High Throughput Sequencing
This is the process of isolating DNA samples and reading the information contained digitally, usually producing millions to billions of “reads” representing short regions of the genome. This will be applied to Rev’s novel strains to computationally reconstruct the full genome sequences.
DNA contains the information in genes that are transcribed into messenger RNA and then translated into proteins to perform tasks within the cell. RNA-seq is the process of sequencing and quantifying the messenger RNA for all genes expressed in a tissue for a given genotype, time point, or environmental growth conditions. Detailed knowledge of messenger RNA abundance across strains provides developmental stage specific genome editing and breeding targets.
Single Nucleotide Polymorphisms (SNPs)- RNA-seq data can also be used to genotype plants across many locations in the genome for single nucleotide polymorphisms (SNPs). Knowing the genotype of thousands of SNPs across the genome provides a “molecular fingerprint” for each strain. This information is crucial for intellectual property protection of new strains.
Quantitative Trait Loci (QTL) Mapping
Many traits such as yield, growth, and disease resistance are not controlled by just a single gene, but rather a suite of genes scattered throughout the genome. These traits are considered “quantitative”. The SNP information from each strain will be statistically associated with the trait information from each strain thereby indicating genomic regions of interest. Once the region of the genome is narrowed, RNA-seq data will be used to identify gene candidates for genome editing as part of Rev’s molecular breeding pipeline.