Looking back on the sequencing of the soybean genome

JGI: https://jgi.doe.gov/jgi-at-25-strengthening-soybean/

Maximizing soybean yield is critical to energy independence in the U.S. Not only does it pair with maize, the dominant source of bioethanol, in crop rotation, but soybean (Glycine max) also has the advantage of reducing the need for nitrogen fertilizer. These impressive environmental and energy advantages explain why soybean is a flagship genome of the JGI’s Plant Program.

While soybean has desirable properties as a liquid transportation fuel, it simply doesn’t yield enough gallons of fuel per acre to compete with gasoline. Yet. 

In 2010, soybean became the first legume species with a published complete draft genome sequence. At the time, the vital global source of both protein and oil was also the largest plant project completed by the JGI. It has since been cited more than 5,400 times, including a number of projects that point to the potential of seed oils as biofuel.

After analyzing the original sequence, Gary Stacey of the University of Missouri said he and his colleagues had identified 1,110 genes involved in lipid metabolism. 

“There’s still a lot of thinking that truck fuel and airplane fuel and things like that are not going to be replaced by electricity anytime soon,” Stacey said when we caught up with him recently. “So, there’s going to be a need for these biofuels and that’s a good niche market for soybean.” 

Upon its initial release in 2009, the soybean genome sequence immediately spurred further research and additional discoveries. Stacey noted that even prior to the sequence being published in Nature, immediate progress had already been made positionally cloning genes involved in agronomic traits related to nutritional quality and disease resistance due to the sequence’s availability via Phytozome. In 2015, a new and revised version brought the soybean sequence up to date with current technology. 

In addition to supporting work on the soybean plant in order to maximize yields for biofuel, the JGI has also helped researchers understand a fungus that threatens these crops as they grow. Asian Soybean Rust is a major problem. Leaves grow discolored and rust pustules develop as the pathogen feeds on its soybean host, which is maintained alive. Once a crop is infected, ASR can decimate up to 60-90% of its yield. 

(Learn more about the soybean genome sequence and ASR in this JGIota, a Genome Insider podcast minisode.)

In 2016, the JGI accepted a proposal from Sebastien Duplessis of the French National Institute for Agricultural Research (INRAE) to sequence a reference genome for the fungus Phakopsora pachyrhizi, a major pathogen of soybean that causes ASR.

“I love working with these guys,” said Duplessis, who has collaborated with the JGI on multiple projects involving rust pathogens. “All along the way, it was just like rediscovering genetics, with the evolution of sequencing technologies and the evolution of bioinformatics.” 

P. pachyrhizi has a very large and complex genome with lots of repetitions, making it very difficult to sequence — roughly 1.25 billion Gb (gigabasepairs — most fungi are around 50 million Mb, or megabases, in size). So, the JGI helped a consortium of researchers from various institutions, including INRAE as well as the Sainsbury Institute, by annotating not just one but three genomes for P. pachyrhizi, which are available on MycoCosm

“We work on making good resistance traits against this disease for use in the field,” said Peter van Esse of the Sainsbury Institute, who works extensively on ASR. “Having the genomes of a crop like soybean ensures that what we bring to the grower is novel … We’re a long way there; we are developing traits with key partners, both Corteva and Bayer, and that’s going really well. And having the sequence data available for us to enable that research will have a great impact for growers.”