University debuts cotton gold-standard genome sequence

An international consortium, led by Professor Andrew Paterson of the University of Georgia, has made publicly available the first ‘gold-standard’ genome sequence for cotton.

Cotton was among the first plants studied at the molecular level, and the sequence obtained by Paterson and his team is the culmination of a 20-plus year effort in the analysis of cotton genes and genomic DNA. This critical sequence will be invaluable to better understanding and optimizing the production and sustainability of the cotton plant.

The research effort of Paterson and others gained momentum in 2007 when a proposal from 22 leading cotton scientists representing the world’s seven largest cotton-producing nations was approved by the United States Department of Energy (DOE) Joint Genome Institute (JGI) Community Sequencing Program.

The study established the strategy that was used for ‘gold-standard’ sequencing of the New World cotton progenitor, Gossypium raimondii; which was chosen by the worldwide cotton community to be the first of 50 cotton species to be sequenced.

“This achievement, and the ongoing research community annotations of our cotton genome, will speed continued improvement of cotton production and help sustain one of the world’s largest industries,” said Professor Paterson.

The cotton sequence is among the highest-quality flowering plant sequences yet produced. A novel strategy integrating “next-generation” and conventional sequencing methods was used. Critical to the effort was information about the cotton hereditary blueprint, which had been accumulated over more than 20 years of research funded by the U.S. National Science Foundation, the U.S. Department of Agriculture, Cotton Incorporated, and other public and private agencies.

“This cotton data will help accelerate the study of gene function, particularly cellulose biosynthesis as it is fundamental to improved biofuels production,” said Jeremy Schmutz, head of the DOE JGI Plant Program and a faculty investigator at the HudsonAlpha Institute for Biotechnology, who led the effort to assemble the sequence.

“In addition, the unique structure of the cotton fiber makes it useful in bioremediation, and accelerated cotton improvement also promises to improve water efficiency and reduce pesticide use.”

Cotton production contributes heavily to many economies. The value of cotton fiber grown in the U.S. is typically about $6 billion per year. Cottonseed oil and meal byproducts add nearly $1 billion more of value. More than 430,000 domestic jobs are related to cotton production and processing, with an aggregate influence of about $120 billion on the annual US gross domestic product and an estimated annual $500 billion worldwide.

Professor Paterson noted that “The cotton community is delighted at the sequence quality resulting from integration of accumulated and new information by the skilled team of Mr. Jeremy Schmutz and Dr. Dan Rokhsar of the DOE JGI. We are enthusiastically pursuing next steps to improve sustainability of cotton production and increase its role in the more bio-based economy of the future.”

Dr. Don Jones, Director of Agricultural Research responsible for biotechnology research at Cotton Incorporated, said this Gossypium raimondii gold standard sequence will be the foundation for sequencing upland cotton, Gossypium hirsutum.

“This sequencing effort demonstrates that wise investment of grower supplied Cotton Incorporated funding produces cutting edge research which benefits the greater cotton community. "

"This sequence is a cornerstone that will help advance our knowledge so we more thoroughly understand the biology that leads to enhanced yield, improved fiber quality, and better stress tolerance, all improvements that will benefit growers in the not-too-distant future.”

Cotton Incorporated, funded by U.S. growers of upland cotton and importers of cotton and cotton textile products, is the research and marketing company representing upland cotton. The Program is designed and operated to improve the demand for and profitability of cotton.