Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism markers

Abstract

The genetic diversity and relationships among populations of Chinese-endemic rugged rose (Rosa rugosa) were studied at the molecular level, to provide theoretical guidance and technical support for the scientific evaluation, preservation and development of the germplasm resources of this endangered species. DNA samples of 120 specimens of R. rugosa, originating from six different Chinese source populations were amplified with CDDP (conserved DNA-derived polymorphism) primers. A total of 121 polymorphic loci out of the 128 total bands (94.53%) were recovered using 13 informative and reliable primers. The average number of amplified bands per primer was about 9.84. The number of specific bands was 8, accounting for 6.25%. Nei's gene diversity (H), Shannon's information index (I) and the effective number of alleles (Ne) were 0.3057, 0.4646 and 1.5131, respectively. A UPGMA (unweighted pair group method with arithmetic mean) cluster analysis suggested that these populations of rugged rose could be divided into six major groups, with a similarity coefficient of 0.81. Here we show that the CDDP marker technique can effectively reveal the genetic diversity among Chinese-endemic populations of the rugged rose. Based on the results from the cluster analysis, we suggest that although the population genetic structure mirrors the geographic structure to some extent, it is clear that other factors besides geographic distance contribute to the generation of genetic variation.

Analysis of the genetic diversity of the coastal and island endangered plant speciesElaeagnus macrophyllavia conserved DNA-derived polymorphism marker

“…In the present study, the Ht and Hs of E. macrophylla were 0.1706 and 0.1149, respectively. Compared with endangered and Chinese secondary protected plants (Fu & Jin, 1992), including R. rugosa, in previous CDDP-based (Ht = 0.2770, Hs = 0.1522) studies (Jiang & Zang, 2018), E. macrophylla in the present study showed low diversity. Similarly, the diversity values in the present study were lower than those estimated via CDDP markers for the plant species C. japonica (Ht = 0.2874, Hs = 0.2518 ;Juan, 2018).…”

“…By amplifying these conserved sequences, which tend to be linked to phenotypic traits, CDDP markers can provide advantages for plant genetic diversity assessment (Andersen & Lübberstedt, 2003). Since Poczai first successfully used CDDP markers and within-target markers to investigate the genetic diversity and group structure of Solanum dulcamara (Poczai et al, 2011), CDDP markers have proven useful in the analysis of several other plant species, such as Chrysanthemum (Li et al, 2014), Paeonia suffruticosa (Li, 2013), Vaccinium vitis-idaea (Fang et al, 2016), and Rosa rugosa (Jiang & Zang, 2018). However, CDDP markers have not yet been used to study E. macrophylla.…”

Peer Review #1 of "Analysis of the genetic diversity of the coastal and island endangered plant species Elaeagnus macrophylla via conserved DNA-derived polymorphism marker (v0.1)"

“…In the present study, the Ht and Hs of E. macrophylla were 0.1706 and 0.1149, respectively. Compared with endangered and Chinese secondary protected plants (Fu & Jin, 1992), including R. rugosa, in previous CDDP-based (Ht=0.2770, Hs=0.1522) studies (Jiang & Zang, 2018), E. macrophylla in the present study showed low diversity. Similarly, the diversity values in the present study were lower than those estimated via CDDP markers for the plant species C. japonica (Ht=0.2874, Hs=0.2518; Juan, 2018).…”

“…By amplifying these conserved sequences, which tend to be linked to phenotypic traits, CDDP markers can provide advantages for plant genetic diversity assessment (Andersen & Lübberstedt, 2003). Since Poczai first successfully used CDDP markers and within-target markers to investigate the genetic diversity and group structure of Solanum dulcamara (Poczai et al, 2011), CDDP markers have proven useful in the analysis of several other plant species, such as Chrysanthemum (Li et al, 2014), Paeonia suffruticosa (Li et al, 2013), Vaccinium vitis-idaea (Fang et al, 2016), and Rosa rugosa (Jiang & Zang, 2018). However, CDDP markers have not yet been used to study E. macrophylla.…”

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“…By amplifying these conserved sequences, which tend to be linked with phenotypic traits, CDDP can provide advantages in plant genetic diversity assessment (Andersen & Lübberstedt, 2003). Since Poczai first successfully used CDDP molecular markers and in-targeting markers to investigate the genetic diversity and group structure of Solanum dulcamara (Poczai et al, 2011), CDDP molecular markers have proven useful in the analysis of several other plant species, such as Chrysanthemum (Li et al, 2014), Paeonia suffruticosa (Li et al, 2013), Vaccinium vitis-idaea (Fang et al, 2016), and Rosa rugosa (Jiang et al, 2018). However, CDDP markers have not yet been used to study E. macrophylla.…”