A bioinformatics approach to the study of polyphenols and antioxidant capacity in Vaccinium vitis-idaea L.

Alam, Md. Zobayer (2017) A bioinformatics approach to the study of polyphenols and antioxidant capacity in Vaccinium vitis-idaea L. Masters thesis, Memorial University of Newfoundland.

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Abstract

Lingonberry (Vaccinium vitis-idaea L.) rich in nutrients and biochemical properties beneficial for human health is one of the less studied crops of the Ericaceae family. In this study, we identified regions within Newfoundland and Labrador, Canada where wild berries contained a higher phenolic content and antioxidant capacity. Notably, berries within the North Shore forest and high temperatures had higher phenolic content. Having DNA markers to characterize lingonberry plants in terms of their metabolite production would be useful, however lingonberry’s genomic sequences are unavailable. We applied next generation sequencing technology to discover single nucleotide polymorphisms (SNPs). Specifically, we investigated the association of SNPs with phenolic compound and antioxidant activity variation in lingonberry grown under different environmental conditions in Newfoundland and Labrador. After processing 144 million single-end DNA sequence reads, 1586 high-quality putative SNPs were identified. A Chi-square test identified 260 SNPs that were significantly correlated with at least one environmental variable, phenolic compound and/or antioxidant activity. Annotation of the 260 SNP-containing sequences, based on BLAST similarity searches, identified 128 genes that were involved in phenolic compound biosynthesis, transcription regulation, transport, drought and water pH resistance. The SNP markers discovered in this study will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high-density quantitative trait locus (QTL) analysis, and association mapping. The identified candidate genes containing the SNPs need further studies on their adaptation ability in lingonberry.

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