scholarly journals Genetic Diversity and Variety Identification of Panax Species Based on EST-SSR Markers

2021 ◽  
Author(s):  
xin-yuan fan ◽  
He-tong Hui ◽  
Tian-qi Wang ◽  
Ming-hui Wang ◽  
Mo-Yi Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Panax Ginseng ◽  
Ssr Markers ◽  
Economic Value ◽  
Plant Morphology ◽  
Panax Notoginseng ◽  
Variety Identification ◽  
Panax Quinquefolium ◽  
Wild Ginseng

Abstract Background: The roots of Panax species are widely used in the East because of their high medicinal and economic value. They are similar in plant morphology and chemical composition, but have quite differences in medicinal properties and efficacy, therefore, genetic diversity and variety identification of Panax species is particularly important. Methods: We screened 7 Simple Sequence Repeat (SSR) markers from expressed sequence tags (ESTs) database of Panax species in NCBI. Using these markers test SSR polymorphism in Panax species. Results: Seven SSR markers could successfully identify Panax ginseng, Panax quinquefolium, Panax notoginseng, and their commercial products. Among three ginseng varieties, garden ginseng, forest ginseng, and wild ginseng, the polymorphism of EST-SSR markers decreased gradually, which may be related to age and environment. Two pairs of EST-SSR primers can specifically identify three ginseng cultivars. The phylogenetic relationships analysis showed that Panax ginseng and Panax quinquefolium were closer than Panax notoginseng. Compared with wild ginseng, the relationship between the garden ginseng and the forest ginseng was closer. Conclusion: SSR molecular markers have high repeatability and can be used as reliable molecular markers for genetic diversity and variety identification of Panax species.

EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences

2018 ◽  
Vol 17 (03) ◽  
pp. 280-284 ◽  
Author(s):  
Katina F. Olodo ◽  
Mame C. Gueye ◽  
Caroline Calatayud ◽  
Baye M. Diop ◽  
Ndjido A. Kane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
West Africa ◽  
Ssr Markers ◽  
Related Species ◽  
Evolutionary History ◽  
Genetic Difference ◽  
Transcriptome Sequences ◽  
Ssr Development ◽  
Digitaria Exilis

AbstractDigitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

scholarly journals Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

2022 ◽  
Author(s):  
Huiling Wang ◽  
Kuan Yang ◽  
Liwei Guo ◽  
Lifen Luo ◽  
Chi He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Yunnan Province ◽  
Polymorphic Information Content ◽  
Polyacrylamide Gel Electrophoresis ◽  
Panax Notoginseng ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

Establishment of an effective set of simple sequence repeat markers for sunflower variety identification and diversity assessment

2005 ◽  
Vol 83 (1) ◽  
pp. 66-72 ◽  
Author(s):  
L S Zhang ◽  
V Le Clerc ◽  
S Li ◽  
D Zhang
Keyword(s):  
Genetic Diversity ◽  
Helianthus Annuus ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Inbred Lines ◽  
Variety Identification ◽  
Large Set ◽  
Sequence Repeat ◽  
Diversity Assessment ◽  
Simple Sequence

The objective of this study was to identify an efficient set of simple sequence repeat (SSR) markers for sunflower (Helianthus annuus L.) variety fingerprinting, relying on semi-automated analysis conditions. Based on criteria such as quality of amplification products, co-dominant and single locus, 78 SSR markers were selected and used to assess the genetic variability among a large set of 124 sunflower inbred lines, including 67 female maintainers (M lines) and 57 male restorers (R lines). They revealed a total of 276 alleles across the 124 elite inbred lines, with a mean of 3.5 alleles per SSR locus. The polymorphism index content per locus varied from 0.06 to 0.81, with an average of 0.51. Relationships among the inbred lines were studied using estimations of Rogers' distances. The great majority of the distance estimates ranged between 0.4 and 0.6, but distances between some pairs of lines were less than 0.1. The genetic diversity value was similar within each subset of R and M lines and low, but significant differentiation was found (GST = 0.049) between the two pools. The selected set of SSRs proved to be useful both for sunflower fingerprinting and genetic diversity assessment.Key words: genetic diversity, genotyping, Helianthus annuus, multiplex PCR, simple sequence repeats (SSR).

scholarly journals Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Nor Asiah Ismail ◽  
M. Y. Rafii ◽  
T. M. M. Mahmud ◽  
M. M. Hanafi ◽  
Gous Miah
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Peninsular Malaysia ◽  
Molecular Characteristics ◽  
Etlingera Elatior

Fifty-seven accessions of torch ginger (Etlingera elatior) collected from seven states in Peninsular Malaysia were evaluated for their molecular characteristics using ISSR and SSR markers to assess the pattern of genetic diversity and association among the characteristics. Diversity study through molecular characterization showed that high variability existed among the 57 torch ginger accessions. ISSR and SSR molecular markers revealed the presence of high genetic variability among the torch ginger accessions. The combination of different molecular markers offered reliable and convincing information about the genetic diversity of torch ginger germplasm. This study found that SSR marker was more informative compared to ISSR marker in determination of gene diversity, polymorphic information content (PIC), and heterozygosity in this population. SSR also revealed high ability in evaluating diversity levels, genetic structure, and relationships of torch ginger due to their codominance and rich allelic diversity. High level of genetic diversity discovered by SSR markers showed the effectiveness of this marker to detect the polymorphism in this germplasm collection.

scholarly journals High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in Capsicum frutescens

Horticulturae ◽  
2021 ◽  
Vol 7 (7) ◽  
pp. 187
Author(s):  
Yangmin Zhong ◽  
Yuan Cheng ◽  
Meiying Ruan ◽  
Qingjing Ye ◽  
Rongqing Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Capsicum Frutescens ◽  
Next Generation Sequencing Technology ◽  
High Productivity ◽  
Ssr Primers ◽  
Pepper Genome ◽  
Plant Pathogenesis ◽  
Insight Into

Capsicum frutescens, one of the domesticated species of pepper grown worldwide, is thought to be highly advantageous due to its strong resistance against plant pathogenesis, high productivity, and intense aroma. However, a shortage of molecular markers limits the efficiency and accuracy of genetic breeding for pepper. With the newly developed next-generation sequencing technology, genome sequences of C. frutescens can be generated, which are now available for identifying SSR markers via data mining. In this study, a total of 278,425 SSRs were detected from the pepper genome using MISA software. It was observed that trinucleotides were the dominant repeat motif. This was followed by dinucleotides, tetranucleotides, pentanucleotides, and the hexanucleotides repeat types. (AT)n (TTG)n (AAAT)n (AAATA)n (TATAGA)n is known to be the most common repeat motifs corresponding to dinucleotide to hexanucleotide repeats, respectively. In addition, a total of 240 SSR primers evenly distributed over all 12 chromosomes were designed and screened against 8 C. frutescens cultivars. Of these, 33 SSR markers that have high polymorphism, have been scrutinized for 147 accessions from 25 countries. The dendrogram constructed clustered these accessions into seven major groups. The groups were found to be consistent with their origins. The results obtained in this study provided resources of SSR molecular markers and insight into genetic diversity of the C. frutescens.

Antiplatelet and anticoagulant effects of Panax notoginseng: Comparison of raw and steamed Panax notoginseng with Panax ginseng and Panax quinquefolium

2009 ◽  
Vol 125 (3) ◽  
pp. 380-386 ◽  
Author(s):  
Aik-Jiang Lau ◽  
Ding-Fung Toh ◽  
Tung-Kian Chua ◽  
Yun-Keng Pang ◽  
Soo-On Woo ◽  
...  
Keyword(s):  
Panax Ginseng ◽  
Panax Notoginseng ◽  
Panax Quinquefolium

scholarly journals Use of Molecular Markers to Assist the Development of Inbred Lines under Open Field Conditions: the Case of Criollo Peppers (Capsicum annuum L.) from Mexico

2017 ◽  
Vol 45 (2) ◽  
pp. 365-368
Author(s):  
Leandro PEREIRA-DIAS ◽  
Gustavo CHÁVEZ-GONZÁLEZ ◽  
Miguel BRACHO-GIL ◽  
Ana M. FITA ◽  
Santiago VILANOVA ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Molecular Markers ◽  
Capsicum Annuum ◽  
Open Field ◽  
Ssr Markers ◽  
Inbred Lines ◽  
Open Pollination ◽  
Adaptation To Climate Change ◽  
Chile Peppers

Chile peppers are one of the most important crops in Mexico and a plethora of ecotypes can be found there. Most of them are ancient open-pollinated (OP) landraces selected by farmers for uniform phenotype but with an inherent level of genetic diversity, called criollos. In this work 15 pepper accessions, encompassing 2 criollo lines, their open-pollinated progenies, and 5 controls, were characterized with a set of 36 IPGRI descriptors and 23 SSR markers to assess the effect of open pollination in the inbreeding process. Heterozygosity levels were comprised between 12 and 47% in the progenies, which were similar or lower than those values from parent plants and similar or higher than control cultivars. Also, both progenies and parents showed similar levels of agronomic and morphological uniformity. Our results suggest that this OP program is efficient in terms of reaching enough agronomic uniformity in criollo Ancho peppers while preserving certain genetic diversity to confer adaptation to climate change.

scholarly journals Genetic diversity and population structure of Vernonia [Vernonia galamensis (Cass.) Less] populations from Ethiopia revealed by SSR markers

2020 ◽  
Author(s):  
Alemneh Mideksa Egu ◽  
Kassahun Tesfaye ◽  
Kifle Dagne New ◽  
Xuebo Hu New
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
In Situ Conservation ◽  
Germplasm Conservation ◽  
Pharmaceutical Products ◽  
Gene Pools ◽  
Vernonia Galamensis ◽  
Diversity Assessment

Abstract Background: Vernonia (Vernonia galamensis) is a potential novel industrial crop due to high demand for its natural epoxidized oil, which can be used for the manufacturing of oleochemicals such as paints, plastic formulations (polyvinyl chloride), and pharmaceutical products. This study was initiated for the systematic and intensive genetic diversity assessment of V. galamensis accessions by SSR molecular markers to minimize the existing research gaps, provide a clue for germplasm conservation and further research. Results: Twenty SSR markers were used for genetic diversity analyses of 150 individual V. galamensis accessions representing 10 populations, from which a total of 79 bands were identified for the 20 loci. All the loci used showed high polymorphism that ranged from 0.50 to 0.96, while the mean observed heterozygosity (Ho) was 0.15 across all the 20 markers evaluated. The molecular variance analysis (AMOVA) showed significant variations among populations which accounted for 11% of the variations. Populations clustering showed that the dendrogram and principal coordinate’s analysis roughly classified the accessions into four groups. However, the Bayesian model-based clustering (STRUCTURE) grouped into 6 (K = 6) major gene pools. Since, the cluster and the STRUCTURE analyses did not group the populations into sharply distinct clusters, due to presence of gene flow and mode of reproduction of the plant. Conclusions: The SSR molecular markers used in this study are highly polymorphic. Among the ten populations, East Showa and East Hararghe revealed higher genetic diversity, signaled that these areas are the hotspots for in-situ conservation of V. galamensis. In addition, the values of SSR markers such as heterozygosity, Shannon‘s index, polymorphic information content, and population clusters are important baseline information for future V. galamensis cultivation, breeding and genetic resource conservation endeavors in Ethiopia.

Sign in / Sign up

Export Citation Format

Share Document