Genetic diversity of <i>Herpetospermum caudigerum</i> (Ser.) Baill using AFLP and chloroplast microsatellites

Xu, Frank F.; Pei, Lei; Jiang, Mingquan; Sang, Liqun; Guan, Fang; Meng, Fanjuan; Hong, Quan

doi:10.1080/13102818.2019.1642798

Cited by 5 publications

(5 citation statements)

References 45 publications

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“…All these indices based on AFLP data indicated a very close sibship between J. regia and J. sigillata. Moreover, the parameter values for these two species were relatively high compared with Herpetospermum caudigerum (Na ¼ 1.352, Ne ¼ 1.188, H ¼ 0.111 and I ¼ 0.168) [12], comparable to that of Glehnia littoralis (Na ¼ 1.224, Ne ¼ 1.235, H ¼ 0.149, I ¼ 0.238) [11], but much lower Table 2. Summary of the AFLP markers scored for J. regia, J. sigillata and the hybrids using 9 primer combinations.…”

Section: Genetic Diversity Indicesmentioning

confidence: 89%

“…Genetic diversity and cultivar discrimination studies of non-wood-product forests are currently supported by molecular methods, such as molecular makers and genome sequencing [11]. Amplified fragment length polymorphism (AFLP) technique is a reliable genetic marker with low cost, superior repeatability and high resolution [12]. Thus, AFLP markers have been with broad application in systematics [13], genetic diversity [11,12,14], genetic linkage map construction [15] and association analysis [16] till now.…”

Section: Introductionmentioning

confidence: 99%

“…Amplified fragment length polymorphism (AFLP) technique is a reliable genetic marker with low cost, superior repeatability and high resolution [12]. Thus, AFLP markers have been with broad application in systematics [13], genetic diversity [11,12,14], genetic linkage map construction [15] and association analysis [16] till now. Here, 35 clonal cultivars selected from the main cultivating area in China were applied in AFLP analysis.…”

Section: Introductionmentioning

confidence: 99%

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Molecular genetic variability of Juglans regia L. and Juglans sigillata D. as revealed by fluorescent amplified-fragment length polymorphism

Zhang

Pei

2020

Biotechnology & Biotechnological Equipment

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Juglans regia L. and J. sigillata D. have a long cultivation history in China. With the purpose of detecting interspecific and intraspecific genetic variation, 35 clonal cultivars of J. regia, J. sigillata, J. sigillataÂJ. regia and J. hopeiensis Hu. (J. mandshurica Maxim. ÂJ. regia) were selected from a broad geographic range and applied in amplified-fragment length polymorphism (AFLP) analysis. Clear-cut AFLP profiles were produced using 9 EcoR I/Mse I primer combinations. As for J. regia, J. sigillata and their hybrids, the percentages of polymorphic bands (PPBs) averaged 93.86%, 93.94% and 60.46%; the observed number of alleles (Na) averaged 1.5370, 1.6389 and 1.2593; the effective number of alleles (Ne) averaged 1.2582, 1.2543 and 1.1646; Nei's gene diversity (H) scored 0.1560, 0.1556 and 0.0951; Shannon's information index (I) averaged 0.2402, 0.2459 and 0.1414, respectively. These results implied a moderate level of genetic diversity within the investigated species. The total gene diversity (H t ¼ 0.1596) can be distributed into intra-(H s ¼ 0.1356) and inter-(D st ¼ 0.0240) species gene diversity. The proportion of the distributed genetic diversity among populations (G st ) was 0.1505, indicating that only 15% of the total gene diversity was attributed to differences between species. The factorial correspondence analysis (FCA) and unweighted pair-group method of arithmetic averages (UPGMA) analysis revealed a close genetic distance between these two species.

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Section: Genetic Diversity Indicesmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular genetic variability of Juglans regia L. and Juglans sigillata D. as revealed by fluorescent amplified-fragment length polymorphism

Zhang

Pei

2020

Biotechnology & Biotechnological Equipment

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“…For all species, the most frequent motif type was mononucleotide, which is normally the most abundant repeat type in angiosperms chloroplast genomes 34 , 36 , 37 , 47 , 53 . Chloroplast microsatellites have been pointed out as highly informative regions, being useful for evolutionary, populational and genetic structure studies 54 – 56 .…”

Section: Discussionmentioning

confidence: 99%

Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily

Castro

Nunes

Carvalho

et al. 2023

Sci Rep

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Uncaria species are used in traditional medicine and are considered of high therapeutic value and economic importance. This work describes the assembly and annotation of the chloroplast genomes of U. guianensis and U. tomentosa, as well as a comparative analysis. The genomes were sequenced on MiSeq Illumina, assembled with NovoPlasty, and annotated using CHLOROBOX GeSeq. Addictionaly, comparative analysis were performed with six species from NCBI databases and primers were designed in Primer3 for hypervariable regions based on the consensus sequence of 16 species of the Rubiaceae family and validated on an in-silico PCR in OpenPrimeR. The genome size of U. guianensis and U. tomentosa was 155,505 bp and 156,390 bp, respectively. Both Species have 131 genes and GC content of 37.50%. The regions rpl32-ccsA, ycf1, and ndhF-ccsA showed the three highest values of nucleotide diversity within the species of the Rubiaceae family and within the Uncaria genus, these regions were trnH-psbA, psbM-trnY, and rps16-psbK. Our results indicates that the primer of the region ndhA had an amplification success for all species tested and can be promising for usage in the Rubiaceae family. The phylogenetic analysis recovered a congruent topology to APG IV. The gene content and the chloroplast genome structure of the analyzed species are conserved and most of the genes are under negative selection. We provide the cpDNA of Neotropical Uncaria species, an important genomic resource for evolutionary studies of the group.

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“…A total of 100 ISSR primers (University of British Columbia, Vancouver, BC, Canada) were tested with nine (UBC #808, #824, #827, #836, #841, #842, #847, #857, and #873) showing high reproducibility and accuracy selected for PCR amplification. The PCR reaction was performed as described in literature with a minor modification [36]. The optimal reaction condition of ISSR-PCR amplification contained 2.5 µL template DNA, 2 µL 10× PCR buffer, 1.5 µL dNTPs, 0.2 µL Taq polymerase, 0.5 µL primer, 13.3 µL ddH 2 O to make the total volume of 20 µL.…”

Section: Pcr Amplification Of Issr Markermentioning

confidence: 99%

Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

et al. 2021

Self Cite

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Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

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Genetic diversity of Herpetospermum caudigerum (Ser.) Baill using AFLP and chloroplast microsatellites

Cited by 5 publications

References 45 publications

Molecular genetic variability of Juglans regia L. and Juglans sigillata D. as revealed by fluorescent amplified-fragment length polymorphism

Molecular genetic variability of Juglans regia L. and Juglans sigillata D. as revealed by fluorescent amplified-fragment length polymorphism

Chloroplast genome characterization of Uncaria guianensis and Uncaria tomentosa and evolutive dynamics of the Cinchonoideae subfamily

Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

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