JGI at 25: Studying Sorghum’s Survival Skills

2022 marks the JGI’s 25th anniversary. Over the next few months, we’ll be revisiting a number of notable achievements that showcase our collaborations and capabilities to enable great science that will help solve energy and environmental challenges.

An animated gif that shows the number of citations resulting from the original Sorghum bicolor reference genome.

A graphic of the papers, patent applications, and patents citing the JGI’s Sorghum bicolor reference genome. (Neil Byers, Menaka Wilhelm)

Sorghum stands out as a candidate feedstock for biofuels thanks to its drought and flood hardiness. Even with little water, full sunlight and hot temperatures, sorghum plants can photosynthesize and thrive — some varieties grow their leafy stalks 16 to 18 feet into the air. Beyond being a staple grain eaten around the world, sorghum’s potential to adapt and thrive in our changing climate has earned it a place on the JGI’s Flagship Plant Genome roster.

Sorghum has an important feature in common with certain other cereal crops: It performs C4 photosynthesis, which is the fastest way for plants to convert carbon dioxide and water into sugars and oxygen. Both sugarcane and corn share this photosynthetic pathway. However, neither crop shares sorghum’s hardiness, so understanding sorghum’s survival secrets could change not only how we use and grow sorghum, but other important crops as well.

In 2009, the JGI sequenced and analyzed the first reference genome for Sorghum bicolor. Since then, 2,993 publications, 107 patent applications, and 53 patents have cited that genome.

Since publishing that original reference genome, the JGI has also continued to collaborate on research to understand how sorghum fares so well in harsh conditions, and how to engineer sorghum’s strengths into other plants.

A brief timeline of sorghum projects at the JGI:

2009: JGI and collaborators use whole-genome shotgun sequencing to analyze the 730-megabase Sorghum bicolor (L.) Moench genome. Sorghum was the second cereal crop with a fully sequenced genome (following rice in 2002) and the first C4 crop to be fully analyzed.
2014: The JGI updates its Sorghum bicolor reference genome and releases it to the community.
2014: GENCODE project begins. To support growing sorghum and other C4 plants for biofuel production, John Mullet (Texas A & M and Great Lakes Bioenergy Research Center) and his team set out to compare different varieties of sorghum. Initially, the project looks at how each variety stores sugars and sequesters carbon.
2015: Epigenetic Control of Drought Tolerance in Sorghum (EPICON) begins. Peggy Lemaux (UC Berkeley) and her team studied sorghum plants in drought conditions for three years (2016-2018) in the field in Parlier, California at the UC Kearney Agricultural Research and Extension Center.
2017: The JGI and collaborators sequence and annotate the Sorghum bicolor reference genome, BTx623 for the third time, this time aligning it with over 50 other diverse sorghum genomes. Deep sequencing and genetic linkage analysis improve the genome’s accuracy, and increase its length by 29.5 Megabasepairs.
2017: Pan-genome analysis of sorghum begins. Enabled by the JGI’s Community Science Program, Todd Mockler and his team collect diverse lines of sorghum to understand what genes exist across the species. Earlier pan-genomes for other plants, like the soybean relative Glycine max (2014) and the grass Brachypodium distachyon (2017), have identified many more genes than found in the single reference genome, including traits useful for adapting to harsh conditions.
2019: JGI and collaborators analyze the sweet sorghum RIO reference genome. Compared to shorter, grain-producing varieties previously sequenced, this line is sweeter, taller, and grows more biomass.

In ongoing work, JGI and collaborators are continuing to generate sorghum genomes to better understand sorghum’s toughness and energy storage. The S. bicolor reference genome, BTx623, recently received its fifth update. Another 31 varieties have also been sequenced, and the EPICON studies are still informing work on sorghum’s drought tolerance.

A brief timeline of sorghum projects at the JGI:

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