The Genotyping Services Lab (GSL),  has been created to support the needs of rice breeding programs within the Global Rice Science Partnership. Our group has optimized the sample preparation workflow to increase the efficiency of rice leaf tissue sampling, DNA extraction, and DNA quality control in preparation for Single nucleotide polymorphism (SNP) genotyping.

At the GSL, we selected sets of informative SNPs for different germplasm groups and genome regions from the 44K SNP chip developed at Cornell University. Fixed sets of 384 SNPs for Indica germplasm and 384 SNPs for Indica/Japonica material are now routinely used for genetic diversity analysis, QTL mapping, and marker-assisted backcrossing (MABC).

Likewise, SNP fingerprinting databases are being developed to support variety identification and diversity analysis. Flexible sets of 24 and 96 SNPs on a Fluidigm EP1 system are now available to enable rapid, low-cost genotyping of markers targeted to specific QTLs and genes controlling traits of interest, and to provide quality control tests to detect seed labeling errors. Functional SNPs and allele-specific SNP haplotypes for breeding-relevant genes are being validated to provide custom sets of markers tailored to different rice breeding programs. These services are now available for both IRRI and non-IRRI clients for SNP genotyping in rice at the GSL.


The GSL team:

Tobias Kretzschmar

Tobias_GSL

Dr. Tobias Kretzschmar received a PhD in Molecular Plant Physiology from the University of Zurich, Switzerland, in 2009. After joining IRRI in 2011 he was involved in Gene Discovery work for abiotic stress tolerance, before taking over as Head of GSL in 2015. His areas of expertise include molecular biology, molecular genetics and functional genomics. Contact Tobias


Maria Reveche

Mayee is in charge of the services and over-all operations of the Genotyping Services Laboratory (GSL). She takes care of relations with other service units at IRRI that help the GSL function smoothly. Contact Mayee











Geraldine Ann M. Layaoen

EJ_ GSL

"EJ"  is a Researcher-Genetics working under GSL. She works with Infinium data decoding using GenomeStudio Software and provides the Nucleotide Matrix Data to clients. She also attends to inquiries on Infinium 6K data. Contact EJ.


Geisha Shaina Lyn Sanchez   

Sha_GSL
As one of the Researchers at GSL, "Sha" performs SNP genotyping protocols that the laboratory offers as services. She is the main person responsible for Fluidigm EP1 System operations and data analysis. She also performs Illumina 6K genotyping, Fragment Analyzer, DNA extraction, and other related molecular biology work. Contact Sha.


Ann Jarana

"An" is a researcher in GSL who leads the Fragment Analyzer and Infinium 6k genotyping activities. She also coordinates the field sampling & DNA extraction works and performs data analysis & other related services offered by the unit. Contact An.









Venice Juanillas

Venice works as a Bioinformatics software developer for molecular data handling and storage at GSL. She is currently developing GSL-Galaxy, which will in-house all tools for the GenomeStudio to Alchemy Workflow, Genotyping Data Management System (GDMS) and TASSEL-GBS Pipeline.