Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species

Yang, Ying; Jing, Zhaobin; Ruan, Xiaofeng; Cheng, Jimin

doi:10.4238/2015.january.30.2

Cited by 12 publications

(15 citation statements)

References 22 publications

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“…The DNA evidences obtained in this study clearly support the previous taxonomic proposals that D. deyangensis and D. jinzaoshi should be raised to species rank based on morphological, molecular characteristics and chromosome numbers [ 4 , 9 – 12 ]. In the cpDNA–based tree, the D. kaki lineage and the lineage including the dioecious D. deyangensis and the monoecious D. oleifera shared a common furcation.…”

Section: Discussionsupporting

confidence: 87%

Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros

Li¹,

Liu

Yang

et al. 2018

BMC Plant Biol

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BackgroundFruits of persimmon plants are traditional healthy food in China, Korea and Japan. However, due to the shortage of morphological and DNA markers, the development of persimmon industry has been heavily inhibited.ResultsChloroplast genomes of Diospyros cathayensis, D. virginiana, D. rhombifolia and D. deyangensis were newly sequenced. Comparative analyses of ten chloroplast genomes including six previously published chloroplast genomes of Diospyros provided new insights into the genome sequence diversity and genomic resources of the genus. Eight hyper-variable regions, trnH-psbA, rps16-trnQ, rpoB-trnC, rps4-trnT-trnL, ndhF, ndhF-rpl32-trnL, ycf1a, and ycf1b, were discovered and can be used as chloroplast DNA markers at/above species levels. The complete chloroplast genome sequences provided the best resolution at inter-specific level in comparison with different chloroplast DNA sequence datasets.ConclusionDiospyros oleifera, D. deyangensis, D. virginiana, D. glaucifolia, D. lotus and D. jinzaoshi are important wild species closely related to the cultivated persimmon D. kaki. The hyper-variable regions can be used as DNA markers for global genetic diversity detection of Diospyros. Deeper study on these taxa would be helpful for elucidating the origin of D. kaki.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1421-3) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 87%

Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros

Li¹,

Liu

Yang

et al. 2018

BMC Plant Biol

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“…In their study, they used as many as 12 SSR primers from three pine species (Pinus densiflora, Pinus pinaster and Pinus taeda) to amplify Pinus merkusii DNA, but failed to produce polymorphic allele. In contrast to previous report by Yang et al (2015), 13 (93%) of 14 SSR primers from Diospyros kaki could amplify DNA from Diospyros glaucifolia, Diospyros lotus, Diospyros oleifera and Diospyros sp, and only primer mDP08 could not generate PCR-product in Diospyros glaucifolia.…”

Section: Resultscontrasting

confidence: 96%

Polymorphism of Simple Sequence Repeat Regions of Sulawesi Ebony (Diosphyros Celebica Bakh.) in Experimental Forest of Hasanuddin University Provenance

et al. 2016

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Polymerase Chain Reaction (PCR)-based molecular techniques have been used to detect the polymorphism in plants. The utilization of molecular markers plays essential role in germplasm characterization and plant breeding since the information of DNA marker technology can be exchanged between laboratories and should have standard method to be reproducible. The molecular aspect has been commonly linked to DNA isolation protocol and polymorphic molecular marker, thus can be used for molecular research recommendation purposes. The objectives of this study were to evaluate the capability of microsatellite marker of Ebenaceae Family for amplifying Ebony DNA, and to determine the appropriate PCR annealing temperatures. The DNA isolation of Ebony leaves from Experimental Forest of Hasanuddin University Provenance was carried out using Genomic DNA Mini Kit (Plant) Geneaid protocol. Nine of seventeen selected primers from the Genus Diospyros were able to amplify Ebony DNA. Amplification products produced polymorphic bands with different annealing temperatures (ranged from 53 to 56°C). These nine polymorphic primers will be recommended to use for future studies in genetic diversity as well as pollen dispersal pattern analyses.

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“…Microsatelite markers are co-dominant, highly polymorphic and easily reproducible [ 35 ]. They are important tools to examine genetic diversity, the assessment of genetic relationships and population genetic structure in plants [ 26 ].…”

Section: Discussionmentioning

confidence: 99%

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

et al. 2018

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BackgroundClematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their petals with different colors and shapes make the genus the “Queen of the Vines”. However, the genomic information and phylogeny of Clematis based on existing molecular studies are limited. In this paper, new microsatellites (SSR) markers were identified from the transcriptome data of C. finetiana obtained using the Illumina paired-end sequencing technology.ResultsSequences on a total of 71,900 high-quality unigenes with the mean length of 865 bp were produced in this study. There were 6192unigenes annotated and classified into 49 functional sub-groups in three main ontology categories in GO (Gen Ontology) database,14,022 unigenes mapped to COGs (Clusters of Orthologous Groups) database and classified into 25 functional categories, and 21,494 unigenes obtained and divided into 128 pathways of KEGG (Kyoto Encyclopedia of Genes) Database. A total of 7532 SSRs were discovered from 6337 unigenes. We randomly tested 210 primer pairs, of which 52 primer pairs were able to generate specific products, and 19 possessed polymorphism in the 13 wild populations of six species from Clematis, which were used as a test material.ConclusionsThe dataset of C. finetiana transcriptome and the identified new SSR markers will promote genetic research and breeding effort in Clematis.Electronic supplementary materialThe online version of this article (10.1186/s41065-018-0060-x) contains supplementary material, which is available to authorized users.

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Development of simple sequence repeat markers in persimmon (Diospyros L.) and their potential use in related species

Cited by 12 publications

References 22 publications

Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros

Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros

Polymorphism of Simple Sequence Repeat Regions of Sulawesi Ebony (Diosphyros Celebica Bakh.) in Experimental Forest of Hasanuddin University Provenance

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

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