Genetic diversity of the endangered and medically important Lycium ruthenicum Murr. revealed by sequence-related amplified polymorphism (SRAP) markers

Liu, Zenggen; Shu, Qingyan; Wang, Lei; Yu, Minfeng; Yanping, Hu; Zhang, Huaigang; Tao, Yanduo; Shao, Yuchuan

doi:10.1016/j.bse.2012.07.017

Cited by 50 publications

(26 citation statements)

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“…For L. ruthenicum, the available molecular markers are insufficient, which makes it difficult to distinguish the individuals or populations of this genus. To date, the genetic diversity analysis of L. ruthenicum is restricted to sequence-related amplified polymorphism markers (Liu et al, 2012). EST sequences are important resources for the development of SSR markers.…”

Section: Establishment and Application Of Novel Microsatellite Markersmentioning

confidence: 99%

“…However, as an important traditional Chinese herbal plant with distinguished abiotic stress resistance, the Lycium genus is markedly less reported than other genera within the family. L. ruthenicum is widely distributed in the salinized and alkalinized desert of Northwest China (Liu et al, 2012), mainly in the Qinghai and Gansu Provinces and Xinjiang Uygur Autonomous Region of China. The species is often used for the treatment of heart disease, irregular menstruation, and menopause (Liu Y.L.…”

Section: Introductionmentioning

confidence: 99%

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Physiological characterization, transcriptomic profiling, and microsatellite marker mining of Lycium ruthenicum

Chen

Zhang

et al. 2017

J. Zhejiang Univ. Sci. B

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Lycium ruthenicum is a perennial shrub species that has attracted considerable interest in recent years owing to its nutritional value and ability to thrive in a harsh environment. However, only extremely limited transcriptomic and genomic data related to this species can be found in public databases, thereby limiting breeding research and molecular function analysis. In this study, we characterized the physiological and biochemical responses to salinealkaline mixed stress by measuring photochemical efficiency, chlorophyll content, and protective enzyme activity. We performed global transcriptomic profiling analysis using the Illumina platform. After optimizing the assembly, a total of 68 063 unique transcript sequences with an average length of 877 bp were obtained. Among these sequences, 4096 unigenes were upregulated and 4381 unigenes were down-regulated after saline-alkaline mixed treatment. The most abundant transcripts and over-represented items were assigned to gene ontology (GO) terms or Kyoto Encyclopedia of Genes and the Genomes (KEGG) categories for overall unigenes, and differentially expressed unigenes were analyzed in detail. Based on this set of RNA-sequencing data, a total of 9216 perfect potential simple sequence repeats (SSRs) were identified within 7940 unigenes with a frequency of 1/6.48 kb. A total of 77 primer pairs were synthesized and examined in wet-laboratory experiments, of which 68 loci (88.3%) were successfully amplified with specific products. Eleven pairs of polymorphic primers were verified in 225 individuals from nine populations. The inbreeding coefficient and the polymorphism information content value ranged from 0.011 to 0.179 and from 0.1112 to 0.6750, respectively. The observed and expected heterozygosities ranged from 0.064 to 0.840 and from 0.115 to 0.726, respectively. Nine populations were clustered into three groups based on a genetic diversity study using these novel markers. Our data will be useful for functional genomic investigations of L. ruthenicum and could be used as a basis for further research on the genetic diversity, genetic differentiation, and gene flow of L. ruthenicum and other closely related species.

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Section: Establishment and Application Of Novel Microsatellite Markersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Physiological characterization, transcriptomic profiling, and microsatellite marker mining of Lycium ruthenicum

Chen

Zhang

et al. 2017

J. Zhejiang Univ. Sci. B

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“…Molecular markers have been widely used to characterize the population genetic structures of plant species (Liu et al, 2012), and DNA-based markers have been particularly informative because, unlike morphological and biochemical markers, they are not prone to environmental influence. Random amplified polymorphic DNA (RAPD) is a useful method to determine several genetic parameters of rare and endangered plants, as it requires low amounts of plant tissue (Trindade et al, 2012) and obtains DNA fingerprints without accessing genome sequence information (Liu et al, 2012;Rodrigues et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

“…Random amplified polymorphic DNA (RAPD) is a useful method to determine several genetic parameters of rare and endangered plants, as it requires low amounts of plant tissue (Trindade et al, 2012) and obtains DNA fingerprints without accessing genome sequence information (Liu et al, 2012;Rodrigues et al, 2013). Despite its vulnerable status and scattered distribution, no investigation has been undertaken on G. microrrhynchum using molecular markers, except for the study by Chang et al (2005) using allozymes.…”

Section: Introductionmentioning

confidence: 99%

Conservation implications of the genetic diversity of Gymnospermium microrrhynchum in Korea

2016

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ABSTRACT. Gymnospermium microrrhynchum (Berberidaceae) is an ephemeral perennial herb with a limited distributional range in the Baekdudaegan mountain areas of the Korean Peninsula, and is designated a rare plant by the Korean Forest Service. Information about its genetic variation and structure is important for developing successful conservation strategies. To investigate the genetic variation within and among seven G. microrrhynchum populations, random amplified polymorphic DNA data were obtained for 207 individuals. The populations exhibited relatively low genetic diversity: the percentage of polymorphic bands (PPB) ranged from 32.1 to 66.7% (mean = 51.4%) and Nei's gene diversity (H E ) ranged from 0.116 to 0.248 (mean = 0.188). However, genetic diversity at the species level was relatively high (PPB = 98.7%, H E = 0.349). An analysis of molecular variance revealed high differentiation among populations (F ST = 0.6818), but the low gene flow value (N m = 0.117) suggests a low level of gene exchange occurs among populations. Principal coordinates analysis revealed that individuals were separated according to population. The high level of genetic differentiation and restricted gene flow among G. microrrhynchum populations, which resulted from their isolation in alpine areas after the Ice Age, indicates that it is essential to protect and manage all populations, rather than focus on specific populations, in order to maintain the genetic diversity of this species.

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“…Molecular markers have been widely used to characterize the genetic structure of plant populations (Liu et al, 2012). The random amplified polymorphic DNA (RAPD) method has some advantages, such as the high polymorphism generation and the fact that it does not require previous knowledge of the genome.…”

Section: Introductionmentioning

confidence: 99%

Genetic Variation of Paliurus Ramosissimus (Lour.) Poiret (Rhamnaceae): Implication for Conservation Strategies

Lee¹

2017

Appl Ecol Env Res

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Abstract. Paliurus ramosissimus (Rhamnaceae) is a deciduous shrub found on the seashore of Jeju Island, located at the southern tip of the Korean peninsula, and has been designated a rare plant species by the Korea Forest Service. Random amplified polymorphic DNA was used to investigate the genetic variation within and among P. ramosissimus populations on Jeju Island. Populations of P. ramosissimus showed a relatively low genetic diversity. The percentage of polymorphic bands (PPB) ranged from 33.3% to 63.6% (average = 51.4%), Shannon's information index (I) ranged from 0.213 to 0.352 (average = 0.316), and Nei's gene diversity (H) ranged from 0.149 to 0.239 (average = 0.218). Analysis of molecular variance and Nei's gene differentiation coefficient showed low genetic differentiation among populations (Φst = 0.207 and Gst = 0.186). The level of gene flow was sufficient to counter population divergence due to genetic drift (Nm = 0.109). Population genetic information obtained from this study could provide a valuable baseline for conservation and management plans for this species; P. ramosissimus on Jeju Island have to be protected through in situ conservation. The populations Pyo-sun and Il-gwua with high genetic diversity have conservation priority. In particular, Pyo-sun population protection must be the highest priority, as this population was revealed to have a high genetic diversity despite its small size.

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Genetic diversity of the endangered and medically important Lycium ruthenicum Murr. revealed by sequence-related amplified polymorphism (SRAP) markers

Cited by 50 publications

References 47 publications

Physiological characterization, transcriptomic profiling, and microsatellite marker mining of Lycium ruthenicum

Physiological characterization, transcriptomic profiling, and microsatellite marker mining of Lycium ruthenicum

Conservation implications of the genetic diversity of Gymnospermium microrrhynchum in Korea

Genetic Variation of Paliurus Ramosissimus (Lour.) Poiret (Rhamnaceae): Implication for Conservation Strategies

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