Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice
While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (<i>Oryza sati...
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| Format: | Article |
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MDPI AG
2022-10-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/12/10/1542 |
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| author | Noraikim Mohd Hanafiah Acga Cheng Phaik-Eem Lim Gomathy Sethuraman Nurul Amalina Mohd Zain Niranjan Baisakh Muhamad Shakirin Mispan |
| author_facet | Noraikim Mohd Hanafiah Acga Cheng Phaik-Eem Lim Gomathy Sethuraman Nurul Amalina Mohd Zain Niranjan Baisakh Muhamad Shakirin Mispan |
| author_sort | Noraikim Mohd Hanafiah |
| collection | DOAJ |
| description | While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (<i>Oryza sativa</i>) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources. |
| first_indexed | 2024-03-09T03:34:52Z |
| format | Article |
| id | doaj.art-ba5e544b70164ba79f3c11af6cab728d |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T03:34:52Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-ba5e544b70164ba79f3c11af6cab728d2023-12-03T14:50:00ZengMDPI AGLife2075-17292022-10-011210154210.3390/life12101542Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy RiceNoraikim Mohd Hanafiah0Acga Cheng1Phaik-Eem Lim2Gomathy Sethuraman3Nurul Amalina Mohd Zain4Niranjan Baisakh5Muhamad Shakirin Mispan6Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, MalaysiaInstitute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, MalaysiaInstitute of Ocean and Earth Science, Universiti Malaya, Kuala Lumpur 50603, MalaysiaInstitute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, MalaysiaInstitute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, MalaysiaSchool of Plant, Environmental and Soil Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USAInstitute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, MalaysiaWhile previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (<i>Oryza sativa</i>) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources.https://www.mdpi.com/2075-1729/12/10/1542agarose gel electrophoresisamylose contentbacterial leaf blightblastfragrancemultiplex polymerase chain reaction |
| spellingShingle | Noraikim Mohd Hanafiah Acga Cheng Phaik-Eem Lim Gomathy Sethuraman Nurul Amalina Mohd Zain Niranjan Baisakh Muhamad Shakirin Mispan Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice Life agarose gel electrophoresis amylose content bacterial leaf blight blast fragrance multiplex polymerase chain reaction |
| title | Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice |
| title_full | Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice |
| title_fullStr | Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice |
| title_full_unstemmed | Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice |
| title_short | Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice |
| title_sort | novel pcr based multiplex assays for detecting major quality and biotic stress in commercial and weedy rice |
| topic | agarose gel electrophoresis amylose content bacterial leaf blight blast fragrance multiplex polymerase chain reaction |
| url | https://www.mdpi.com/2075-1729/12/10/1542 |
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