Method for reference-genome independent gene discovery and cloning

Technology ref: J20BW1

Proposed use

This invention enables cloning of genes from accessions of a wild plant species lacking advanced agronomic traits, allowing discovery of genes in breeding or pre-breeding germplasm and the development of gene-specific markers for marker-assisted selection.

Problem addressed

Trait discovery in species with no reference genome was time-consuming and unviable.

Traditionally, SNP-based Genome-Wide Association Study (GWAS) was used for trait discovery and marker development, which requires a high-quality reference genome and captures only a limited proportion of the species diversity.

This invention not only enables trait discovery without strictly relying on a high-quality reference genome, but also allows capture of species diversity using multiple low-to-medium quality reference genomes, if they are available.


  • The method presents a technology for reference genome-independent gene discovery and cloning
  • On provision of a database of genetic samples from a population, this significantly reduces the amount of additional crossing or mutagenesis required for gene identification

Technology overview

A single reference genome can only capture limited information about the genetic variation present in the species complex. Therefore, genes that are under diversifying selection might escape detection using traditional methods, such as SNP-GWAS.

This invention dramatically increases the amount of the genetic variation captured from a species by using k-mer based association genetics in combination with multiple low-to-medium quality reference genomes.

The methodology includes:

  1. Obtaining information of a diversity panel from a DNA sequence whole genome shotgun database
  2. Identifying the presence or absence of k-mers
  3. Phenotyping the diversity panel for any phenotypic traits and associate it with the presence/absence k-mer analysis
  4. 4rdering contigs in the reference genome
  5. Identifying genes associated with the selected phenotype

Intellectual property information

Pending PCT Application (unpublished) – “Association Mapping Method”.

Published papers

Gaurav K., Arora S., …, Wulff B.B.H. ‘Evolution of the bread wheat D-subgenome and enriching it with diversity from Aegilops tauschii

Inventor information

  • Dr Kumar Gaurav – A former postdoctoral scientist in wheat research and genomics in the Wulff group at the John Innes Centre
  • Dr Brande Wulff – An Associate Professor at the King Abdullah University of Science and Technology (KAUST), formerly a group leader in wheat pathogen-omics and genomic research at the John Innes Centre