HudsonAlpha plant genomics researchers surprised by cotton genome

New reference-grade assemblies published in Nature Genetics

April 20, 2020 (Huntsville, Ala.) – Plant genomics researchers at HudsonAlpha Institute for Biotechnology announce the surprising results of a cotton sequencing study led by Jane Grimwood, PhD, and Jeremy Schmutz, who co-direct the HudsonAlpha Genome Sequencing Center (HGSC). The goal of the project was to identify differences among wild and domesticated cotton that could be used to reintroduce agriculturally beneficial traits like disease or drought resistance. The results, however, surprised the researchers and led them to unexpected conclusions, as described in their paper in Nature Genetics.

Jane Grimwood, PhD

“The importance of this study is that it helps us understand more about cotton fiber development,” said Grimwood, who is a faculty investigator at HudsonAlpha. “But perhaps more importantly, it reinforces the surprising concept that wild and domesticated cotton is remarkably similar, leading us to the conclusion that we will need to work on other approaches to generate diversity for cotton species.”

For the study, the group sequenced and assembled reference-grade genomes for five different species of allotetraploid cotton and compared them with two diploid cotton genomes. Their genomic analysis showed that two ancestral diploid cotton genomes came together to form what is basically the modern tetraploid cotton between 1 and 1.6 million years ago.

Then, about 8,000 years ago, humans began to domesticate cotton for agriculture. They selected wild plants for cultivation that had desirable traits like stronger fiber or more cotton on each plant. Humans then continued to choose plants for breeding that would improve yield and the quality of the harvested crop.

“When we compared the wild cotton plants to domesticated cotton, we expected to see a genetic bottleneck where many wild traits had been discarded,” said Schmutz, a faculty investigator at HudsonAlpha. “What you typically see with these crops is that all the selection has gone into improving production, potentially at the cost of losing beneficial genetic material from the wild species.”

What they found, however, surprised them.

The wild and domesticated genomes, it turns out, were incredibly similar.

Jeremy Schmutz

“In all of the cotton tetraploids, there’s less diversity between what are supposed to be different species of cotton than between two humans or even within different cells in a single human body,” Schmutz said.

This lack of diversity means that researchers won’t be as easily able to reach back into the wild cotton gene pool to introduce lost traits like disease resistance back into cultivated cotton plants.

“We can’t only rely on the gene pool to make changes to the plant architecture because those wild genes don’t exist. Exploring the route of mining natural diversity won’t work. The only real way forward to improve cotton as a crop will be genome editing,” Schmutz said.

The result of this surprising discovery has been the launch of new projects for Schmutz, Grimwood and their team at HudsonAlpha. To begin with, they now have complete comparison genomes for multiple species of the same crop plant. This knowledge allows them to “walk” from one species to the other to introduce desirable traits to cultivated cotton.

“We are the first group to do these sorts of large projects where we are sequencing multiple high-quality references from the germplasm with the goal of getting direct comparisons across multiple species,” Grimwood said.

“We just sequenced a cotton genome in two days,” Schmutz added. “The promise of that speed is that we can start to move from inferred variation where you look at a single reference and infer the variation to looking at multiple references and directly comparing the differences.”

One ongoing project in the HGSC in collaboration with Clemson University, then, is trying to accelerate targeted gene editing in cotton. The group is looking at genetic mechanisms that enable fast transformation in cotton so they can bump up the rate of making targeted modifications.

In addition, while the group was surprised to find so much similarity among the cotton genomes, they did find some useful variation. Wild cotton, for instance, does have some more disease resistance triggers than cultivated cotton varieties, which tend to be more vulnerable.

“This is the basis from which we can start to compare what else we can do with existing cotton diversity,” Grimwood said. “Breeders have selected for ‘improved’ strains of cotton based on phenotype changes but they don’t necessarily have a full understanding of the changes they are making on the genetic side. With this new information, they can look at what their selections are doing on a genetic level.”

Even though the project results were unexpected, the entire team is confident that the newly assembled cotton genomes will lead to direct benefits for cotton producers and the cotton industry.

Don Jones, the Director of Agricultural Research at the nonprofit Cotton Incorporated, said these reference grade assemblies are significant advancements for improving the sustainability of cotton production.

“The results described in this Nature Genetics publication will facilitate deeper understanding of cotton biology and lead to higher yield and improved fiber while reducing input costs. Growers, the textile industry, and consumers will derive benefit from this high impact science for years to come,” Jones said.

This work is supported by grants from the National Science Foundation, U.S. Department of Agriculture and Cotton Incorporated. In addition to the HudsonAlpha team, the publication included researchers from 12 other institutions: the University of Texas at Austin; Nanjing Agricultural University in Nanjing, China; Texas A&M University in College Station, Texas; the U.S. Department of Agriculture in Raleigh, N.C., and Stoneville, Miss.; Zhejiang A&F University in Lin’an, China; Clemson University in Clemson, S.C.; Iowa State University in Ames, Iowa; the U.S. Department of Energy Joint Genome Institute in Walnut Creek, Calif.; Mississippi State University; Alcorn State University in Lorman, Miss.; and Cotton Incorporated in Cary, N.C.

About HudsonAlpha: HudsonAlpha Institute for Biotechnology is a nonprofit institute dedicated to developing and applying scientific advances to health, agriculture, learning, and commercialization. Opened in 2008, HudsonAlpha’s vision is to leverage the synergy between discovery, education, medicine, and economic development in genomic sciences to improve the human condition around the globe. The HudsonAlpha biotechnology campus consists of 152 acres nestled within Cummings Research Park, the nation’s second largest research park. The state-of-the-art facilities co-locate nonprofit scientific researchers with entrepreneurs and educators. HudsonAlpha has become a national and international leader in genetics and genomics research and biotech education and includes more than 30 diverse biotech companies on campus. To learn more about HudsonAlpha, visit

Media Contact:
Margetta Thomas
[email protected]