How potato breeders use Flex-Seq to battle against late blight disease

Potato (Solanum tuberosum) is the world’s third most important food crop after wheat and cereal and is a staple food for over 1.3 billion people. The overall value of the potato crop to the global economy largely comes from the processing of potatoes, with the industry in the USA alone valued at over $100B employing over 700,000 people¹. The global significance of potatoes heightens the importance of combating the potato’s nemesis, late blight (Phytophthora infestans). Late blight, a quickly spreading disease, is caused by the oomycete pathogen and can have a devastating impact on the potato industry. 

Figure 1: FAOSTAT, New Food Balances, February 2020

Image credit: Moctar Kante, CIP. Late blight susceptible clone.

 

The International Potato Centre (CIP) in Peru, a CGIAR research centre with a focus on potato, sweet potato and Andean roots and tubers. CIP delivers innovative science-based solutions to enhance access to affordable nutritious food, foster inclusive sustainable business and employment growth. CIP also drives the climate resilience of root and tuber agri-food systems. Headquartered in Lima, Peru, CIP has a research presence in more than 20 countries in Africa, Asia and Latin America. 

 

CIP has made significant advances in the use of advanced biotechnology and molecular methods to transfer late blight-free resistance from wild relative crops to cultivated potatoes. These varieties were then thoroughly evaluated at the ILRI-BecA (Biosciences eastern and central Africa) Hub in Kenya and the National Agricultural Research Organization in Uganda and are currently resistant to late blight. These blight resistant potatoes are grown in several countries. Three late blight resistant varieties were released in 2023 in Peru.⁴ 

 

These new potato cultivars have been bred using resistance genes against P. infestans (Rpi genes) that originate from wild relatives of potato, and imported material, but such programmes are complex and long. New approaches focus on identifying key Rpi genes through GWAS studies followed by genetic engineering to construct what are known as "gene pyramids" or combinations of multiple Rpi genes. Single gene resistance strategies can often be overcome by rapidly evolving pathogens.

Image credit: Moctar Kante, CIP. CIP observational study.

 

Flex-Seq targets individual regions using the two Flex-Seq probes, often focusing on a single SNP. Probes can be designed to flexibly bind on either side of the SNP, leading to greater ability to recover desired targets. Once both probes bind, the complementary sequence is synthesised between the probes and the target region is amplified from the genomic DNA. The genomic DNA and non-specific binding products are removed. The proprietary Flex-Seq probes enable high levels of target multiplexing in a single reaction. 

 

Tuber samples were from pre-breeding material from CIP in Peru. The samples were selected based on diversity between families and their late blight resistance rating.

Image credit: Moctar Kante, CIP. Sample preparation at CIP.

 

We asked lead CIP scientist Moctar Kante what benefits genotyping can deliver for breeders. 

 

"Cost efficiency is the key benefit; the possibility to select for a trait or a group of traits in early stages of the breeding cycle, and the possibility to select for parents in early stages of the breeding cycle can increase short-term genetic gain. Accurate phenotypic evaluation for key traits can be expensive, and disease evaluation when the disease does not naturally occur in field plots can reveal resource inefficiencies. So, using molecular markers when managing large number of clones for disease characterization is a useful option. For other traits, depending on the breeding focus, the use of markers can happen in early stages or late stages, or the fixed effect of some markers can be accounted for in prediction models." M. Kante Associate Scientist-Potato Breeder, CIP 

Image credit: Moctar Kante, CIP. The negative impact of heat stress.

Upon receiving the Flex-Seq 20K loci results CIP were able to request the discovery mode data which delivered around 200K of SNPs. They found that the obtained reads were on average 4 times longer than GBS’s typical 50 bases with Flex-Seq giving 200 nucleotides-long reads. Moctar is currently analysing the data. 

 

In the future they are hoping to look at disease resistance traits for Potato virus Y (PVY) and bacterial wilt - the second and third most significant potato diseases. Innovative research is needed to understand bacterial wilt pathogenicity and virulence before durable resistance can be developed to that disease. They will also be investigating traits for higher yield, dry matter content, biotic stress tolerance including heat stress, good quality tuber and hybrid breeding.

 

• US Dept of Agriculture dives into blueberry and cranberry genotyping
• For more information on the work of CIP visit CIP - International Potato Center.
• To find out more about the work of the University of Wisconsin Potato Breeding & Genetics laboratory visit Potato Breeding & Genetics
•  Read about CGIAR's research work