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Identification of Indica-Japonica Subspecies Rice by Duplex Fluorescence PCR Detection for Chloroplast DNA and Endogenous gos Gene

Received: 17 August 2021     Accepted: 6 September 2021     Published: 23 September 2021
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Abstract

Asia cultivated rice are classified into two subspecies, indica and japonica rice (hsien and keng rice called in China, separately). It is necessary to establish a convenient and effective method to identify two subspecies because of the different quality characteristics between the rice products of them, which lead to different processing uses and commodity values. The identification method of PCR based on the difference of chloroplast DNA is convenient and effective, to be attempted to establish. Based on 69 bp fragment deletion of chloroplast DNA (cpDNA) found in ORF100 region nucleotides within the cpDNA Pst I-12 fragment in indica rice but not in japonica, the primer pair and a probe located on the specific cpDNA fragment in japonica rice were designed to identify indica and japonica rice. Another primer pair and probe used to detect endogenous gene gos in rice were combined with above primer pair and probe for detecting cpDNA to establish duplex fluorescence PCR to amplify cpDNA and gos gene for improving detection accuracy, to avoid the false negative results caused by DNA extraction error. The duplex fluorescence PCR detection method was established using typical japonica rice (pearl rice) and typical indica rice (Taixian 11). The accuracy of the method was validated with 547 samples including 177 samples of rice seed and eaten rice known as conventional japonica varieties and japonica type hybrid combinations and 370 samples of rice seed and eaten rice known as conventional indica rice varieties and indica type hybrid combinations. In 177 japonica samples, 170 samples with both positive results of cpDNA marker and gos gene, a coincidence rate of 96.05% agreement japonica rice, and 7 samples with positive results of gos gene and negative of cpDNA marker, not agreement japonica rice with non-coincidence rate of 3.95%, were detected. Of the 370 samples of indica rice seed and eaten rice, with positive results of gos gene and negative of cpDNA marker were detected in 340 samples, the rate of coincidence to indica rice was 91.89%. Other 30 samples with both positive results of cpDNA marker and gos gene, were detected, and the non-coincidence rate with indica rice was 8.11%. These identification results were in good agreement with known indica and japonica varieties, and the coincidence rate of japonica varieties was higher than indica. This method can be used to identify indica and japonica subspecies rice, especially suitable to identify conventional rice varieties.

Published in International Journal of Nutrition and Food Sciences (Volume 10, Issue 5)
DOI 10.11648/j.ijnfs.20211005.12
Page(s) 101-107
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2021. Published by Science Publishing Group

Keywords

Indica (hsien) Rice Seed/Eaten Rice, japonica (keng) Rice/Eaten Rice, Chloroplast DNA (cpDNA), Endogenous gos Gene, Duplex Fluorescence PCR, Identification

References
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    Biying Shao, Tingyu Miao, Juan Peng, Bin Chen, Wenbing Chen. (2021). Identification of Indica-Japonica Subspecies Rice by Duplex Fluorescence PCR Detection for Chloroplast DNA and Endogenous gos Gene. International Journal of Nutrition and Food Sciences, 10(5), 101-107. https://doi.org/10.11648/j.ijnfs.20211005.12

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    Biying Shao; Tingyu Miao; Juan Peng; Bin Chen; Wenbing Chen. Identification of Indica-Japonica Subspecies Rice by Duplex Fluorescence PCR Detection for Chloroplast DNA and Endogenous gos Gene. Int. J. Nutr. Food Sci. 2021, 10(5), 101-107. doi: 10.11648/j.ijnfs.20211005.12

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    AMA Style

    Biying Shao, Tingyu Miao, Juan Peng, Bin Chen, Wenbing Chen. Identification of Indica-Japonica Subspecies Rice by Duplex Fluorescence PCR Detection for Chloroplast DNA and Endogenous gos Gene. Int J Nutr Food Sci. 2021;10(5):101-107. doi: 10.11648/j.ijnfs.20211005.12

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  • @article{10.11648/j.ijnfs.20211005.12,
      author = {Biying Shao and Tingyu Miao and Juan Peng and Bin Chen and Wenbing Chen},
      title = {Identification of Indica-Japonica Subspecies Rice by Duplex Fluorescence PCR Detection for Chloroplast DNA and Endogenous gos Gene},
      journal = {International Journal of Nutrition and Food Sciences},
      volume = {10},
      number = {5},
      pages = {101-107},
      doi = {10.11648/j.ijnfs.20211005.12},
      url = {https://doi.org/10.11648/j.ijnfs.20211005.12},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijnfs.20211005.12},
      abstract = {Asia cultivated rice are classified into two subspecies, indica and japonica rice (hsien and keng rice called in China, separately). It is necessary to establish a convenient and effective method to identify two subspecies because of the different quality characteristics between the rice products of them, which lead to different processing uses and commodity values. The identification method of PCR based on the difference of chloroplast DNA is convenient and effective, to be attempted to establish. Based on 69 bp fragment deletion of chloroplast DNA (cpDNA) found in ORF100 region nucleotides within the cpDNA Pst I-12 fragment in indica rice but not in japonica, the primer pair and a probe located on the specific cpDNA fragment in japonica rice were designed to identify indica and japonica rice. Another primer pair and probe used to detect endogenous gene gos in rice were combined with above primer pair and probe for detecting cpDNA to establish duplex fluorescence PCR to amplify cpDNA and gos gene for improving detection accuracy, to avoid the false negative results caused by DNA extraction error. The duplex fluorescence PCR detection method was established using typical japonica rice (pearl rice) and typical indica rice (Taixian 11). The accuracy of the method was validated with 547 samples including 177 samples of rice seed and eaten rice known as conventional japonica varieties and japonica type hybrid combinations and 370 samples of rice seed and eaten rice known as conventional indica rice varieties and indica type hybrid combinations. In 177 japonica samples, 170 samples with both positive results of cpDNA marker and gos gene, a coincidence rate of 96.05% agreement japonica rice, and 7 samples with positive results of gos gene and negative of cpDNA marker, not agreement japonica rice with non-coincidence rate of 3.95%, were detected. Of the 370 samples of indica rice seed and eaten rice, with positive results of gos gene and negative of cpDNA marker were detected in 340 samples, the rate of coincidence to indica rice was 91.89%. Other 30 samples with both positive results of cpDNA marker and gos gene, were detected, and the non-coincidence rate with indica rice was 8.11%. These identification results were in good agreement with known indica and japonica varieties, and the coincidence rate of japonica varieties was higher than indica. This method can be used to identify indica and japonica subspecies rice, especially suitable to identify conventional rice varieties.},
     year = {2021}
    }
    

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  • TY  - JOUR
    T1  - Identification of Indica-Japonica Subspecies Rice by Duplex Fluorescence PCR Detection for Chloroplast DNA and Endogenous gos Gene
    AU  - Biying Shao
    AU  - Tingyu Miao
    AU  - Juan Peng
    AU  - Bin Chen
    AU  - Wenbing Chen
    Y1  - 2021/09/23
    PY  - 2021
    N1  - https://doi.org/10.11648/j.ijnfs.20211005.12
    DO  - 10.11648/j.ijnfs.20211005.12
    T2  - International Journal of Nutrition and Food Sciences
    JF  - International Journal of Nutrition and Food Sciences
    JO  - International Journal of Nutrition and Food Sciences
    SP  - 101
    EP  - 107
    PB  - Science Publishing Group
    SN  - 2327-2716
    UR  - https://doi.org/10.11648/j.ijnfs.20211005.12
    AB  - Asia cultivated rice are classified into two subspecies, indica and japonica rice (hsien and keng rice called in China, separately). It is necessary to establish a convenient and effective method to identify two subspecies because of the different quality characteristics between the rice products of them, which lead to different processing uses and commodity values. The identification method of PCR based on the difference of chloroplast DNA is convenient and effective, to be attempted to establish. Based on 69 bp fragment deletion of chloroplast DNA (cpDNA) found in ORF100 region nucleotides within the cpDNA Pst I-12 fragment in indica rice but not in japonica, the primer pair and a probe located on the specific cpDNA fragment in japonica rice were designed to identify indica and japonica rice. Another primer pair and probe used to detect endogenous gene gos in rice were combined with above primer pair and probe for detecting cpDNA to establish duplex fluorescence PCR to amplify cpDNA and gos gene for improving detection accuracy, to avoid the false negative results caused by DNA extraction error. The duplex fluorescence PCR detection method was established using typical japonica rice (pearl rice) and typical indica rice (Taixian 11). The accuracy of the method was validated with 547 samples including 177 samples of rice seed and eaten rice known as conventional japonica varieties and japonica type hybrid combinations and 370 samples of rice seed and eaten rice known as conventional indica rice varieties and indica type hybrid combinations. In 177 japonica samples, 170 samples with both positive results of cpDNA marker and gos gene, a coincidence rate of 96.05% agreement japonica rice, and 7 samples with positive results of gos gene and negative of cpDNA marker, not agreement japonica rice with non-coincidence rate of 3.95%, were detected. Of the 370 samples of indica rice seed and eaten rice, with positive results of gos gene and negative of cpDNA marker were detected in 340 samples, the rate of coincidence to indica rice was 91.89%. Other 30 samples with both positive results of cpDNA marker and gos gene, were detected, and the non-coincidence rate with indica rice was 8.11%. These identification results were in good agreement with known indica and japonica varieties, and the coincidence rate of japonica varieties was higher than indica. This method can be used to identify indica and japonica subspecies rice, especially suitable to identify conventional rice varieties.
    VL  - 10
    IS  - 5
    ER  - 

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Author Information
  • Technology Center of Fuzhou Customs District, Fuzhou, China

  • Technology Center of Fuzhou Customs District, Fuzhou, China

  • Technology Center of Fuzhou Customs District, Fuzhou, China

  • Technology Center of Fuzhou Customs District, Fuzhou, China

  • Technology Center of Fuzhou Customs District, Fuzhou, China

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