Dissecting DNA Damage Responses in Arabidopsis: A High-Throughput Sequencing Approach Public Deposited

http://ir.library.oregonstate.edu/concern/undergraduate_thesis_or_projects/mw22v744q

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  • A unique, permanent root-growth arrest phenotype was observed in UV-B irradiated Arabidopsis thaliana roots lacking the DNA damage response kinase ATR. Segregation analysis suggests the dependence of this phenotype on another, unidentified gene, termed ursu. High-throughput sequencing technologies were used to map and identify the causal ursu mutation. Illumina HiSeq 2000 short sequence reads were analyzed using bioinformatics command line tools for Next-Generation Mapping (NGM) and Mapping and Alignment with Short Sequences (MASS) programs. Several putative candidate genes were identified, including auxin response factor 13 (arf13) and resistance to Peronospora parasitica protein 8 (rpp8). Sanger sequencing verified the presence of a single nucleotide polymorphism (SNP) and a frameshift mutation caused by a 26-bp deletion in arf13 in ursu atr plants. Although additional sequencing and complementation tests are still necessary, a causative mutation in arf13 could provide clues linking the DNA damage response kinase ATR with the key growth and development phytohormone auxin.
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