AdaptiveTarget: Accessing haplotype variation at complex loci with optimized targeting and adaptive sampling

Introduction

Genetic variation at resistance loci is crucial for sustained crop yield, given the challenges and increased pest and pathogen pressures resulting from a warming climate. Despite recent advances in massively parallel sequencing, disease resistance loci and other complex genomic regions of great practical, economical, and scientific importance remain challenging to study.

Challenges in Current Methods

The severe limitations of current methods pose a major problem for fully understanding and harnessing genetic variation for crop improvement.

Development of AdaptiveTarget

We will develop AdaptiveTarget as a bioinformatic method based on targeted long-read sequencing. This method will allow researchers and breeders to:

• Quickly obtain population-level haplotype information
• Efficiently analyze complex genomic regions such as resistance genes and self-incompatibility loci in plants
• Inexpensively conduct studies on genetic variation

Research and Validation

To explore the innovation potential of our ERC-funded research, we will first undertake research to test and validate the project idea. Validation will benefit from known haplotype data for the complex S-locus supergene, produced in the ERC-funded project SuperGenE.

Application of the Method

To demonstrate the general utility of the method, we will apply it to real-world examples consisting of complex loci of agronomic importance.

Future Steps

Once the method is validated, we will investigate options for patenting and licensing the method.

Impact of AdaptiveTarget

Our AdaptiveTarget method for fast and efficient targeted sequencing of complex genomic regions could greatly facilitate the assessment of genetic variation at complex genomic regions of outstanding scientific, practical, and economic interest.

Therefore, our method could help drive innovation in several ways, including:

1. Allowing the development of more efficient methods for precision breeding
2. Enhancing disease and pest resistance in crops