Genetic diversity and population structure of Eucommia ulmoides Oliver, an endangered medicinal plant in China

Abstract

ABSTRACT. Eucommia ulmoides Oliver, one of the tertiary relict species found only in China, is the only extant species of Eucommiaceae. Using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers, we studied the genetic diversity and population genetic structure of 187 accessions from 17 E. ulmoides populations throughout its main distribution in China. A total of 65 bands were amplified using eight ISSR primers, of which 50 bands (76.9%) were polymorphic. Meanwhile, another 244 bands were observed using eight SRAP primer combinations and 163 (66.8%) of these were polymorphic. The analysis of molecular variation (AMOVA) indicated that 88.8 and 92.4% of the total variation resided within populations based on ISSR and SRAP analysis, respectively. Moreover, we found that the E. ulmoides populations were clustered into six distinct groups using ISSR and SRAP markers via the unweighted pair-group method (UPGMA). Furthermore, STRUCTURE analysis showed that these 17 populations could be classified into four groups using ISSR markers, but only two groups using SRAP markers. No 2471-2483 (2015) significant relevancy was observed between genetic and geographic distances among the sampled populations. The results of this study support the view that exchange of seeds among local farmers plays an important role in shaping the present genetic distribution pattern. "Core collection" is suggested for genetic diversity conservation of E. ulmoides in China.

Whole-Genome Comparison Reveals Heterogeneous Divergence and Mutation Hotspots in Chloroplast Genome of Eucommia ulmoides Oliver

“…The genetic markers of SSR, AFLP and SRAP have been developed and used for the population genetics studies of E. ulmoides [ 18 , 20 , 21 ]. However, the above fingerprinting markers [ 23 , 24 ] may provide insufficient genetic information to resolve the population structure and history of E. ulmoides . The relationships among natural and cultivated populations of E. ulmoides are elusive at present [ 18 , 24 ].…”

“…However, the above fingerprinting markers [ 23 , 24 ] may provide insufficient genetic information to resolve the population structure and history of E. ulmoides . The relationships among natural and cultivated populations of E. ulmoides are elusive at present [ 18 , 24 ]. SNP markers are ample in plant cp genomes, making them useful candidates for population genetics studies.…”

“…Amplified fragment length polymorphism (AFLP) and sequence-related amplified polymorphism (SRAP) have been used to construct genetic maps of E. ulmoides [ 20 , 21 ]. The genetic markers of random amplified polymorphic DNA (RAPD), chloroplast microsatellite (cpSSR) and inter-simple sequence repeat (ISSR) have also been uncovered [ 22 , 23 , 24 ]. Nevertheless, the variability of these developed fingerprinting markers in E. ulmoides is relatively low, with limited population genetics information.…”

Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses

“…In total 119,411 putative SNPs were detected in the gene regions with an average of one SNP per 980 bp, showing more than five folds higher of density than in the rubber tree ( H. brasiliensis ) gene regions (one SNP per 5.2 kb) [ 74 ]. The dioecious sexual system of E. ulmoides may be one of the factors contributing to the high level of its genetic diversity [ 73 , 75 ]. Furthermore, the plentiful SNP markers detected here could use to construct finer genetic maps of E. ulmoides compared to the previously published ones [ 76 , 77 ] to improve the molecular breeding process of E. ulmoides .…”

Analysis of chemotypes and their markers in leaves of core collections of Eucommia ulmoides using metabolomics

“…E. ulmoides was a monotypic species of Eucommiaceae. Germplasm genetic diversity of E. ulmoides had been evaluated by morphological traits, major active metabolites, and a number of molecular markers from RAPD to SNP ( Wu et al., 2011 ; Yao et al., 2012 ; Yu et al., 2015 ; Du et al., 2017 ; Liu et al., 2022 ). Most results tended to believe that the genetic diversity of E. ulmoides at the intra-population level was higher than at the inter-population level, and its genetic distance was not evidently correlated to geographical distribution.…”