The challenge

The application of genomics can improve the effectiveness and efficiency of developing new varieties that achieve complex crop profile targets while decreasing costs. Within breeding programs, applied genomics is used for trait discovery, pedigree verification, parent identification, genomic selection, and verification of farmer uptake of new varieties. Successful integration of applied genomics has been achieved by large and well-funded breeding programs. The aim of the ILCI genomics team is to co-develop resources, tools, and pipelines that are available and accessible to small public breeding programs globally for crops species such as sorghum, millets, cowpea, and common bean.

Our approach

ILCI’s approach incorporates genomics within a total crop improvement framework that includes disciplines as diverse as gender science, nutrition, phenomics, and informatics. In this way genomics is not a stand-alone tool; it is embedded into breeding pipelines that are guided by decision-support and inclusive and adoptable product profiles. ILCI genomics aims to co-develop the tools, technologies, and methods to enable full adoption and control by National Agricultural Research Institutes to achieve sustainable genetic gains for farmers and communities within their target regions. 

Recent highlights

International partnerships

Working together with Excellence in Breeding (EiB), CoIs, and other international researchers to leverage and collate existing genomics data, reference genomes, and markers for time and cost savings

Customized software

Re-designing current software applications for use by applied users in small public breeding programs

Centers of Innovation

Innovating with CoIs on existing software applications to improve genomic prediction accuracy

Research from our experts

In progress

  • Outsourcing low-cost and high-quality DNA extraction and genotyping with Excellence in Breeding (EiB) so scientists can focus on developing bioinformatics expertise
  • Conducting in silico testing to ensure genotyping platforms cover the diversity present in CoI crop germplasm
  • Assembling high-quality reference genomes for CoI crops lacking reference genomes in collaboration with Excellence in Breeding (EiB)
  • Establishing cloud computing for genomic analyses at small public breeding programs
  • Applying cost and time-efficient approaches to genomic breeding using the Practical Haplotype Graph (PHG)
  • Incorporating functional gene-level data into genomic prediction models for improved accuracy
  • Adapting and updating TASSEL for use by plant breeders

Publications from our experts (external from ILCI funding)

Genomics team

Bethany Econopouly

International Applied Genomics Lead

Ed Buckler portrait

Ed Buckler

Genomics Lead

Cinta Romay

Buckler Lab Project Manager