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Breeding higher yielding dry beans

Is there a single gene allele (or gene form) responsible for high yields in dry beans? Ten years ago, this might have been an impossible question to answer; today, the answer isn’t far off. In fact, researchers at the University of Guelph recently discovered a gene in canola that influences yield, and preliminary studies show the same gene exists in dry bean (Phaseolus vulgaris).

“Most breeders would say you can’t find a yield gene, because so many things contribute to yield in the end,” says Karl Peter Pauls, a professor in the University of Guelph’s department of plant agriculture. “Yield is not generally considered to be simply an inherited trait, but rather a lot of things correspond ultimately to give you a higher yielding plant.”

However, it is possible to discover quantitative trait loci (QTL) – or sections of DNA that correlate with a particular set of characteristics – and an underlying set of genes contributes to those QTLs, Pauls says.

In other words, many things contribute to high yields, and one of those factors is undeniably genetics. In this case, the gene under investigation for its effects on yield is called BnMicEmUp.

Pauls is heading a joint Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA) and University of Guelph three-year study examining yield/anti-yield gene alleles in dry bean, with the goal of streamlining breeding projects focused on introducing varieties with improved resource use efficiencies.

He says BnMicEmUp was discovered almost by accident, when John Chan, a PhD student, discovered the gene in embryonic cells for canola. “Since it wasn’t identified, we had no idea what its gene function might be,” Pauls says.

Another PhD student, Fariba Shahmir, took the gene and implanted it in a model plant, Arabidopsis – a close relative of canola – using transgenic tools to “upregulate” or over-express the gene in some materials, and “turn it down,” or under-express it, in other materials.

“So we had Arabidopsis plants where the gene was turned down and plants where it was upregulated,” Pauls explains. “Once you had that spread between it being over- and under-expressed, some of the effects on vegetative growth and seed production became obvious.

“If you turned the gene down you increased seed yield, and if you turned it up you inhibited seed production.”

Because the gene had an observable impact on Arabidopsis seed numbers, and this can be translated into a rough estimate of yield, Pauls’ team decided to look for the gene in dry beans – a crop they’d been working on for years. “We thought, well, let’s take a look,” he says.

Using the recently released genome sequence for dry beans, the team was able to quickly zero in on BnMicEmUp because they knew what they were looking for.

How it works
BnMicEmUp is part of a class of genes that occurs in many plant species; according to Pauls, it appears to mimic a gene type that is involved in plant stress response.

“This is how I try to explain the ‘anti-yield’ gene. I think it’s related to a brake on a car – when the conditions are not good for vegetative growth, the plant doesn’t invest in vegetative growth in its response to stress,” he says. “It’s not actively growing; it’s protecting whatever physiological processes it needs for survival. And some plants turn on the brakes early – say, in a period of drought – and are not willing to take a risk.”

In the first phase of Pauls’ study, a masters student, Yanzhou Qi, measured the activity of the gene in a range of materials that vary significantly in terms of yield potential – a small set of 20 dry bean varieties – and found what they expected: a negative but not statistically significant correlation between gene expression and yield.

In 2015, Pauls’ research associate, Yarmilla Reinprecht, bean breeding technician Tom Smith, and Annie Cheng, a summer student in Pauls’ program, conducted a field trial with an expanded set of 100 varieties. Now, Reinprecht and Erika Cintora, an exchange student from Mexico, are analyzing gene activity within samples from the large field trial, looking for correlations between gene activity and yields.

The work can also be applied to soybeans, Pauls says, as dry beans and soybeans are closely related.

“We can find the locations of that gene in the genomes, and it corresponds with yield QTLs both in beans and soybeans. And then we can begin to look at polymorphisms between different forms of this gene so that in the end we have markers for an allele from a high-yielding versus an allele from a low-yielding bean,” he says.

The next step is to get markers in the gene, which can be used to screen germplasm for positive alleles for a high-yield trait. “If we can prescreen germplasm that we use for making crosses for the genes that we think contribute to the traits we’re interested in, then we are a step ahead in breeding superior varieties,” Pauls says.

“Conventional breeding adds about one per cent per year in terms of yield potential to bean varieties. What we hope is that we’ll be able to do an even better job in terms of breeding varieties with higher yield potential.”

Yield isn’t the only desirable ingredient in new bean varieties: Pauls’ team is also working on common bacterial blight and anthracnose disease resistance, cooking qualities, folate content and nitrogen fixation. It might be 10 years before Canadian bean growers can benefit directly from the yield/anti-yield gene research, but new high yielding and disease resistant varieties, like OAC Inferno and Mist, developed by the Guelph bean breeding program, are
already making an impact.


April 19, 2016  By Julienne Isaacs

Annie Cheng (left) and Yarmilla Reinprecht (right) at the field trial in Elora Is there a single gene allele (or gene form) responsible for high yields in dry beans?


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