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Unlocking the potato’s potential: A deep dive into the potential of diploid breeding

This article was written by Jorge Luis Alonso G., an information consultant specializing
in the potato crop.

Husain I. Agha, Laura M. Shannon, and Peter L. Morrell, researchers at the University of Minnesota, completed a review of a recent scientific paper published in the journal Cell Genomics titled: “Unloading potatoes: Potato breeding moves forward with only half the genome“.

The article below is a summary of this review.

On the sprawling battlefields of agriculture, the potato is a titan, reigning as the world’s most widely grown vegetable. But unlike other staples, potato yields haven’t improved in a century. Why is that? The culprit is its complex genetic blueprint known as the autotetraploid genome, the bane of commercial potato growers outside of South America. This genetic complication limits the use of traditional breeding techniques critical to other crops, such as creating inbred lines or integrating favorable traits through introgression.

Historically, the first crop breeding crusades were aimed at creating self-compatible lines that remained true to essential traits. In the labyrinthine world of autotetraploidy, however, this is a virtually Sisyphean task. Today, the potato breeding odyssey begins with sowing an army of tens of thousands of genetically unique individuals, only to find that only 1% meet market class standards based on visual criteria.

For the past decade, a coalition of public and private researchers has been working to revolutionize the potato world. Their bold goal is to move the potato from an autotetraploid clonal crop to a more manageable diploid inbred hybrid crop. This bold project aims to give breeders the ability to lock in favorable traits, introduce beneficial stress resistance from wild diploid cousins, and flexibly adapt to fluctuating environments and market demands.

However, the quest to breed a diploid potato is a Herculean task. Attempts to create inbred lines are hampered by lethal levels of inbreeding depression, caused largely by the segregation of recessive alleles that were benign in the heterozygous state. To circumvent this obstacle, strategies have been employed to target large-effect deleterious alleles, but these methods are costly and require the selection of starting material with relatively few such deleterious alleles.

The Challenge: Breeding Diploid Potatoes and Overcoming the ‘Domestication Cost’

Diploid potatoes, first domesticated in the Andes of South America, haven’t seen the focused intensity of modern breeding efforts. While the domestication and genetic improvement of crops increase traits that are beneficial for human use, it also imposes a “domestication cost” through reductions in effective population size (Ne) or the number of individuals contributing to the domesticated population.

This reduction leads to an increase in genetic drift and a decrease in selection efficacy throughout the genome. As Ne shrinks, linkage selection becomes more important, potentially driving deleterious variants to higher frequencies and contributing to mutational load in domesticated populations.

Many cultivated species have evolved over millennia, selected over a wide geographic range, and often with multiple independent origins. Both of these factors buffer demographic effects and potentially mitigate the genetic toll of crop domestication and subsequent improvement. However, intensive modern breeding threatens to drastically reduce Ne and impose a severe limit on the genetic diversity of improved crops. The consequences could be a devastating loss of useful genetic variants and a sharp increase in fixed mutational load.

Identification of deleterious variants in diploid potato germplasm is key to the development of inbred hybrid lines. Once the deleterious variants with large effects are identified, they can be avoided, reducing the fixed load in breeding populations and accelerating the development of elite inbred potato lines.

Strategies to address the deleterious variation in diploid potatoes, such as the formation of heterotic groups, are being explored. Understanding the distribution of fixed and segregating loads in specific breeding populations could facilitate the formation of heterotic groups that maximize fixed loads within each group while minimizing segregating loads between groups. However, heterotic groups are not a silver bullet — they cannot compensate for the need to improve the population.

A critical factor to consider is the fitness and dominance effects of all variants. The distribution of fitness effects is notoriously difficult to characterize. While dominance is an important component of heterosis, understanding it is only part of the larger puzzle. More research is needed to understand the phenotypic cost of individual deleterious variants in order to truly optimize the breeding process.

Pioneering Approaches: Wu et al.’s Insights into Deleterious Variation and Heterotic Groups

Recent research by Wu et al. has taken a leap toward these goals. They propose a future where plant breeding efforts are informed and guided by an understanding of the nature and impact of variants present in breeding lines. In their study, they have revealed the sheer magnitude of deleterious variation in diploid potato germplasm.

Wu et al. suggest a strategic approach to inbred lines by focusing on the zygosity of deleterious variants. They show that a lower heterozygous load, even at the expense of homozygous load, maybe a more promising starting point for inbreeding. When creating breeding “populations,” it’s also important to consider the difference between fixed and segregating load.

Although it’s a challenging task, removing the fixed load from breeding populations might be possible through the use of introgression or possibly genome editing. Segregating load, on the other hand, can be reduced by identifying offspring with less load than their parents.

This delicate balancing act involves an inherent trade-off between short-term inbreeding efficiency and long-term, stable improvements in agricultural performance. Although Wu et al. emphasize that inbreeding efficiency improves with individuals carrying a lower heterozygous load, it’s important to remember that inbreeding is not the ultimate goal.

One potential approach to managing deleterious variation in diploid potatoes is the development of heterotic groups. These groups rely on the complementation of deleterious alleles, with more diverse sets of deleterious alleles increasing the potential benefits of heterotic groups. However, even these groups cannot fully compensate for the need to improve the population. Adequate Ne within heterotic groups is essential to facilitate effective recombination.

Ultimately, Wu et al. point the way to a future where plant breeding campaigns are guided by a deep understanding of the genetic variants present in breeding lines. Their findings and recommendations serve as a beacon, guiding researchers and breeders to develop strategies that minimize fixed load while maximizing potential improvements in agricultural performance.

Source: Agha, H. I., Shannon, L. M., & Morrell, P. L. (2023). Unloading potatoes: Potato breeding moves forward with only half the genome. Cell Genomics, 3(6), 100343.
Photo: Credit image by tonodiaz on Freepik

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