School of Bioinformatics · Genomics & transcriptomics
Plant & Agricultural Genomics
Genomics is changing how crops are bred and studied. This course teaches the bioinformatics behind plant genome analysis and molecular breeding, with the complications that make plant genomes different: polyploidy, repeats and large genome sizes.
Course overview
Plant & Agricultural Genomics covers plant genome resources and their quirks, variant discovery in diverse germplasm, development of molecular markers, and transcriptomics of stress and development.
The breeding half teaches association mapping in crop panels and genomic selection, where genome-wide markers predict breeding value, using public rice, wheat and maize data. The course suits plant-science students and breeders who want to work with their own sequence data.
Learning outcomes
By the end of the course you will be able to:
- Navigate plant genome databases and their annotation conventions
- Discover variants across germplasm, including in polyploid genomes
- Design SNP and SSR markers for breeding applications
- Run GWAS on a crop diversity panel
- Build and evaluate a genomic-selection model
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- Bioinformatics Foundations or equivalent
- Undergraduate genetics
Best suited to
- Agriculture, horticulture and plant-biotechnology students
- Plant breeders and crop scientists
- Researchers at agricultural universities and institutes
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- Genome size, repeats and polyploidy
- Ensembl Plants, Phytozome and crop databases
- Pan-genomes
Topics
- Resequencing diverse lines
- Calling variants in polyploids
- Diversity statistics
Topics
- SNP and SSR markers
- KASP assay design concepts
- Marker-assisted selection
Topics
- Population structure in crop panels
- Mixed-model GWAS
- Candidate genes
Topics
- GBLUP and ridge regression
- Training populations
- Prediction accuracy
Topics
- Question
- Analysis
- Recommendation
Practical sessions and projects
Capstone project
Support a breeding decision
Use variant, association or genomic-prediction analysis on public crop data to make and justify a recommendation for a breeding programme.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Plant genomes
Compare gene content between rice reference genomes and explore a crop pan-genome.
- Variants in germplasm
Call and filter SNPs across a panel of rice accessions and summarise their diversity.
- Markers for breeding
Design markers flanking a known trait locus and check their specificity.
- Association mapping
Run a GWAS for a grain trait and shortlist candidate genes near significant loci.
- Genomic selection
Predict breeding values in a public wheat dataset and measure accuracy by cross-validation.
- Project: a breeding analysis
Analyse a public crop dataset and recommend markers or selection strategies for a breeding objective.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- 3,000 Rice Genomes Project: Diversity and association mapping.IRRI / public SNP-Seek resources
- Public wheat and maize genomic-selection datasets: Genomic prediction.Published open data
Core reading
- Varshney RK, Bohra A, Yu J, Graner A, Zhang Q, Sorrells ME (2021). Designing future crops: genomics-assisted breeding comes of age. Trends in Plant Science 26:631–649.
- Crossa J et al. (2017). Genomic selection in plant breeding: methods, models, and perspectives. Trends in Plant Science 22:961–975.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Plant & Agricultural Genomics, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Plant & Agricultural Genomics
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
Continue learning