/species with unequivocal resolution.</p>

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Comparative Efficacies of Different DNA-Based Markers for Diversity Analysis and Species Discrimination in Ziziphus spp.

  • 期刊论文

  • 发表日期：

    2026年3月25日

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  • Sheel Yadav,
  • Samriddhi Shree,
  • Joyesh Sahu,
  • Ratna Kumari,
  • Vijay Singh Meena,
  • Lalu Prasad Yadav,
  • Rakesh Singh,
  • Ambika B. Gaikwad

摘要

Jujube/ber (Ziziphus spp.), belonging to the buckthorn family Rhamnaceae, is an important fruit crop, best suited to grow in harsh environmental conditions. Genetic improvement in jujube relies on identification of genetically diverse germplasm, which can be utilized for crop improvement. In the present study, we have compared the relative efficacies of different DNA-based markers to estimate the genetic diversity among twenty-four different accessions of ber. This included the ISSR (Inter-Simple Sequence Repeat), CBDP (CAAT Box Derived Polymorphism), SSR (Simple Sequence Repeat) and the plastidial rpoC1 markers. While the highest number of mean polymorphic bands were obtained with ISSRs, the average PIC (Polymorphism Information Content) of the CBDP markers was highest (0.31). The SSR markers on the other hand had the least average PIC (0.25) and resolving power (2.46). Two accessions, IC-0625869 and IC-0625864, both belonging to Z. oenoplia, were consistently clustered separately from the remaining accessions depicting species divergence during evolution. The CBDP markers (CBDP 19 and 22) allowed successful discrimination of the two accessions, which were otherwise non-distinguishable by other markers. The rpoC1 marker successfully established the genetic distinctness of the Ziziphus spp., allowing distinct clustering of Z. oenoplia from the other Ziziphus spp. The population structure analysis, based on combined analysis utilizing all the marker data, depicted presence of two distinct populations (K = 2) with an allele frequency divergence and the mean FST (fixation index) of 0.28 and 0.48, respectively, depicting limited gene flow between the two populations. This study provides novel insights into the diversity within ber germplasm and identifies novel markers which can be used to identify different genotypes/species with unequivocal resolution.