Successful hunt for ‘P’ gene to pay dividends for bean growers

Darkening pinto bean problem solved by gene discovery, which benefits breeders and farmers

Darkening in pinto beans has an economic cost for growers and processors, and that spurred researcher Sangeeta Dhaubhadel to hunt for the gene that causes darkening.
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Can one small gene really affect an entire crop or does it amount to only a hill of beans?

It does matter if we’re talking about pinto beans.

“Most beans keep the same look after growers harvest and store them,” said Sangeeta Dhaubhadel, a research scientist at the London Research and Development Centre.

“With pinto beans however, the older they are, the darker they become. This is causing serious economic issues for bean farmers and processors. We needed to find the gene responsible.”

Older, darker beans take about 20 per cent longer to cook, so are less popular with consumers who want convenience. They’re also harder to sell, so their price is discounted. And longer cooking times mean higher energy costs for food processors.

The top row shows slow-darkening pinto beans before they have aged (on left) and after (on right). The bottom row is the regular-darkening pinto bean. photo: AAFC

Those problems spurred Dhaubhadel to look for a solution, and she and her team recently discovered the gene that causes pinto beans to darken with age. Their findings are helping bean breeders create new, slow-darkening varieties more quickly.

There are slow-darkening pinto beans but they lack some desirable agronomic traits, such as high yield and improved disease resistance. So they are less popular even though their seed coat darkens more slowly after harvest.

While scientists have known the genetic location of the traits for some time, no one had found the specific gene that controls the slow-darkening trait. Dhaubhadel investigated proanthocyanidins (compounds experts thought were causing the seed coat darkening) and when comparing slow-darkening (SD) beans to regular-darkening (RD) ones, the latter had more of this compound. She and her team then searched for the ‘P’ gene among the 27,433 genes in pinto bean genome.

‘P’ stands for ‘pigment’ and scientists have linked this gene to colour in other plant species. During tests, the ‘P’ gene reacted as the research team expected — it changed the colour of the seed coats.

Still curious why RD pinto beans darken faster than SD varieties, researchers further clarified that a single mismatch in the ‘P’ gene sequence between RD and SD pinto beans may be responsible for the higher protein activity in ‘P’ gene of the RD varieties.

“It took four years to find this gene and solve the puzzle of seed coat darkening,” said Nishat Islam, a PhD student hired for the gene analysis work.

“Cloning this gene for testing was very challenging, but when we found the correct gene, we were thrilled. It was a ‘Wow!’ moment.”

This research helps breeders look at gene sequence earlier which speeds up the breeding process. With more than a third of dry bean acres in Canada being dedicated to pinto beans, bean breeders can now breathe — and breed — a little easier.

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