Understanding the genetic diversity and population structure of Dendrobium chrysotoxum Lindl.-An endangered medicinal orchid and implication for its conservation

Tikendra, Leimapokpam; Potshangbam, Angamba Meetei; Amom, Thoungamba; Dey, Abhijit; Nongdam, Potshangbam

doi:10.1016/j.sajb.2021.01.002

Cited by 21 publications

(4 citation statements)

References 88 publications

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“…Our estimates of number of migrants per generation ( Nm ) between populations throughout the region ranged from 0.229–1.080 and the mean was less than 1, suggesting that genetic divergence is marked and could become progressively entrenched ( Luo et al., 2019 ). However, whilst low compared with other similarly widespread (but more generalist) orchids ( Simmons et al., 2017 ; Tikendra et al., 2021 ), these values are comparable to or even higher than those calculated for several other terrestrial habitat specialists ( Rossetto et al., 2008 ; Mallet et al., 2014 ; Nistelberger et al., 2015 ; Lexer et al., 2016 ). Moreover, Nm estimates were significantly higher among populations belonging to each of the two genetic clusters ( Nm = 1.295 for HN group, Nm = 0.961 for IC group) than the mean for the species as a whole, suggesting greater gene flow at the scale of either landmass.…”

Section: Discussionsupporting

confidence: 47%

Exploring island syndromes: Variable matrix permeability in Phalaenopsis pulcherrima (Orchidaceae), a specialist lithophyte of tropical Asian inselbergs

Zhang

Li²,

Suddee³

et al. 2023

Front. Plant Sci.

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IntroductionPlants confined to island-like habitats are hypothesised to possess a suite of functional traits that promote on-spot persistence and recruitment, but this may come at the cost of broad-based colonising potential. Ecological functions that define this island syndrome are expected to generate a characteristic genetic signature. Here we examine genetic structuring in the orchid Phalaenopsis pulcherrima, a specialist lithophyte of tropical Asian inselbergs, both at the scale of individual outcrops and across much of its range in Indochina and on Hainan Island, to infer patterns of gene flow in the context of an exploration of island syndrome traits.MethodsWe sampled 323 individuals occurring in 20 populations on 15 widely scattered inselbergs, and quantified genetic diversity, isolation-by-distance and genetic structuring using 14 microsatellite markers. To incorporate a temporal dimension, we inferred historical demography and estimated direction of gene flow using Bayesian approaches.ResultsWe uncovered high genotypic diversity, high heterozygosity and low rates of inbreeding, as well as strong evidence for the occurrence of two genetic clusters, one comprising the populations of Hainan Island and the other those of mainland Indochina. Connectivity was greater within, rather than between the two clusters, with the former unequivocally supported as ancestral.DiscussionDespite a strong capacity for on-spot persistence conferred by clonality, incomplete self-sterility and an ability to utilize multiple magnet species for pollination, our data reveal that P. pulcherrima also possesses traits that promote landscape-scale gene flow, including deceptive pollination and wind-borne seed dispersal, generating an ecological profile that neither fully conforms to, nor fully contradicts, a putative island syndrome. A terrestrial matrix is shown to be significantly more permeable than open water, with the direction of historic gene flow indicating that island populations can serve as refugia for postglacial colonisation of continental landmasses by effective dispersers.

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Section: Discussionsupporting

confidence: 47%

Exploring island syndromes: Variable matrix permeability in Phalaenopsis pulcherrima (Orchidaceae), a specialist lithophyte of tropical Asian inselbergs

Zhang

Li²,

Suddee³

et al. 2023

Front. Plant Sci.

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“…Thus, the extensive use of neutral molecular markers targeting different regions is conducive to the comprehensive elucidation of plant genetic diversity and relationships ( Gogoi et al, 2020 ). To date, many applications combining multiple molecular marker techniques have been employed to evaluate the genetic diversity and genetic relationships of plants ( Antony et al, 2015 ; Thakur et al, 2021b ; Tikendra et al, 2021 ). The combination of 45 ISSR and SCoT primers produced a higher number of alleles (508) with an average of 69% and 78% (P), demonstrating the usefulness of the selected primers for identifying the genetic variability between the studied cultivars.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L

ALshamrani

Safhi²,

Alshaya³

et al. 2022

Front. Genet.

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The genetic diversity and the relationships among sesame cultivars were investigated using physiological and cyto/molecular analysis. To our information, no studies have yet been conducted on the genetic evaluation of sesame genotypes based on cyto/molecular analysis in Saudi Arabia. This study showed that genotype Bah-312 had the highest values from physiological and biochemical traits (plant height, harvest index, total plant dry matter, seed yield, oil content, and fatty acids content). Using 20 ISSR and 25 SCoT primers, the studied genotypes amplified 233 and 275 alleles, while the average polymorphism percentage (P%) was 65.32% (ISSR) and 77.8% (SCoT) across all the studied genotypes, respectively. To assess the markers efficiency analysis the polymorphism information contents (PIC), Marker Index (MI), Effective Multiplex Ratio (EMR), Resolving Power (Rp) were estimated. In general, primers (ISSR 2 & SCoT 21) and (ISSR 4 & SCoT 3) revealed the highest and lowest values for P %, PIC, MI, and EMR%. Furthermore, 188 positive and negative unique bands were detected, out of which ISSR generated 84, while 104 were amplified by SCoT analysis. In this regard, genotype Bah-312 generated 41 unique amplicons, and Jiz-511 genotype 23 unique amplicons. In the same context, the population genetics parameters, number of different alleles (Na), number of effective alleles (Ne), Shannon’s index (I), expected heterozygosity (He), and Unbiased Expected Heterozygosity (uHe), were calculated. ISSR marker showed the highest values for all the estimated parameters. In this regard, genotype Bah-312 exhibited the highest values (1.35, 1.37, 0.31, 0.21, 0.29) & (1.31, 1.35, 0.30, 0.20, 0.27) while, genotype Ahs-670 revealed the least values (1.29, 1.31, 0.26, 0.16, 0.23) &(1.14, 1.26, 0.22, 0.15, 0.20) for ISSR and SCoT markers respectively. For cytological data, according to the highest asymmetry index (AsK%) and lowest total form percentage (TF%) values, genotype Ahs-670 was the most advanced cultivar, and genotype Bah-312 was the most primitive one. According to the degree of asymmetry of karyotype (A) and intrachromosomal asymmetry index (A1), sesame genotype Ahs-670 was the most asymmetrical, and Bah-312 was the most symmetrical genotype. This study gives some helpful information about the genetic diversity of six sesame landraces. The variation harbored by these landraces could be used in sesame breeding programs.

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“…The population structure analysis showed that SCoT markers could not differentiate the two species of Tinospora from T. cordifolia accessions from Delhi, UP states. Similar studies with SCoT markers showed pure and admixture individuals in medicinal plants like Dendrobium and Crepidium with three (K = 3) and two (K = 2) populations, respectively [ 56 , 57 ]. AMOVA analysis showed a 4% variation among the population which was observed at 34% in Clerodendrum serratum [ 58 ].…”

Section: Discussionmentioning

confidence: 58%

Molecular Characterization of Tinospora cordifolia (Willd.) Miers Using Novel g-SSR Markers and Their Comparison with EST-SSR and SCoT Markers for Genetic Diversity Study

Paliwal

Singh

Choudhury

et al. 2022

Genes

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In the present study, novel genomic-SSR (g-SSR) markers generated in our laboratory were used to characterize Tinospora cordifolia and related species. The g-SSR marker was also compared with EST-SSR and SCoT markers used earlier in our laboratory to assess the genetic diversity of T. cordifolia. A total of 26 accessions of T. cordifolia and 1 accession each of Tinospora rumphii and Tinospora sinensis were characterized using 65 novel g-SSR markers. A total of 125 alleles were detected with 49 polymorphic g-SSR markers. The number of alleles per locus varied from 1–4 with a mean value of 2.55 alleles per locus. Mean PIC, gene diversity, and heterozygosity were estimated to be 0.33, 0.41, and 0.65, respectively. The two species, namely T. rumphii and T. sinensis, showed cross-species transferability of g-SSRs developed in T. cordifolia. The success rate of cross-species transferability in T. rumphii was 95.3% and 93.8% in T. sinensis, proving the usefulness of this marker in genetic diversity studies of related species. The Tinospora accessions were also used for molecular characterization using SCoT and EST-SSR markers and compared for genetic diversity and cross-species transferability. The PIC, gene diversity, heterozygosity, and principal coordinate analysis showed that g-SSR is the better maker for a genetic diversity study of T. cordifolia. Additionally, high cross-species transferability of g-SSRs was found (95.3% and 93.8%) compared to EST-SSRs (68.8% and 67.7%) in T. rumphii and T. sinensis, respectively.

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Understanding the genetic diversity and population structure of Dendrobium chrysotoxum Lindl.-An endangered medicinal orchid and implication for its conservation

Cited by 21 publications

References 88 publications

Exploring island syndromes: Variable matrix permeability in Phalaenopsis pulcherrima (Orchidaceae), a specialist lithophyte of tropical Asian inselbergs

Exploring island syndromes: Variable matrix permeability in Phalaenopsis pulcherrima (Orchidaceae), a specialist lithophyte of tropical Asian inselbergs

Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L

Molecular Characterization of Tinospora cordifolia (Willd.) Miers Using Novel g-SSR Markers and Their Comparison with EST-SSR and SCoT Markers for Genetic Diversity Study

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