How Diverse Are the Genes of the Potato?

Published online: Jun 28, 2018 Articles
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Source: Laboratory Equipment

The potato is a crop vital to feeding the teeming human species worldwide.

When colonialism first disseminated the spud widely from its South American beginnings, it became a staple crop of a booming global population of billions. When it failed, like with fungal blight of the mid-19thcentury in Northern Europe and Ireland, millions died or were displaced.

The 21st century implications are clear: as billions more people are going to need sustenance, the rich source of a wide swath of vitamins and minerals is likely to be as important as ever.

At the same time, some critics have pointed out that the dangers of monocultures proven by privations of the past have yet to be learned by societies great and small.

All this is to say that plant biologists have a tuber controversy on their hands as deep as the DNA of the spud itself.

The latest scientific debate has played out in the Proceedings in the National Academy of Sciences.

Last fall, a team led by plant biologists at Michigan State University did a massive survey of potato samples, both cultivated and wild. Their samples were taken from the U.S. Department of Agriculture’s potato gene bank that included wild species from South America, traditional cultivars in North America.

DNA was purified from leaf samples using the Qiagen DNeasy Plant Tissue Kit. Paired-end sequencing libraries were sequenced on an Illumina HiSeq 2500 system at Michigan State, according to the paper. The researchers found a staggering amount of variety.

“Cultivated potato harbored striking levels of diversity… exceeding estimates from previous crop-resequencing studies and overturning historic assumption of low founder diversity,” the scientists said.

What’s more, the wild specimens of Solanum found in South America could offer a huge shot of further diversity, assisting breeders worldwide who have “struggled to produce new varieties that outperform those released over a century ago,” according to the paper.

“This study uncovers a historic role of wild Solanum species in the diversification of long-day-adapted tetraploid potatoes, showing that extant natural populations represent an essential source of untapped adaptive potential,” the researchers add.

But another group of scientists said in a letter in the same journal that the diversity is just the product of a flawed methodology in the previous paper.

The new letter is from scientists at the University of Oxford, the University of Wisconsin-Madison and the Novogene Bioinformatics Institute in Beijing. Their recent studies have included next-generation resequencing of major crops that include soybean, cotton, tomato and cotton, among others.

Their look into the potato differed greatly, as shown in the number of SNPs counted.

For instance, the first Michigan State study identified 46,797,252 SNPs in 20 accession of diploid wild species. For the new next-gen count, that number dropped to 10,473,482.

From the 10 diploid land-race genotypes of the potato, the number dropped from 26,560,638 SNPs in the Michigan state count to 8,108,352 SNPs in the latest look, according to the letter.

The reason for the greater diversity reported in the earlier study is that there were “greatly relaxed procedures” that did not effectively filter out candidates, according to the latest letter.

“We suggest that the large number of SNPs (in the first study) resulted from relaxed filtration procedures, likely leading to an overestimate of diversity,” the researchers write. “In sum, their analysis likely retained many false SNPs, which led to overestimates of diversity.”

The key difference, the researchers argue, is the use of a hard filter known as the Genome Analysis Toolkit (GATK) and the SAMtools.

While the Michigan State team used GATK, they did not apply two filtering criteria to the raw SNPs that still counted the low confidence samples.

The Michigan State authors also responded to the letter to defend last year’s study, as C. Robin Buell, the director of the Plant Resilience Institute at MSU, told Laboratory Equipment in an email.

The Michigan State team used multiple filters to detect low-confidence variants, the researchers said said. Additionally, the GATK best practices cited by the critics were designed for human genomics and medical research, and were not necessarily accurate for assessing plant genes.

“We contend that arbitrary extension of filtering parameters established for humans to plants in which heterozygosity, repetitive sequence, structural variation and divergence from reference genomes are several orders higher demonstrates a reductive approach to genomic research failing to account for studies involving more diverse species or, in our study, numerous species,” the MSU team writes.

Whichever the correct analysis, the true genetic palette of the spud could be vital to future sustainability.

The monoculture of the Irish Lumper established by most farmers on the Emerald Isle by the 19th century is the single biggest reason the arrival of the Phytophthora infesans in 1845 was so uniquely devastating, as Laboratory Equipment reported in March.

An estimated 1 million died of starvation, and another million left Ireland for other parts of the world.