2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA)
| Format: | General Document |
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| building | INTELEK Repository |
| collection | Online Access |
| collectionurl | https://intelek.unisza.edu.my/intelek/pages/search.php?search=!collection3 |
| copyright | Copyright©PWB2025 |
| country | Malaysia |
| date | 2022-04-20 |
| format | General Document |
| id | 15505 |
| institution | UniSZA |
| internalnotes | Sila masukkan subject wajib Dissertations, Academic untuk semua tesis.. Terima kasih |
| originalfilename | DETECTION OF ALIEN INVASIVE AUSTRALIAN REDCLAW CRAYFISH, Cherax quadricarinatus USING WATER ENVIRONMENTAL DNA (eDNA) (MASTER_2022).pdf |
| person | Muhammad Syafiq Aiman Bin Mohd Nasir |
| recordtype | oai_dc |
| resourceurl | https://intelek.unisza.edu.my/intelek/pages/view.php?ref=15505 |
| sourcemedia | Server storage Scanned document |
| spelling | 15505 https://intelek.unisza.edu.my/intelek/pages/view.php?ref=15505 https://intelek.unisza.edu.my/intelek/pages/search.php?search=!collection3 General Document Malaysia Library Staff (Top Management) Library Staff (Management) Library Staff (Support) Terengganu Faculty of Bio-resources & Food Industry English application/pdf 1.5 Server storage Scanned document Universiti Sultan Zainal Abidin UniSZA Private Access UNIVERSITI SULTAN ZAINAL ABIDIN SAMBox 2.3.4; modified using iTextSharp™ 5.5.10 ©2000-2016 iText Group NV (AGPL-version) 2022-04-20 138 DETECTION OF ALIEN INVASIVE AUSTRALIAN REDCLAW CRAYFISH, Cherax quadricarinatus USING WATER ENVIRONMENTAL DNA (eDNA) (MASTER_2022).pdf Muhammad Syafiq Aiman Bin Mohd Nasir Copyright©PWB2025 2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA) The expansion of an alien Australian redclaw crayfish (Cherax quadricarinatus) population is continuously increasing into the wild ecosystem in Malaysia. The intentional and unintentional release of this species has caused disturbances towards the native biodiversity and ecosystem. Hence, monitoring the distribution of this invasive species is necessary to minimize their effect. The conventional monitoring method consumes a lot of time and energy. The use of environmental DNA (eDNA) method for monitoring offers more rapid result within a short period with the help of the species-specific primer. The current study aimed to develop species-specific primer sets and probe for C. quadricarinatus from mitochondrial DNA (mtDNA) COI gene, to validate the specificity and workability of the designed primer sets in detecting the targeted species from water (eDNA, and to detect the eDNA of C. quadricarinatus from controlled aquatic environment. The species-specific primer was designed using Primer3 Pro software from the extracted C. quadcarinatus sequence. The primer validation process was done by amplifying the sequences from C. quadricarinatus, C. destructor, Procambarus clarkii and Macrobrachium rosenbergii to ensure only C. quadricarinatus sample was amplified. The workability test was conducted by extracting DNA from aquarium containing the C. quadricarinatus and tilapia fish, which served outgroup species and further amplified using the conventional PCR (cPCR). The eDNA detection from controlled aquatic environment was conducted via testing the presence of eDNA sampled from aquariums which divided into two conditions which were (i) density and (ii) time dependent. Two sets of primers were designed namely CQCOI_F1_F2 and CQCOI_F2_R3 and product sizes of 119 base pairs (bp) and 175bp respectively. Annealing temperature at 64°C found to be the most optimum for both primer sets. Only CQCOI_F2_R3 primer set was selected to be tested for workability due to its longer primer length which can increase the specificity. The workability test has also proven success as only C. quadricarinatus water eDNA sample were amplified when tested with tilapia eDNA sample, with the band size of 175bp. The specificity of the designed probe was confirmed using quantitative PCR (qPCR). Results from controlled aquatic environment using cPCR were a success as 11 of 12 samples were successfully amplified. qPCR results from the first and second aquatic condition found out higher density and longer day left found to have lower eDNA concentration compared to lower density and shorter day. Generally, the objective was achieved as at least one samples from each treatment was successfully amplified via cPCR an qPCR Cherax quadricarinatus Environmental DNA (eDNA) Dissertations, Academic Sila masukkan subject wajib Dissertations, Academic untuk semua tesis.. Terima kasih Cherax Quadricarinatus Australian Redclaw Crayfish Thesis |
| spellingShingle | 2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA) |
| state | Terengganu |
| subject | Cherax quadricarinatus Dissertations, Academic |
| summary | The expansion of an alien Australian redclaw crayfish (Cherax quadricarinatus) population is continuously increasing into the wild ecosystem in Malaysia. The intentional and unintentional release of this species has caused disturbances towards the native biodiversity and ecosystem. Hence, monitoring the distribution of this invasive species is necessary to minimize their effect. The conventional monitoring method consumes a lot of time and energy. The use of environmental DNA (eDNA) method for monitoring offers more rapid result within a short period with the help of the species-specific primer. The current study aimed to develop species-specific primer sets and probe for C. quadricarinatus from mitochondrial DNA (mtDNA) COI gene, to validate the specificity and workability of the designed primer sets in detecting the targeted species from water (eDNA, and to detect the eDNA of C. quadricarinatus from controlled aquatic environment. The species-specific primer was designed using Primer3 Pro software from the extracted C. quadcarinatus sequence. The primer validation process was done by amplifying the sequences from C. quadricarinatus, C. destructor, Procambarus clarkii and Macrobrachium rosenbergii to ensure only C. quadricarinatus sample was amplified. The workability test was conducted by extracting DNA from aquarium containing the C. quadricarinatus and tilapia fish, which served outgroup species and further amplified using the conventional PCR (cPCR). The eDNA detection from controlled aquatic environment was conducted via testing the presence of eDNA sampled from aquariums which divided into two conditions which were (i) density and (ii) time dependent. Two sets of primers were designed namely CQCOI_F1_F2 and CQCOI_F2_R3 and product sizes of 119 base pairs (bp) and 175bp respectively. Annealing temperature at 64°C found to be the most optimum for both primer sets. Only CQCOI_F2_R3 primer set was selected to be tested for workability due to its longer primer length which can increase the specificity. The workability test has also proven success as only C. quadricarinatus water eDNA sample were amplified when tested with tilapia eDNA sample, with the band size of 175bp. The specificity of the designed probe was confirmed using quantitative PCR (qPCR). Results from controlled aquatic environment using cPCR were a success as 11 of 12 samples were successfully amplified. qPCR results from the first and second aquatic condition found out higher density and longer day left found to have lower eDNA concentration compared to lower density and shorter day. Generally, the objective was achieved as at least one samples from each treatment was successfully amplified via cPCR an qPCR |
| title | 2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA) |
| title_full | 2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA) |
| title_fullStr | 2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA) |
| title_full_unstemmed | 2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA) |
| title_short | 2022_Detection of Alien Invasive Australian Redclaw Crayfish, Cherax quadricarinatus Using Water Environmental DNA (eDNA) |
| title_sort | 2022_detection of alien invasive australian redclaw crayfish, cherax quadricarinatus using water environmental dna (edna) |