The Right Sequence

The potato genome has been sequenced. What does it mean for growers?

Published in the March 2014 Issue Published online: Mar 16, 2014 Sergio Feingold
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A group of researchers from 14 countries (including partners from North and South America, Europe, Oceania and Asia) has recently released the reference genome for the potato. The ancient Andean crop, domesticated with the dawn of agriculture, is finally unveiling its secret code.

This pioneering effort identified 39,031 putative genes in the 723 out of the estimated 840 Millions of DNA bases that comprises the complete genetic information. By the end of 2013, this endeavor was completed and complemented with the anchoring of this sequence to a potato genetic map of 936 cM , where approximately 96 percent of the predicted genes were located in their respective chromosomes.

From a research point of view, this is a great advance that helps in identifying which genes are responsible for each trait in potatoes. This potentially provides a way to understand how the plant resists pests and diseases and adapts to different environmental conditions and stresses such as drought.

To assist in this task, scientists and breeders can use the information on genetic regions associated to different traits (known as QTLs: Quantitative trait loci) retrieved in the past 30 years or so, and try to identify the responsible gene or genes within these regions. The appearance of new sequencing techniques that can show all the genes that the plant expresses in particular situations and specific tissues can help.

Once a responsible gene is identified, scientists and breeders can look at all the gene variants (alleles) that exist in other cultivated and wild potatoes, and then decide which one behaves most suitably to their breeding needs.

The main question is this: How can breeders use this information to breed a better potato? Unlike wheat, corn or soybeans, backcrossing to recover the original genetic background with an improved gene variant is not possible with the potato due to its heterozygous condition, and the typical failure of selfing. Breeders can make use of marker-assisted breeding to decide the parental genotypes of their breeding populations and then track the presence of the desired gene variant without the need to test for disease resistance or cooking quality at early stages of the breeding process.

This limitation makes potatoes a very suitable crop for conventional genetic modification and despite the fact that genetically modified potatoes are used for the starch industry, until the public perception of GMOs for direct human consumption changes, breeding efforts likely will not be directed to this orientation.

The appearance of a new technique called genomic edition, which directly changes genetic sequences at a target gene, opens a new dimension in genetic modification of organisms, and can overcome some of the concerns facing GMOs. To use genomic edition successfully in plant breeding, there are only two pieces of information that need to be put together: 1)which gene to modify, and 2) which sequence will replace the original one. The sequenced potato genome and the ability to identify the gene or genes responsible for that trait help in the former while the search of allelic gene variants is needed for the latter.

It was long believed that the genetic base of the potato is narrow. This is true for European-bred varieties that migrated from its South American origin in the 15th and 16th centuries and are now cultivated in large areas of high latitude across the world. However, this belief gives no justice to the hundreds of native varieties that are still cultivated in vast areas of the Andean region of South America, from Colombia south to Argentina and Chile.

Andean potatoes produce tubers under short days typical in low latitude regions. The process of adaptation of potatoes to Europe and other low latitude regions involved the ability of improved genotypes to tuberize under long days. The information of a specific region on potato chromosome 5 associated to tuberization under long-day conditions and the availability of the sequenced genome led a group of researchers to the identification of a gene that regulates tuberization and plant life cycle length by acting as a mediator between the circadian clock and a mobile tuberization signal. The identification of allelic genetic variants of this gene in native Andean varieties from different latitudes and their subsequent modification can help in cultivation of diverse Andean potatoes in new regions and with modified crop cycles. Hopefully, this will come with the proper recognition and benefit sharing with the original native farmers, who have been improving the potato for the past 10,000 years.

Likewise, the identification of new genes and alleles involved in disease resistance, water use efficiency and industrial and nutritional quality—along with the understanding on how they work—will lead to new improved varieties of potato in the mid-term.

If breeding new potato varieties is like a maze, having the genome sequenced, ordered and anchored is seeing the labyrinth from above.