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

Biying Shao; Tingyu Miao; Juan Peng; Bin Chen; Wenbing Chen

doi:doi:10.11648/j.ijnfs.20211005.12

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

Biying Shao, Tingyu Miao, Juan Peng, Bin Chen, Wenbing Chen

Published in International Journal of Nutrition and Food Sciences (Volume 10, Issue 5)

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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APA Style

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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ACS 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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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

Biying Shao

Technology Center of Fuzhou Customs District, Fuzhou, China
Tingyu Miao

Technology Center of Fuzhou Customs District, Fuzhou, China
Juan Peng

Technology Center of Fuzhou Customs District, Fuzhou, China
Bin Chen

Technology Center of Fuzhou Customs District, Fuzhou, China
Wenbing Chen

Technology Center of Fuzhou Customs District, Fuzhou, China

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Plain Text BibTeX RIS

APA Style

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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ACS 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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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

Copy | Download

@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}
}

Copy | Download

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  -

Copy | Download