In a groundbreaking achievement led by an international team that includes Clemson scientist Chris Saski, the intricately woven genetic makeup of Upland cotton has been decoded for the first time in the ancient plant’s history.
Saski participated in sequencing the genome, which is a crucial stepping-stone toward further advancements of understanding the inner workings of one of the most complex and treasured plants on the planet.
The future implications of Saski’s research in the short and long terms are both financial and holistic. Upland cotton, which accounts for more than 90 percent of cultivated cotton worldwide and has a global economic impact of $500 billion, is the main source of renewable textile fibers.
The genome sequence, unveiled Monday in the renowned scientific journal Nature Biotechnology, will provide the know-how to engineer superior lines that will clothe, feed and fuel the ever-expanding human population.
“From the discovery standpoint – having a solid foundation to begin measuring genetic diversity and how the genes are organized – this is a game-changer,” said Saski, director of Clemson’s Genomics and Computational Biology Laboratory. “With a genome map and genetically diverse populations, you can reveal the biology and DNA signature underlying cotton fiber development. Then you can use this information to breed cotton lines with advanced fiber elongation and fiber strength, which are crucial to the industry. This first draft of the genome sequence is a solid foundation for unlocking cotton’s mysteries.”
Upland cotton, which has an economic impact of $205 million in South Carolina alone, came into existence more than a million years ago when two separate species hybridized, creating a plant that has multiple genomes. Unlike humans, who have two sets of chromosomes (from a mother and a father), the Upland cotton genome is configured with four sets, adding multiple layers of complexity for scientists such as Saski.
“You can only imagine the confounding problems that can occur when you have multiple genomes,” said Saski. “I’m interested in the process underlying polyploidization and how a better understanding of this complexity can be leveraged to breed better cotton.”
Saski’s U.S based consortium, which includes Brian Scheffler of the U.S. Department of Agriculture, David Stelly of Texas A&M, Don Jones of Cotton Inc. and Jeffrey Chen of the University of Texas at Austin, traveled to Nanjing Agriculture University in eastern China. There they worked with a team led by professors Tianzhen Zhang and Ruiqiang Li to assemble the draft genome.
“China is the largest cotton-producing country in the world,” said Saski, whose initial research on the project began more than four years ago. “In the end, we were successful in setting the stage for using DNA information to inform and benefit breeders.”
Upland cotton is one of South Carolina’s foundational commodity crops. It has been grown since the time of the American Revolution, and it remains a staple crop to this day. It is also South Carolina’s leading agricultural export.
One of Clemson’s DNA sequencers played a role in deciphering the cotton genome.
Image Credit: Jim Melvin / Clemson University
Cotton breeders are being challenged to release new varieties suitable for drought-like conditions and high salinity soils, and that are also better able to resist constant threats from pests and diseases.
“The techniques and approach Saski and his collaborators are applying to decode the complex cotton genome will have a profound impact on the way cotton is improved through breeding,” said Stephen Kresovich, Coker Chair of Genetics and director of Clemson’s Institute of Translational Genomics. “These insights will also advance our understanding of polyploidy genetics, which is so common in crop plants.”
The cotton genome that produces spinnable fibers is extremely complex because of the presence of multiple genomes, a phenomenon that occurs in about 80 percent of all plant species.
“Saski and his colleagues have developed innovative strategies to dissect the cotton genome using comparative genomics, genetics, computational biology and high-performance computing,” said Kresovich. “The results of this work will have a direct impact in the discovery of novel traits in cotton and related species and will set the stage for accelerated agronomic improvement. As the future unfolds, South Carolina will certainly be a major benefactor.”