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Tag: bioinformatics

Fingerprinting bioinformatics pipeline cuts seed purity testing from days to clicks

Written by dmedina on . Posted in Blogs.

A new bioinformatics-driven tool dramatically accelerates seed purity testing, offering fast, automated parental purity checks and hybridity verification—thereby increasing the effectiveness of breeders, seed companies, and regulators.

Waiting days—or even weeks—to analyze Single Nucleotide Polymorphism (SNP) assay data to verify the genetic purity and hybridity of seeds and crosses may soon be a thing of the past. A new bioinformatics-driven seed purity testing pipeline significantly reduces the time required to confirm seed identity, bringing it down to just a few clicks.

The new pipeline uses DNA fingerprinting with SNPs in a fast, accurate, and scalable automated genetic analysis.

Modernizing Genetic Purity and Hybridity Testing

Traditionally, seed producers and certification agencies have relied on grow-out tests and morphological analysis to assess genetic purity. These methods are labor-intensive and time-consuming, often requiring weeks or months of field or greenhouse work by trained technicians.

Although CIMMYT has long used molecular markers to verify parental purity and hybridity, challenges remained—particularly the lack of automated tools and integrated platforms to make the process seamless and accessible.

That is changing, thanks to software developed by Abhishek Rathore and team. The pipeline automatically compares each sample’s genetic profile to its expected reference using a custom algorithm. Based on user-defined thresholds, the tool confirms parental purity, identifies putative F1 hybrids, and flags failed crosses.

“We wanted a tool that breeders and seed companies can use without needing specialized bioinformatics skills,” said Abhishek Rathore, bioinformatics specialist at CIMMYT. “Once the DNA data is generated, the analysis is push-button. The software quickly interprets the SNP results and produces an easy-to-read report on seed purity. It’s about making advanced bioinformatics accessible and routine for parental purity and F1 verifications.”

Speedy, Automated, and User-Friendly

Early implementation of the pipeline has demonstrated large gains in speed and efficiency. What previously required extensive manual effort can now be completed in minutes.

The system is designed with user-friendliness in mind: lab technicians simply upload SNP assay results into an intuitive interface, and the pipeline returns clear metrics—such as “% purity”—while flagging any off-type individuals. With the computational workload fully automated, even seed companies and labs with minimal informatics infrastructure can benefit.

“Automation is key,” added Rathore. “By reducing manual steps and subjective interpretation, we save time and minimize human error. You can process dozens of seed samples overnight and receive a comprehensive genetic report by morning.”

To make this automation accessible to stakeholders across NARS, CIMMYT’s biometrician Roma Das developed a user-friendly web interface, while Peter Kimathi, a bioinformatics and software developer, developed a custom report and deployed the pipeline as a web service on CIMMYT’s servers (link below).

Widespread Adoption Across Africa

Since its rollout, the pipeline has been widely adopted by CIMMYT and partners through the Africa Dryland Crops Improvement Network (ADCIN). Mohan Chejerla, Genomics Expert at CIMMYT, has already applied the pipeline to over 23,000 samples, ensuring quality assurance and quality control (QA/QC) for breeding pipelines across Kenya, Uganda, Mali, Senegal, Burkina Faso, Ethiopia, Tanzania, Niger, Togo, Zambia, and Ghana.

This broad uptake underscores the demand for reliable, scalable seed purity testing—and the pipeline’s value for enhancing crop breeding and seed system integrity.

Additional Information:
🔗 Pipeline Source Code
🔗 CIMMYT Pipeline Implementation

Huihui Li

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Huihui Li is a Senior Scientist – Quantitative Geneticist at CIMMYT in China.

Akshaya Biswal

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Akshaya Biswal is a scientist specialized in plant transformation and tissue culture, working with CIMMYT’s Genetic Resources Program. His current work focuses on application of gene editing to improve host-plant resistance.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9-mediated genome editing has revolutionized our ability to study gene function and alter it to improve biotic and abiotic stress tolerance, increase yield potential of crop plants or even to improve the quality of grains. Various plant diseases cause up to 30% yield loss in cereals. Polyploidy in maize and wheat poses additional difficulty to breeders for developing and deploying resistant lines to pathogens. Some these can be solved by biotechnological intervention with relative ease. Biswal’s team uses gene editing to: control Maize Lethal Necrosis (MLN) in Africa for improved grain harvests; improve stem rust and powdery mildew resistance in wheat; and discover and validate the function of candidate genes underpinning large effect QTLs.

Prior to joining CIMMYT, Biswal completed postdoctoral placements at the International Rice Research Institute (IRRI) and the University of North Carolina. He earned a PhD in Biotechnology at Jawaharlal Technological University, an MSc from Banaras Hindu University, and a BSc from Utkal University, India.

Claudio CĂ©sar Ayala HernĂĄndez

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Claudio Ayala is an experienced Data Management Coordinator with a demonstrated history of working in the research industry. He has a Master’s degree focused on Information Systems and Applied Computing and is skilled in analytics, database management, and the development of tools for effectively capturing, curating, storing and integrating different datasets.

Carolina Paola Sansaloni

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Carolina Sansaloni is a molecular geneticist and leader of the Genetic Analysis Service for Agriculture, a high throughput genotyping platform managed by CIMMYT’s Seeds of Discovery initiative that uses Diversity Arrays Technology. She regularly contributes to projects that have strategic significance in wheat pathology, disease resistance, quality, functional genomics and bioinformatics.

Sansaloni also works on the wheat Global Diversity Analysis, which characterizes and analyses seeds in genebanks at CIMMYT and the International Center for Agricultural Research in Dry Areas (ICARDA). Her team has characterized around 100,000 wheat accessions, including more than 40 species that represent 40 percent of the CIMMYT genebank and almost 100 percent of the ICARDA ‘s genebank wheat collection. This is an incredible and unique resource for wheat scientists that provides a genetic framework to help select the most relevant accessions for breeding.

Juan Burgueño

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Juan Burgueño is a senior scientist and head of CIMMYT’s biometrics and statistics unit. He and his team are committed to developing new mathematical and statistical methodologies, and applying them to solve the problems CIMMYT and partner researchers face.

Burgueño and his team mainly focus on research, consultancy and training on a broad range of topics like experimental design, multi-environment cultivar trials, agronomy, pathology and entomology experiments, genetic resources conservation, mapping quantitative trait loci, genome selection and genetic diversity.

As head of the unit, he coordinates the team’s efforts in these areas and strengthens CIMMYT’s team of biometricians in order to effectively collaborate and help CIMMYT’s staff and partners. Burgueño mainly contributes to experimental design, statistical modeling, genome selection and analysis of high-throughput phenotyping data.