Genotyping-by-Sequencing (GBS) is a method for processing genomic DNA into libraries for next-generation sequencing. GBS is commonly used by plant geneticists because it makes sequencing more high-throughput and affordable. Examples of downstream applications include genetic linkage mapping, genome-wide association studies (GWAS), genomic diversity and association studies, molecular marker discovery and genomic selection (GS). This video specifically uses the double digest restriction-site associated DNA sequencing (ddRADseq) pipeline as it has been demonstrated to work on sweet basil. Although the workflow is typically automated in specialized genomics labs, a more manual workflow is presented for broader accessibility and teaching purposes. Each step of the pipeline is listed below with its time stop:
Background 00:13
What is ddRADseq? 00:28
Why do we use ddRADseq? 00:56
Step 1: gDNA dilution 1:57
Step 2: digest 5:02
Step 3: ligation 7:05
Step 4: clean up DNA 11:14
Step 5: PCR 18:44
Step 6: qubit 20:44
Step 7: pooling 25:36
Acknowledgements 27:07
Citations:
* Poland et al. 2012- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032253
* Pyne et al. 2017- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184319
For more information on the Simon lab and RU basil, visit:
Website: https://newuseag.rutgers.edu/
Instagram: @rutgersbasil
This video was produced by Lara Brindisi, PhD Candidate at Rutgers University
Email: [email protected]
