Unlocking the complex genomes of European potatoes for modern breeding

Introduction

Potato is one of the three most important food crops in the world. Around 1.3 billion people rely on potato as a staple food every day. But despite this exceptional socio-economic importance, the improvement of potato during the past 150 years has been limited. The main reason for this deficit is the highly heterozygous, autotetraploid genome of potato. This complicates several important aspects of breeding, including the fixation of beneficial alleles and the implementation of modern, genomics-assisted breeding techniques.

Challenges in Breeding

Recently, it has been suggested to convert tetraploid potato into a diploid crop, thereby overcoming all the difficulties associated with tetraploid potato breeding. However, the creation of diploid potatoes is hampered by the large number of deleterious recessive mutations that have accumulated in the tetraploid genome and are exposed in the diploid potatoes.

Project Overview

In BYTE2BITE, we will address the fundamental issues that hold back the success of potato breeding. We will generate the first-of-its-kind, near-to-complete pan-genome of potato and use this resource to develop unprecedented genome-graph tools for efficient genotyping and haplotype-resolved genome analysis.

Goals

We will then use this new computational toolbox to establish a genomics-assisted pre-breeding programme in which we will generate novel potato cultivars with low mutational load. This new resource will open the doors to efficient breeding, unleashing the genetic potential of potato and thereby helping to secure the way we feed the world for the decades to come.

Specifically, in BYTE2BITE we want to achieve the following goals:

1. A near-to-complete pan-genome describing almost the entire haplotype diversity of potato.
2. A genome graph tool for cost-efficient genotyping and haplotype-resolved genome analyses.
3. A genomics-assisted pre-breeding programme for potatoes with low mutational load.