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Draft Genome for Upland Cotton—Which Accounts for More Than 90% of the World’s Cultivated Cotton and $500 Billion in Economic Impact—Is Established; Should Prove Resource for Engineering Superior Cotton Lines and Fiber Improvement

In a groundbreaking achievement led by an international team that includes Clemson (South Carolina) scientist Dr. Chris Saski, the intricately woven genetic makeup of Upland cotton has been decoded for the first time in the ancient plant's history. Dr. 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 Dr. Saski's and his colleagues’ 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 draft genome sequence, unveiled April 20, 2015 in an online, open-access article in Nature Biotechnology, will provide the know-how to engineer superior lines that will help clothe, feed, and fuel the ever-expanding human population. The Nature Biotechnology article is titled “Sequencing of Allotetraploid Cotton (Gossypium hirsutum L. acc. TM-1) Provides a Resource for Fiber Improvement.” "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 Dr. 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 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 of chromosomes (tetraploid), adding multiple layers of complexity for scientists such as Dr. Saski. "You can only imagine the confounding problems that can occur when you have multiple genomes," said Dr. Saski. "I'm interested in the process underlying polyploidization and how a better understanding of this complexity can be leveraged to breed better cotton." Dr. Saski's U.S based consortium, which includes Dr. Brian Scheffler of the U.S. Department of Agriculture, Dr. David Stelly of Texas A&M, Dr. Don Jones of Cotton Inc., and Dr. 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 Chinese professors Tianzhen Zhang and Ruiqiang Li to assemble the draft genome of Upland cotton. "China is the largest cotton-producing country in the world," said Dr. 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.

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 Dr. 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." Dr. Kresovich was not involved in this research effort.

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.

"Dr. Saski and his colleagues have developed innovative strategies to dissect the cotton genome using comparative genomics, genetics, computational biology, and high-performance computing," said Dr. 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."

[Press release] [Nature Biotechnology article]