Gene for darkening in pinto beans isolated

Researchers in London and Saskatoon have pinned down the specific gene that causes darkening in pinto beans, a discovery that should help speed new variety development.

“Gene-specific markers are more specific and durable, so (breeders) can track the marker more confidently,” said Sangeeta Dhaubhadel. “So for the breeding of slow-darkening or any desirable cultivar it can be selected early in the breeding process and efforts will be more effective, will be faster.”

Dhaubhadel is a plant molecular biologist with Agriculture Canada’s London Research and Development Centre. She worked with PhD student Nishat Islam over four years to isolate the gene, building on foundation knowledge from the University of Saskatchewan dry bean breeding program.

Pinto beans come in two varieties: slow darkening (SD) and regular darkening (RD). The latter have better disease resistance and yield better, but they need to go to market right away because customers prefer lighter-coloured beans. Darkened beans also don’t take up water as easily, so they take longer to cook, a problem that gets worse as they age.

SD beans can be held back longer, giving producers more flexibility to time sales to take advantage of better prices.

“Our idea has always been that you would market in the spring when all the number ones are gone,” said Kirsten Bett. “So then you march in there as an exporter and say, ‘hey, I’ve still got number one beans,’ when the price is starting to climb.”

Bett is a pulse breeder and geneticist who runs the dry bean breeding program at the U of S and collaborated in the work.

She explained that the SD trait in pinto beans has been known since about 2000. She and her colleagues have developed genetic markers that, while not narrowed to the specific gene, have allowed them to develop SD varieties for producers (any variety carrying the CDC WM-# designation from the U of S Crop Development Centre).

She likens the genetic apparatus behind darkening to a factory. In RD beans, three “gears” turn smoothly, producing the full amount of pigment. In SD beans, one of these “gears” has a few teeth missing, so it only produces pigment some of the time.

The work of Bett and her colleagues at the U of S, together with the publication of the pinto bean genome around the same time, meant Dhaubhadel and Islam didn’t have to look through the whole genome. But the remainder — more than 27,000 genes — still presented a formidable task. In the end, they found the gene just outside the two markers that it was supposed to be between.

In terms of pinto bean development, finding the actual location of the darkening gene is an incremental improvement. However, Bett said she is intrigued by the possibilities it opens up to chase the trait in other pulse crops.

“That darkening isn’t just in beans. It’s most obvious in beans, but it will also happen in lentils and I don’t know if it’s the same gene,” she said. “So understanding it in one species, especially if you understand at that level, allows you to explore it in other species.”

Dhaubhadel also sees potential to better understand how the pigments themselves, called proanthocyanidins, are made in the plant. Building on the U of S work, she and her colleagues found the genes responsible for making them. This class of compounds have drawn extensive interest for their potential health applications against microbial infection and even cancer.

“There is a lot to do because proanthocyanidin synthesis is a very complex and long process, so we’ve been trying to understand how this gene works,” she said. “It would be interesting to see how this gene could affect similar traits in other beans as well.”

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