Genetic diversity and population structure of the medicinal plant Docynia delavayi (Franch.) Schneid revealed by transcriptome-based SSR markers

Peng, Jingyu; Chen, Shi; Wang, Dawei; Shuang-zhi, LI; Zhao, Xin; Duan, Anan; Cai, Na; He, Chengzhong

doi:10.1016/j.jarmap.2021.100294

Cited by 12 publications

(11 citation statements)

References 45 publications

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“…In this study, we explored the G. uralensis genetic diversity and observed that the Ho and He for G. uralensis ranged between 0.492-0.436 and 0.324-0.3, respectively (Supplementary Table 4). These Ho and He values were relatively low compared to other Chinese herbal medicines, including Epimedium (Zhou et al, 2010), Himatanthus drasticus (Baldauf et al, 2011), and Docynia delavayi (Peng et al, 2021). According to previous reports, species with a narrow or endemic distribution reportedly maintained lower genetic diversity than those with a broader distribution (Hamrick and Godt, 1996), which is in line with the current study.…”

Section: Genomic Differentiation Of G Uralensis Populationsupporting

confidence: 90%

Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis

Dang

Zhang

et al. 2022

Front. Plant Sci.

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Glycyrrhiza uralensis is a valuable medicinal legume, which occurs widely in arid and semi-arid regions. G. uralensis demand has risen steeply due to its high medical and commercial value. Interpret genome-wide information can stimulate the G. uralensis development as far as its increased bioactive compound levels, and plant yield are concerned. In this study, leaf nutrient concentration and photosynthetic chlorophyll index of G. uralensis were evaluated to determine the G. uralensis growth physiology in three habitats. We observed that G. uralensis nutrient levels and photosynthesis differed significantly in three regions (p < 0.05). Whole-genome re-sequencing of the sixty G. uralensis populations samples from different habitats was performed using an Illumina HiSeq sequencing platform to elucidate the distribution patterns, population evolution, and genetic diversity of G. uralensis. 150.06 Gb high-quality clean data was obtained after strict filtering. The 895237686 reads were mapped against the reference genome, with an average 89.7% mapping rate and 87.02% average sample coverage rate. A total of 6985987 SNPs were identified, and 117970 high-quality SNPs were obtained after filtering, which were subjected to subsequent analysis. Principal component analysis (PCA) based on interindividual SNPs and phylogenetic analysis based on interindividual SNPs showed that the G. uralensis samples could be categorized into central, southern, and eastern populations, which reflected strong genetic differentiation due to long periods of geographic isolation. In this study, a total of 131 candidate regions were screened, and 145 candidate genes (such as Glyur001802s00036258, Glyur003702s00044485, Glyur001802s00036257, Glyur007364s00047495, Glyur000028s00003476, and Glyur000398s00034457) were identified by selective clearance analysis based on Fst and θπ values. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed significant enrichment of 110 GO terms including carbohydrate metabolic process, carbohydrate biosynthetic process, carbohydrate derivative biosynthetic process, and glucose catabolic process (p < 0.05). Alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways were significantly enriched (p < 0.05). This study provides information on the genetic diversity, genetic structure, and population adaptability of the medicinal legumes, G. uralensis. The data obtained in this study provide valuable information for plant development and future optimization of breeding programs for functional genes.

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Section: Genomic Differentiation Of G Uralensis Populationsupporting

confidence: 90%

Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis

Dang

Zhang

et al. 2022

Front. Plant Sci.

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“…Reports around the globe suggested that the EST-SSR primers show less polymorphism than genomic SSRs in crop plants due to larger sequence conservation in transcribed regions ( Varshney et al., 2005 ). Our result of PIC was lower than Coriandrum sativum (0.38) ( Tulsani et al., 2019 ) Docynia delavayi (0.587) ( Peng et al., 2021 ), Ginkgo biloba (0.781) ( Zhou et al., 2019 ), and Quercus petraea (0.787) ( Lupini et al., 2019 ) identified with EST-SSR markers. The moderate estimates of PIC might be due to the development of SSRs from the metabolic pathway-specific, highly conserved transcribed region of kalmegh.…”

Section: Discussioncontrasting

confidence: 67%

Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh (Andrographis paniculata (Burm. f.) Nee)

et al. 2022

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Andrographis paniculata, commonly known as kalmegh is among the most popular medicinal herbs in Southeast Asia. It is widely cultivated for medicinal purposes. The bioactive molecule, Andrographolide accumulated in herb leaves has immense therapeutic and economic potential. However, comprehensive information regarding genetic diversity is very limited in this species. The present study assessed genetic diversity between and within the six populations (ecotypes) of twenty-four kalmegh accessions using multiple datasets (agro-morphological traits, phytochemical traits, and genic markers). This is the established report where EST-SSR (Expressed sequence tags-Simple Sequence Repeat) markers have been used to unlock genetic variation in kalmegh. Here, we identified and developed ninety-one metabolic pathway-specific EST-SSR markers. Finally, 32 random EST-SSR primer pairs were selected for genetic diversity assessment. Multivariate analysis to unveil the agro-morphological, phytochemical and genotypic variability was helpful in discriminating various germplasms studied in the present study. Among all the morphological discriptors used in present study, days to fifty percent flowering and dry herb yield were found as potential selection index for AP genetic improvement. Hierarchical cluster analysis built with agro-morphological data identified three major groups. However, corresponding analysis with phytochemical and molecular data generated two clear-cut groups among the studied individuals. Moreover, the grouping of individuals into different clusters using multiple datasets was geographically independent, and also showed inconsistency in grouping among agromorphological, phytochemical and molecular dataset based clusters. However, joint analysis using agro-morphological, phytochemical and genotypic information generated two genetic groups, which could be a valuable resource for identifying complementary crossing panels in the kalmegh breeding program. The accessions AP7, AP13, AP5, AP3 belong to cluster I and accessions AP17, AP18 belong to cluster II could be utilized as potential donors for high dry herb yield and andrographolide content, respectively in different selective breeding programs of AP. Thus, our results provided useful information about the overall genetic diversity and variation in economic traits useful for initiating selective breeding programs for contrasting traits of interest and maximizing genetic gain in kalmegh.

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“…All 10 transferable SSR primers used in the present study deviated significantly from the HWE ( p < 0.01), which might reflect that the samples were collected from natural populations affected by complex environmental factors and human activities ( Wang and Shete, 2012 ; Peng et al, 2021 ). The investigation found that E. stauntonii mainly resided beside rivers and valleys at lower altitudes, and its living environment was easily disturbed by tourism, grazing, and farmland planting.…”

Section: Discussionmentioning

confidence: 76%

“…In the current study, gene flow of E. stauntonii ( N m = 1.252) was moderately low, lower than that reported for Eragrostis tef ( N m = 4.742) ( Tadesse et al, 2021 ) and Mucuna pruriens ( N m = 7.48) ( Lepcha and Sathyanarayana, 2021 ), but it was consistent with the high genetic differentiation ( F st = 0.181) ( Balloux and Lugon-Moulin, 2002 ). The low gene flow, which might be caused by the small sampling range and habitat fragmentation, increased the within-population genetic variation and promoted population differentiation ( Young et al, 1996 ; Li et al, 2014 ; Peng et al, 2021 ). Notably, among the 18 populations, the greatest genetic differentiation was observed between the CX and ZQ populations, which may be considered as potential parents for hybrid breeding.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

et al. 2022

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Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (NA), expected heterozygosity (HE), and Shannon’s information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (Nm = 1.252) and high genetic differentiation (Fst = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.

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Genetic diversity and population structure of the medicinal plant Docynia delavayi (Franch.) Schneid revealed by transcriptome-based SSR markers

Cited by 12 publications

References 45 publications

Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis

Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis

Maximizing genetic gain through unlocking genetic variation in different ecotypes of kalmegh (Andrographis paniculata (Burm. f.) Nee)

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

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