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A new frontier in potato breeding: Unlocking the potential of wild potato species for late blight resistance

The following article was prepared by Jorge Luis Alonso G.

Late blight is a significant disease in potato production. Research efforts are currently focused on discovering and characterizing resistant wild potato species to improve resistance breeding.

The Institute for Breeding Research on Agricultural Crops and the University of Rostock have conducted a study that lists all wild potato species recognized by the authors as having resistance, along with their associated genes and quantitative trait loci (QTL). The research team also looked at how these new sources of resistance could be used for future resistance breeding.

The researchers reported their findings in the journal Plant Breeding in 2022 – titled, “Late blight resistance in wild potato species — Resources for future potato (Solanum tuberosum) breeding“.

The article below is a summary of the study and the main findings.

Introduction

Solanum tuberosum L., commonly known as potato, is a globally important crop, but it is susceptible to diseases, especially those that spread rapidly with pathogens such as the oomycete Phytophthora infestans, which causes late blight. This disease alone causes an annual global economic loss of $6.7 billion. The severity of this persistent problem is compounded by the impending expiration of fungicide registrations and a dearth of new products, underscoring the need for sustainable alternatives.

In organic farming, the use of copper-based fungicides is quite common. Unfortunately, these substances are harmful to soil microorganisms, underscoring the need to develop resistant varieties in all types of farming. Despite relentless efforts over the past 160 years, achieving long-term resistance has been challenging. Even promising sources of resistance such as S. demissum have been outcompeted by the highly adaptable P. infestans strains.

The focus of modern breeding efforts has shifted to achieving broad-spectrum resistance. This involves the use of multiple quantitative trait loci (QTL) and a range of resistance genes to circumvent the possibility of single-gene failure. The success of these strategies depends on the discovery of new resistances in either wild tuber species or S. tuberosum landraces.

This study provides a comprehensive review of the known resistances to P. infestans in wild potatoes, delving into the resistance gene loci of their genome. The results indicate a potentially broad spectrum of resistance capabilities. In addition, the limited commercial use of resistant species indicates a promising area of untapped potential that could spur future improvements in potato breeding.

Late blight-resistant wild relatives of potato

Encompassing approximately 1500 species, the genus Solanum of the family Solanaceae is characterized by a significant number of tuber-bearing species found in the section Petota. The taxonomic division of the Petota section is recognized in two main ways: Hawkes’ 1990 taxonomy, which recognizes 232 species, and Spooner et al.’s 2014 revision, which distills these into 107 species based on molecular and morphological evidence.

Interestingly, Hawkes’ taxonomic structure is widely adopted because of its concordance with traditional genetic data. Among the various species, 85 wild species exhibit resistance to P. infestans, as determined by methods such as field tests, leaf tests, and tuber tests, albeit with varying comparative results.

The species S. demissum, S. bulbocastanum and S. microdontum stand out for their inherent resistance. There are twenty-five newly discovered species that suggest potential resistance, but the genetic specifics of these species, particularly S. pampasense and any associated known R gene homologues, warrant further detailed study.

Resistance mechanisms against P. Infestans

Phytophthora infestans, native to central Mexico, is a fascinating case of co-evolution with wild potato species. This process produces a number of virulence genes, such as Avr-sto1, which provide a robust defense against host resistance. In response, corresponding resistance genes, such as Rpi-sto1 from Solanum stoloniferum, recognize these virulence genes.

Most of these resistance genes are of the NLR type, serving as receptors that can distinguish specific pathogen proteins. An important group of these proteins are the effectors of the RXLR class, which serve to suppress plant defenses. It’s striking that the P. infestans genome shows an immense diversity with more than 560 RXLR effector genes.

The zigzag model provides a detailed map of the intricate stages of host-pathogen interaction, highlighting NBS-mediated RXLR recognition as a secondary defense response known as effector-triggered immunity (ETI). There is also a possible primary defense strategy that detects apoplastic effectors through receptor-like proteins (RLPs) and kinases (RLKs). This mechanism, known as MAMP-triggered immunity (MTI), involves pattern recognition receptors (PRRs) that recognize microbe-associated molecular patterns (MAMPs). However, the practical use of PRR genes to breed potatoes resistant to P. infestans has yet to be firmly established.

R genes and QTL for P. infestans resistance in wild potato species

Research on genetic disease resistance in potato has been conducted in 32 of 85 wild species, with 61 resistance (R) genes identified in 27 species and 37 quantitative trait loci (QTL) specified in 11 species. Typically, a single species has been observed to harbor multiple R genes or QTL. Interestingly, there are cases where a gene or QTL can be traced to 12 different species.

The distribution of these genetic elements follows a particular pattern. R genes are clustered predominantly on chromosomes 4, 9, and 11, a clear demonstration of gene clustering. QTLs, on the other hand, show a more dispersed pattern, particularly on chromosomes 10 and 11.

In the R gene landscape, certain genes, such as R2 and Rpi-abpt, make their home in the R2 and R3 clusters on chromosomes 4 and 11, respectively. Other genes, such as Rpi-edn3 and Rpi-avl1, are located in the N cluster on chromosome 11. Introducing genes from different clusters into a single variety has the potential to improve disease resistance.

RenSeq, an advanced technique for sequencing NLR genes, has proven invaluable. This method facilitates the distinction between functional and non-functional R gene alleles and even opens the door to the discovery of new R genes within the NB-LRR gene family.

Interspecific hybridisation with wild potato species

The resistance traits of potato crops are mainly derived from different donor species with different ploidies, including diploid, tetraploid and hexaploid forms. A key aspect in determining their cross-compatibility depends on their respective ploidy levels and endosperm balance number (EBN). Incompatibility is often due to uneven endosperm development.

The majority of potato cultivars are 4x, 4 EBN, in contrast to most tetraploid wild species, which are characterized as 4x, 2 EBN. Interestingly, compatibility is more likely to be found between species with similar EBNs.

To facilitate hybridization between traditionally incompatible species, scientists have turned to ploidy manipulation, either by doubling the chromosome and EBN or by inducing spontaneous duplication in callus culture. Such manipulations could involve raising diploid species to tetraploid levels to achieve compatibility. In addition, diploids naturally synchronize with 4x, 4 EBN species via unreduced gametes.

When considering resistance to P. infestans, the primary gene pool provides a limited number of resistant cultivars. In contrast, the secondary pool provides a more diversified base, with 11 out of 68 species having no hybridization barriers. Meanwhile, the tertiary pool consists mainly of diploid species with an EBN of 1.

Opportunities for diploid breeding

The practice of breeding diploid potato varieties, initiated in the 1950s, offers significant advantages, including the use of Mendelian segregation principles to facilitate the creation of superior potato varieties. In particular, diploid breeding has a notable advantage for P. infestans resistance because of its compatibility with a variety of late blight resistance donor species.

The central goal of these breeding efforts is to develop high-quality inbred lines that can rival the performance of tetraploid varieties. Propagation from true potato seed is not only cost-effective but also significantly reduces the risk of disease. These inbred lines can effectively incorporate resistance genes from diploid wild species while eliminating undesirable wild traits.

Despite these advantages, diploid breeding has been hampered by natural self-incompatibility and inbreeding depression, both of which are associated with adverse effects on plant development. However, the discovery of a self-compatibility inducer in S. chacoense has opened the way to the creation of homozygous diploid inbred lines.

In the future, the potential selection of elite diploid lines through this approach could greatly accelerate scientific research on genetic traits and resistance genes.

Late blight resistance through genetic engineering

The process of developing resistant varieties uses a technique known as introgression, in which resistance genes are introduced into elite inbred lines for diploid hybrid breeding. This strategy has found favor in both traditional breeding and genetic engineering. In particular, the use of genetically modified organisms (GMOs) in this area is controversial due to conflicting political regulations and varying levels of consumer acceptance. However, it’s undeniable that genetic engineering offers certain advantages, such as increased speed and precision.

Take, for example, the use of cis-genesis in varieties such as ‘Fortuna’, which incorporates the Rpi-blb1 and Rpi-blb2 genes from S. bulbocastanum through Agrobacterium-mediated transformation. Similarly, Innate® potato varieties contain a late blight resistance gene from S. venturii (Rpi-vnt1) and other quality traits derived from wild potato species. Cis-genesis provides an efficient pathway for rapid integration of multiple R genes, bypassing the notorious obstacle of linkage drag often encountered in conventional R gene introgression.

Potato varieties exhibit a trait called quantitative resistance, a product of gene interaction that confers a degree of pathogen tolerance without altogether preventing infection. Despite these advances, the jury is still out on whether durable resistance can be successfully engineered.

Conclusion

The potential of introducing new donor species for P. infestans resistance breeding cannot be overstated. Elucidating the exact location and function of these genes is paramount to our understanding and use of these species. Rather than relying solely on individual genes, it is the combination of genes from multiple sources and the application of quantitative resistance that will provide more durable protection.

Diploid-level breeding is emerging as a promising strategy, providing the means to generate improved inbred lines. This not only allows for superior resistance mapping but also provides high-quality material for the development of resistant cultivars. At present, the use of genetic modification is limited. However, the advent of cis-genesis has the potential to strengthen organic agriculture, suggesting a likely need for a re-evaluation of current regulations.

In essence, these strategies are all aimed at the same goal: establishing a sustainable, carbon-neutral form of agriculture that significantly reduces our dependence on synthetic pesticides.

Source: Blossei, J., Gäbelein, R., Hammann, T., & Uptmoor, R. (2022). Late blight resistance in wild potato species — Resources for future potato (Solanum tuberosum) breeding. Plant Breeding, 141(3), 314–331. https://doi.org/10.1111/pbr.13023
Author: Jorge Luis Alonso G., an information consultant specializing in the potato crop.
Photo: Wild potato species growing on a rocky hillside in the Andean highlands. Credit International Potato Center.

Editor & Publisher: Lukie Pieterse


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