Development of molecular markers for blight disease resistance in taro using bioinformatics tools
By: Athul, V S.
Contributor(s): Sreekumar, J (Guide).
Material type:
BookPublisher: Vellayani Department of Plant Biotechnology College of Agriculture 2018Description: 85p.Subject(s): BiotechnologyDDC classification: 660.6 Online resources: Click here to access online Dissertation note: BSc-MSc (Integrated) Abstract: Development of molecular markers using sequential information publicly available in the biological databases has enhanced their credibility over the years. The study entitled “Development of Molecular markers for blight disease resistance in taro using bioinformatics tools” was conducted at the Central Tuber Crop Research Institute (CTCRI) during 2017-2018. The objectives of the study included the development and evaluation of various Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeats (SSR) prediction pipelines, computational prediction and validation of the molecular markers for blight disease resistance in taro. The preliminary data set for the study was obtained from the Sequence Read Archive (SRA) section of NCBI. A total of 6,479,882 sequences obtained initially were reduced to 6,319,834 after pre-processing. The processed sequences were reduced to 79,608 sequences after de novo assembly and were finally assembled to 8547 contigs and 59,242 singlets. The contigs were then processed with various prediction pipelines to predict SSRs and SNPs. The tools, QualitySNP and AutoSNP were employed to detect the SNPs present within the contig sequences. The efficiency of these tools in determining the number of synonymous and non-synonymous SNPs was also analyzed. The tools, MISA and SSRIT were used to detect the SSRs within the sequences. The efficiency in predicting more number and types of reliable repeats were considered. The analysis was done with a wide range of repeats such as mono-, di-, tri-, tetra-, penta-, hexa-, and poly repeats and their numbers. QualitySNP identified 518 synonymous and 44 non-synonymous SNPs from the 8547 contigs. MISA identified 967 mono-, 1484 di-, 558 tri-, 14 tetra-, 2 penta-, 9 hexa-, and 393 compound SSRs. Five SNP and SSR primers were designed and synthesized from the contigs containing SSRs and SNPs. The synthesized SNP and SSR primers were then validated against tolerant and susceptible varieties of taro leaf blight. Among the primers synthesized the SSR primer CeSSR4 and SNP primer CeSNP3 were capable of differentiating leaf blight resistant and susceptible varieties. The markers need to be analyzed further with a large number of samples to develop them as a marker for taro leaf blight. Once analyzed, they could be used in marker-assisted selection and breeding programmes of taro.
| Item type | Current location | Collection | Call number | Status | Date due | Barcode |
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Theses
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KAU Central Library, Thrissur Theses | Reference Book | 660.6 ATH/DE (Browse shelf) | Not For Loan | 174553 |
BSc-MSc (Integrated)
Development of molecular markers using sequential information publicly available in the biological databases has enhanced their credibility over the years. The study entitled “Development of Molecular markers for blight disease resistance in taro using bioinformatics tools” was conducted at the Central Tuber Crop Research Institute (CTCRI) during 2017-2018. The objectives of the study included the development and evaluation of various Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeats (SSR) prediction pipelines, computational prediction and validation of the molecular markers for blight disease resistance in taro. The preliminary data set for the study was obtained from the Sequence Read Archive (SRA) section of NCBI. A total of 6,479,882 sequences obtained initially were reduced to 6,319,834 after pre-processing. The processed sequences were reduced to 79,608 sequences after de novo assembly and were finally assembled to 8547 contigs and 59,242 singlets. The contigs were then processed with various prediction pipelines to predict SSRs and SNPs. The tools, QualitySNP and AutoSNP were employed to detect the SNPs present within the contig sequences. The efficiency of these tools in determining the number of synonymous and non-synonymous SNPs was also analyzed. The tools, MISA and SSRIT were used to detect the SSRs within the sequences. The efficiency in predicting more number and types of reliable repeats were considered. The analysis was done with a wide range of repeats such as mono-, di-, tri-, tetra-, penta-, hexa-, and poly repeats and their numbers. QualitySNP identified 518 synonymous and 44 non-synonymous SNPs from the 8547 contigs. MISA identified 967 mono-, 1484 di-, 558 tri-, 14 tetra-, 2 penta-, 9 hexa-, and 393 compound SSRs. Five SNP and SSR primers were designed and synthesized from the contigs containing SSRs and SNPs. The synthesized SNP and SSR primers were then validated against tolerant and susceptible varieties of taro leaf blight. Among the primers synthesized the SSR primer CeSSR4 and SNP primer CeSNP3 were capable of differentiating leaf blight resistant and susceptible varieties. The markers need to be analyzed further with a large number of samples to develop them as a marker for taro leaf blight. Once analyzed, they could be used in marker-assisted selection and breeding programmes of taro.
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