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International team unravels the cotton genome

chris saski
Chris Saski is the director of Clemson’s Genomics and Computational Biology Laboratory. He was part of an international team that decoded the upland cotton genome. Courtesy Jim Melvin and Clemson University.

Geneticists from around the world have unraveled the intricately woven genetic makeup of upland cotton. This plant is the main source of renewable textile fibers in the world, a strain responsible for more than 90 percent of cultivated cotton worldwide and a global economic impact of $500 billion.

Farmers have grown upland cotton since the time of the American Revolution, and it remains a staple crop to this day. Cotton breeders find drought-like conditions and high salinity soils challenging and look for new varieties better able to resist constant threats from pests and diseases.

“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 study co-author Chris Saski, director of Clemson’s Genomics and Computational Biology Laboratory. “With a genome map, you can reveal the biology and DNA signature underlying cotton fiber development and use this information to breed lines with advanced fiber elongation and fiber strength.”

Saski’s US-based consortium, which includes Brian Scheffler of the US 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.”

sequencer used to unravel the upland cotton genome
One of the sequencers used to unravel the upland cotton genome. Courtesy Jim Melvin and Clemson University.

Unlike humans, who have two sets of chromosomes (from a mother and a father), the upland cotton genome has four. This polyploidy genetic construction occurs in about 80 percent of all plant species. Using the k-mer frequency method of genetic sizing, Saski’s team estimated the size of the upland cotton genome to be 2.5 billion base pairs. The assembled genome is available on the CottonGen database.

“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 genome sequence, recently published in Nature Biotechnology,will provide the know-how to engineer superior lines that will clothe, feed, and fuel the ever-expanding human population.

--Jim Melvin, Clemson public services 

--Lance Farrell

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