Genetic diversity among germplasms of Diospyros kaki based on SSR markers

Liang, Yuqin; Han, Weijuan; Sun, Peng; Liang, Jinjun; Wuyun, Tana; Li, Fangdong; Fu, Jianmin

doi:10.1016/j.scienta.2015.02.015

Cited by 26 publications

(17 citation statements)

References 29 publications

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“…Phylogenetic trees reconstructed using different sequences indicated the closer relationship between D. kaki and D. oleifera . This finding is consistent with that of our previous study based on SSR and ITS regions ( S5 and S6 Figs) [ 71 , 72 ] and with that of a study investigating taxonomy based on morphology [ 73 ]. The morphological characteristics of D. oleifera are similar to those of D. kaki : both have pistillate flowers, styles that are parted, and branches without pellicle.…”

Section: Discussionsupporting

confidence: 93%

Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis

Liu

et al. 2016

PLoS ONE

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Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros ‘Jinzaoshi’ were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. ‘Jinzaoshi’, support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

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Section: Discussionsupporting

confidence: 93%

Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis

Liu

et al. 2016

PLoS ONE

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“…On the other hand, this indicated little or no location specificity among the torch ginger accessions. This finding also is in agreement with Distefano et al [56], Liang et al [57], and Wang et al [58] who studied genetic diversity on different crops using SSR markers. Distefano et al [56] suggested that the genetic variation not only relies on their geographical origin but also is likely the effect of human selection and distribution of the most valuable genotypes.…”

Section: Discussionsupporting

confidence: 92%

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

Ismail

Rafii

Mahmud

et al. 2019

BioMed Research International

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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.

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“…Many studies showed that capillary electrophoresis could provide more comprehensive and accurate information on length polymorphism and sequence polymorphism in DNA fragment polymorphism analysis than those provided by existing technologies. Liang et al (2015) reported that germplasm resources, genetic diversity, and relationships among 133 persimmon populations from China, Japan, and America were analysed using the capillary electrophoresis method, and in the process, 158 alleles and 610 genotypes from 17 SSR loci were obtained. In our study, the genetic diversity of these C. communis populations was analysed by capillary electrophoresis and 12 SSR primers with highly polymorphic, nuclear, singlelocus, and codominant makers were selected from 34 SSRs developed initially for C. communis to thoroughly assess the genetic diversity and population structure of the plants from different locations .…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and population structure of Commelina communis in China based on simple sequence repeat markers

Yang

et al. 2018

Journal of Integrative Agriculture

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Commelina communis (Asiatic dayflower) is a troublesome weed in China. Genetic variation of 46 C. communis populations from different collection sites in our country was investigated using 12 simple sequence repeat (SSR) primer pairs. Polymorphism analysis results showed high level of genetic diversity among these populations. The alleles (bands) were amplified by these primer pairs. The polymorphic proportion was 18.25%, and the average polymorphism information content was 0.1330. The highest effective number of alleles was 1.9915 at locus YP33, and the lowest value was 1.0000 at both loci YP25 and YP31. C. communis showed major average observed heterozygosity value (0.8655) than that of average expected heterozygosity (0.1330). C. communis populations were divided into three groups on the basis of unweighted pair-group method with arithmetic mean cluster analysis (Dice genetic similarity coefficient=0.772) and genetic structure analysis (K=3), and a principal coordinate analysis. The results of this study further illustrated that C. communis populations contained abundant genetic information, and the 12 SSR markers could detect the microsatellite loci of C. communis genomic DNA. These results might indicate that C. communis maintains high genetic diversity among different populations.

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Genetic diversity among germplasms of Diospyros kaki based on SSR markers

Cited by 26 publications

References 29 publications

Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis

Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis

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

Genetic diversity and population structure of Commelina communis in China based on simple sequence repeat markers

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