The cerrado, a sprawling savannah that stretches across central and southern Brazil, was dismissed as worthless land for most of human history. As is also the case in other tropical areas, the acidic soils contain a form of aluminum that’s notoriously toxic to food crops and farmers knew no way to plant in them. Over the past decades, though, Brazilian plant scientists have developed methods to change the soil conditions, and have bred crops, through repeated selection, that can withstand the aluminum. Now, in a new PNAS Early Edition paper, researchers have revealed the genetic basis for such aluminum tolerance in maize plants. The findings help them understand what it takes for plants to survive in extreme soils, and could help them select for aluminum tolerance during plant breeding.
“It’s estimated that up to half the world’s potentially arable lands still available for agriculture are highly acidic,” says Leon Kochian, the director of the Cornell University USDA lab and an author of the new work. “And if you look at a map of these, they’re concentrated in the tropics and subtropics, so it’s a major problem limiting agriculture in developing countries.”
Aluminum is the most abundant metal in the earth’s crust, but in most places, it’s bound to other elements and forms stable molecules that have no effect on plants. In areas with highly acidic soil, though, the aluminum is dissolved into a charged cation form that attacks plant roots—first accumulating in their outermost cell walls, then moving inward and blocking signalling pathways and genes.
“You have multiple problems in acidic soils, but aluminum is the big one,” says Kochian.
His lab has studied the basis of aluminum tolerance in sorghum, wheat, and rice plants, and most recently turned their attention to corn. When they analyzed the root tips of maize plants from Brazilian plant breeders that grew best in acidic soils, they found that the roots contained up to three times more of a protein called MATE1. The protein, when it senses toxic aluminum cations, produces compounds that bind to the aluminum, stabilizing it and keeping it from entering the plant’s roots. But Kochian’s group couldn’t determine what was causing the aluminum-tolerant plants to have more MATE1. The MATE1 gene had no unique mutations, nor did the regulatory DNA flanking the gene, which can often impact how much protein is made.
“We were trying to figure out the molecular basis for this, and running into these dead ends,” says Kochian. Then, a member of his lab, first author of the new paper Lyza Maron, decided to look at the number of copies of the MATE1 gene that each plant had. The aluminum-tolerant plants, Maron and Kochian found, had three copies of MATE1, while the others had only one copy, explaining the difference in how much protein each produced. Because of the way experiments looking for mutations are done, the copy number variations (CNVs) hadn’t been revealed earlier.
In humans, CNVs have been linked to physical traits and disease susceptibilities. Researchers knew that CNVs were frequent in plants, but had never pinpointed a particular CNV with such importance.
“I think this is one of the first examples in plants of copy number variation being a regulator of a key agriculture trait,” says Kochian.
The knowledge that extra copies of MATE1 helps corn plants resist aluminum toxicity can help plant breeders who want to select for such tolerance—they can determine whether a particular plant line is aluminum tolerant without waiting to measure its growth in different soil types.