Soybean genome turns out to be soysoybeanbean

Chromosomes copied themselves at least twice

Scientists finally do know beans about soybeans, thanks to a newly unveiled genome sequence.

SPILLING BEANS Researchers have released a draft of the genetic blueprint of the soybean plant, one of the larger plant genomes to be sequenced so far. Image: Roy Kaltschmidt

The plant’s DNA contains a surprising amount of duplication, says geneticist Scott Jackson of Purdue University in West Lafayette, Ind. Having the soybean’s genetic blueprint, he says, should help scientists both improve crop varieties and study the evolutionarily important process of genome doubling.

Soybean’s set of chromosomes has copied itself at least twice, approximately 59 million years ago the first time and then again about 13 million years ago, Jackson and his colleagues report in the Jan. 14 Nature. Redundant genes often retool or vanish, but soybean plants still have multiple copies of almost three-quarters of their genes, the researchers say.

Making extra copies of a genome, leading to what’s called polyploidy, brings the risk of molecular mayhem when it’s time for chromosomes to pair up during reproduction, Jackson explains. A genetic traffic jam can leave a plant sterile, yet duplications happen. “We don’t know why they happen; we don’t know how they happen,” he says.

Most, if not all, flowering plants have copied their genetic material at some time in their histories, comments Keith Adams of the University of British Columbia in Vancouver, Canada. “What is particularly interesting about the soybean is that it has an evolutionarily recent ‘paleopolyploidy’ event,” he says.

Even in its modern, duplicated form, the soybean genome is small for a plant, Jackson says — only a third of the size of the maize genome, for example. Yet it’s one of the larger plant genomes that geneticists have managed to sequence so far: genetically 10 times the size of the lab staple Arabidopsis.

The new draft, based on a soy variety called Williams 82, covers 85 percent of the 1.1 billion pairs of nucleotide bases that form the building blocks of the plant’s DNA. The plant has some 46,000 protein-coding genes, the researchers say.

About a third of these genes fall into an awkward place as far as plant breeders are concerned, Jackson says. This portion of the genes lies in nonrecombining zones, where genes don’t shuffle around to create new mixes of traits.

In addition to the protein-coding genes, researchers found, about 59 percent of the soy genome is composed of repetitive stretches of DNA called transposable elements, which typically stick copies of themselves around the genome.

Studying a group of these elements has revealed for the first time that a “dead” element, one that has lost the ability to copy itself, can regain its powers, says soybean geneticist Jianxin Ma, a coauthor also from Purdue. The dead element revives by exchanging genetic material with a functional counterpart, he and colleagues report in a separate paper to be published in the Plant Cell.

The soybean’s sequence will boost biologists’ understanding of relatives in the legume family as well, says Nevin Young of the University of Minnesota in St. Paul. He’s a coordinator of the effort to sequence the legume Medicago truncatula, whose genome is now available in an early form.

Legumes rank as the third largest family of flowering plants. Peanuts and lentils, as well as important crops in Africa and India such as the common bean, belong to the family, as do many of the trees in the Amazon Rainforest. The family has evolved a knack for corralling microbes into nodules that turn atmospheric nitrogen into a form that the rest of life on Earth can use. So Young hails the soybean genome as “quite an accomplishment that’s important for both applied agricultural research as well as basic plant genetics.”

Susan Milius is the life sciences writer, covering organismal biology and evolution, and has a special passion for plants, fungi and invertebrates. She studied biology and English literature.

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