High Levels of Genetic Diversity within One Population of Rheum tanguticum on the Qinghai-Tibet Plateau have Implications for Germplasm Conservation

Ma, Xiaochong; Xie, Chao; Guan, Meng; Xu, Xiuhai; Miki, Eiji; Takeda, O.; Xin, Tianyi; Zheng, Shu-Jian; Yao, Hui; Shi, Linchun; Song, Jingyuan; Chen, Shilin

doi:10.2174/2210290601405010001

Cited by 8 publications

(3 citation statements)

References 38 publications

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“…Although “pollen limitation” was invoked by Yan et al [30] to explain the low levels of genetic variation they observed in R. sachalinensis populations, recent studies have demonstrated that bumblebees play a positive role in pollen dispersal of alpine plants [33] , [34] . These characteristics, i.e., a dual reproductive system and pollen dispersal, can be viewed as a strategy for maximal heterozygosity and reproductive success, and are common in alpine plants exposed to such drastic environments [35] , [36] .…”

Section: Discussionmentioning

confidence: 99%

Genetic, Epigenetic, and HPLC Fingerprint Differentiation between Natural and Ex Situ Populations of Rhodiola sachalinensis from Changbai Mountain, China

Zhao

Shi

et al. 2014

PLoS ONE

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Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = –0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.

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Section: Discussionmentioning

confidence: 99%

Genetic, Epigenetic, and HPLC Fingerprint Differentiation between Natural and Ex Situ Populations of Rhodiola sachalinensis from Changbai Mountain, China

Zhao

Shi

et al. 2014

PLoS ONE

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“…Contigs were compared using the MUSCLE multiple sequence alignment algorithms supplemented with the CodonCode Aligner. Genetic variations were analyzed with a Kimura 2-parameter distance matrix, which was constructed using MEGA5.0 software (Ma et al 2014 ) and ClustalW (Sun and Chen 2013 ). A phylogenetic tree was created using the NJ method.…”

Section: Methodsmentioning

confidence: 99%

Differentiation of the Chinese minority medicinal plant genus Berchemia spp. by evaluating three candidate barcodes

et al. 2016

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The genus Berchemia comprises important Chinese plants with considerable medicinal value; however, these plants are often misidentified in the herbal medicinal market. To differentiate the various morphotypes of Berchemia species, a proficient method employing the screening of universal DNA barcodes was used in this work. Three candidate barcoding loci, namely, psbA-trnH, rbcL, and the second internal transcribed spacer (ITS2), were used to identify an effective DNA barcode that can differentiate the various Berchemia species. Additionally, PCR amplification, efficient sequencing, intra- and inter-specific divergences, and DNA barcoding gaps were employed to assess the ability of each barcode to identify these diverse Berchemia plants authentically; the species were differentiated using the Kimura two-parameter and maximum composite likelihood methods. Sequence data analysis showed that the ITS2 region was the most suitable candidate barcode and exhibited the highest interspecific divergence among the three DNA-barcoding sequences. A clear differentiation was observed at the species level, in which a maximum distance of 0.264 was exhibited between dissimilar species. Clustal analysis also demonstrated that ITS2 clearly differentiated the test species in a more effective manner than that with the two other barcodes at both the hybrid and variety levels. Results indicate that DNA barcoding is ideal for species-level identification of Berchemia and provides a foundation for further identification at the molecular level of other Rhamnaceae medicinal plants.

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“…However, two barcodes are not precise enough because of the low identification rate [ 22 , 23 ]. The psbA - trnH , ITS, and ITS2 were subsequently suggested [ 23 – 25 ]. Additionally, the amplification efficiency of ITS is lower than that of ITS2, because of the multiple functional copies exist in many taxa [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of Hippophae species (Shaji) through DNA barcodes

et al. 2015

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BackgroundThe morphological identification of different Hippophae species (Shaji) was difficult. This study aims to discriminate between medicinal and non-medicinal Hippophae species by DNA barcodes, the ITS2, psbA-trnH, and a combination of ITS2 and psbA-trnH (ITS2 + psbA-trnH).MethodsDNA was extracted from the dried fruit samples. Primer pairs ITS2F/3R for ITS2 and psbAF/trnHR for psbA-trnH were used for PCR amplification. The purified PCR products were bidirectionally sequenced. Genetic distances were calculated according to the Kimura 2 parameter model and phylogenetic tree was constructed based on neighbor-joining (NJ) method, barcoding gap was also analyzed to assess identification efficiency.ResultsAmplification and sequencing efficiencies for both ITS2 and psbA-trnH were 100 %. Sequence data revealed that ITS2 + psbA-trnH was the most suitable candidate barcode at the species and subspecies level. The closely related Hippophae species were effectively differentiated in the NJ tree.ConclusionThe combination of the two loci, ITS2 + psbA-trnH is applicable to the identification of medicinal and non-medicinal Hippophae species.

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High Levels of Genetic Diversity within One Population of Rheum tanguticum on the Qinghai-Tibet Plateau have Implications for Germplasm Conservation

Cited by 8 publications

References 38 publications

Genetic, Epigenetic, and HPLC Fingerprint Differentiation between Natural and Ex Situ Populations of Rhodiola sachalinensis from Changbai Mountain, China

Genetic, Epigenetic, and HPLC Fingerprint Differentiation between Natural and Ex Situ Populations of Rhodiola sachalinensis from Changbai Mountain, China

Differentiation of the Chinese minority medicinal plant genus Berchemia spp. by evaluating three candidate barcodes

Identification of Hippophae species (Shaji) through DNA barcodes

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