Cassava is genetically decaying, putting staple crop at risk

April 28, 2017 by Amanda Garris, Cornell University
A cassava farm in Nigeria, which is the world’s largest producer of the crop. Credit: Cornell University

For breeders of cassava, a staple food for hundreds of millions in the tropics, producing improved varieties has been getting harder over time. A team at Cornell used genomic analysis of cassava varieties and wild relatives to make a diagnosis: Mutations have corroded the genome, producing many dysfunctional versions of genes and putting at risk a crop crucial to the survival of one-tenth of the world's population.

"The analysis was cleanly able to show that is genetically decaying," said Ed Buckler, a research geneticist at the U.S. Department of Agriculture-Agricultural Research Service and adjunct professor of plant breeding and genetics at the Institute for Genomic Diversity (IGD) in Cornell's Institute of Biotechnology. "It's getting worse through time as it picks up more and more mutations, so when breeders do make crosses they're having to put more and more effort into finding the few offspring that contain at least one functional version of each gene."

Cassava's challenging position – described by Buckler as "pointed in the direction of extinction" – is likely due to a reduction in diversity during domestication as well as the fact that cassava is spread through cuttings rather than seeds. Without sexual reproduction and the concomitant purging of mutations through recombination, approximately 30 new mutations per generation are accumulating.

The research, published April 17 in Nature Genetics, was a test of whether genomewide mutations could be identified computationally. It's a question the group initially set out to answer in maize through a project funded by the Bill & Melinda Gates Foundation, but it was fast-tracked in cassava after a request from the foundation.

The data provide a way forward for breeders to bring greater food security to the tropics by shoring up a key crop that feeds an estimated 800 million people – primarily smallholder farmers – in areas with marginal soils and unpredictable rainfall.

Punna Ramu and Fei Lu, research associates with IGD, used a combination of deep sequencing – collecting enough data to sequence 241 cassava types 30 times – and predictive tools based on evolution to identify which mutations were likely to interfere with a gene's function.

While the frequency of was high at 26 percent, they also uncovered widespread genetic evidence that breeders have been successfully compensating for the dysfunctional alleles in their pursuit of higher productivity and yield. Nearly two-thirds of mutations occurred only in the presence of a second, functional version of the gene.

"Most deleterious mutations are recessive, meaning they are only a problem if the plant has two copies of the mutated gene at the same place," Lu said. "The high heterozygosity in cassava was really the most interesting thing we found – that breeding efforts had successfully masked the deleterious mutations with functional versions."

The findings are already being incorporated into the breeding models of the Cornell-based NextGeneration Cassava Breeding project, also funded by the Gates Foundation. The NextGen project – managed by Chiedozie Egesi in International Programs at the College of Agriculture and Life Sciences, who collaborated on the research – is developing strategies to selectively breed materials to eliminate the mutations, but that's just the start of the ways that the technology could be used.

"In the long run, using genome editing, we could provide the equivalent of personalized medicine to breeding lines," Buckler said. "Essentially these mutations are like in humans. And we're getting to the point where we can identify those deleterious and correct them."

Explore further: Comparative analysis highlights impacts of previous breeding programs on cassava genome

More information: Punna Ramu et al. Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation, Nature Genetics (2017). DOI: 10.1038/ng.3845

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rrwillsj
2.3 / 5 (3) Apr 28, 2017
I was recently searching online material for sweet potatoes, yams and cassava for a couple of storylines I'm working on.

As an important food stock, Cassava has many advantages as a source of starches. The ability to thrive in times of drought being foremost. And resistance to a multitude of pests and diseases that afflict other crops. Also the leaves have nutritional value.

However, the cassava plant survives by producing protective poisons that result in the need to carefully process the harvest before animal and human consumption.

For millennium, Humans have been choosing to breed less toxic, 'sweet' cassavas. Advantageous for food but another target of opportunity for pests.

And as this article so graphically points out, the advantages for survival through thee genetic crapshoot of sexual reproduction versus the obvious accumulation of damaged genes via cloning. As in breeding race horses using the pseudo-science of eugenics.
Porgie
1 / 5 (3) Apr 28, 2017
This is a lame attempt at justifying apposition to GMO. And its lame really. GMO uses less water ,less insecticides, less fertilizer, and produces more per acre and have been around for 3000 years. And believe me your children are not fat and lazy because of GMO. They are because of you.
Shootist
2.3 / 5 (3) Apr 29, 2017
This is a lame attempt at justifying apposition to GMO. And its lame really. GMO uses less water ,less insecticides, less fertilizer, and produces more per acre and have been around for 3000 years. And believe me your children are not fat and lazy because of GMO. They are because of you.


Oh the anti-science is strong in this one.
bhouse1273
not rated yet Apr 29, 2017
The pattern repeats in many contexts. Nature's processes are interfered with by humans having an incomplete understanding of the long-term consequences, leading to various unexpected detriments. In each domain, people then develop proposals to compensate -- artificial bees to pollinate, genetic engineering to combat loss of genetic diversity, seed banks to preserve lost species, etc. And then there is the sell -- these techniques will produce wonder products! The operative word being "product". When nothing exists but corporate organisms and their choice-less consumers, then we will glorify the good old days in corporate media, but wish we still had wildlife to wonder at.
rrwillsj
1 / 5 (2) Apr 29, 2017
I suspect that I am being mistaken for someone who does not enjoy eating...voraciously! Try convincing my waistline...Yeah it ain't listening.

First of all, I doff my hat in solemn tribute to the thousands of generations of women. Whose shrewd foresight and back-breaking labor (you try carrying twenty-odd pounds of wiggling baby on your back or belly, out in the hot sun, while hoeing and weeding and gleaning)

Whose collective efforts across millennia developed all the food you stuff into your maw without the slightest expression of gratitude from your over-entitled, over-fed egotism.

I don't give a steaming pile of fertilizing manure about the fake debate between ignoranting pro-GMO and ignoranting anti-GMO. Nothing you eat is unaltered, nothing!

Not having read the original research paper, based solely on my interpretation of this posted article. I can only hope, urge that people smarten up enough to find and implement solutions to these looming biological disasters.
Pooua
not rated yet Apr 29, 2017
Based on evolutionary theory, with all those mutations, cassava ought to begin walking upright any day now!
rrwillsj
1 / 5 (2) Apr 30, 2017
Good one Pooua!

However, if the shambling muta-cassava's are smart? They'll follow the example set by Orangutans.

Some smart-ass banyol will tell you, with a straight face, that the reason Orangutans refuse to talk? Is to avoid paying taxes....

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