Project description:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping
Project description:Purpose: SMXL6 is a key repressor in strigolactone signaling. The goal of this study is to identify the targeted genes of SMXL6 in the model plant Arabidopsis thaliana. Methods: The stable pSMXL6:SMXL6-HA transgenic line in the smxl6/7/8 background and the smxl6/7/8 mutant were grown for two weeks in 0.5 x MS medium and collected for extraction of the protein-DNA complexes. After ChIP analyses, DNA profiles were generated by deep sequencing, in double replicate, using Illumina system Novaseq 6000. The sequence reads were analyzed using BWA software and SAMtools. ChIP-qPCR validation was performed using Bio-Rad CFX 96 real-time PCR detection system. Results: We identified 1665 and 1401 peaks in replicate experiment 1 and 2.