STARKVILLE, Miss.– A Mississippi State University researcher is part of an international team that has described the first “gold-standard” genome sequence for cotton.
Published in the Dec. 20 issue of Nature –one of the world’s most prestigious scientific journals –the research is the culmination of a 20-plus year effort in the analysis of cotton genes, chromosomes and their evolution, according to Daniel G. Peterson, director of Mississippi State’s Institute for Genomics, Biocomputing and Biotechnology.
The research consortium includes representatives from most of the world’s major cotton producing countries, and is led by Regents Professor Andrew Paterson of the University of Georgia.
The effort gained momentum in 2007 when a proposal from Paterson, Peterson and others was approved by the United States Department of Energy Joint Genome Institute Community Sequencing Program. A “gold-standard” sequence was produced for Gossypium raimondii, chosen by the worldwide cotton community to be the first of 50 cotton species to be sequenced as the best model for the New World progenitor of commercially important Upland and Pima cottons.
The IGBB at MSU and the USDA-ARS augmented the scope and impact of the research by producing “draft” sequences of a model for the other Upland and Pima (Old World) progenitor, G. herbaceum, as well as the commercially important Upland cotton (G. hirsutum) cultivar ‘Acala Maxxa,’ and a wild relative, G. longicalyx.
The cotton genome sequence will be invaluable both on the farm and in the biotechnology laboratory, Peterson said.
On the farm, the identification of key cotton genes and their importance will accelerate understanding and provide data crucial to increasing cotton production, quality and sustainability.
In the lab, the comparison of an elite cotton cultivar to its wild ancestors provides new insights into how a “polyploidy” becomes “more than the sum of its progenitors.”
All flowering plants have experienced polyploidy, a process by which the entire hereditary blueprint of an organism is doubled. This is the first time that a polyploid plant has been compared to its progenitors over the entire genome, illuminating evolutionary processes salient to all plants and providing a strategy to better understand the genome of many other crops such as canola, wheat and peanuts.
Peterson has been involved in the project from its inception.
In 2000 while a postdoc at the University of Georgia, he constructed one of the key molecular resources used in mapping the G. raimondii genome. As a faculty member in Mississippi State’s Department of Plant and Soil Sciences, Peterson co-authored the successful 2007 Department of Energy proposal that resulted in initiation of G. raimondii genome sequencing.
As IGBB director, Peterson, in partnership with Brian Scheffler of the USDA-ARS at Stoneville, used an existing IGBB/USDA cooperative agreement to conduct targeted DNA sequencing critical in assembly of the G. raimondii genome. Additionally, the IGBB/USDA team sequenced the three Gossypium genomes to which the G. raimondii reference was compared.
“With a high-quality Gossypium reference sequence in hand, we can quickly assay DNA diversity within and among cotton species. This diversity is the key to generating cotton cultivars suited to various and variable environments, something that is particularly important in light of increasing climate instability,” Peterson noted.
Other IGBB co-authors on the paper were research associate Kurt Showmaker and postdoctoral associate William S. Sanders, both of whom were involved in DNA sequencing, data management, and identification of sequence differences between species.
The cotton sequence is among the highest-quality flowering plant sequences yet produced. Ironically, the sequence revealed it to also be among the most complex of flowering plant genomes, experiencing at least 30-fold multiplication of its genetic complement since its origin from an ancestral flowering plant.
Critical to understanding this complexity was information accumulated over more than 20 years of research funded by the U.S. National Science Foundation, the U.S. Department of Agriculture, Cotton Incorporated, the Consortium for Plant Biotechnology Research, Bayer Crop Science, and other public and private agencies.
“This cotton data will help accelerate the study of gene function, particularly cellulose biosynthesis, the understanding of which 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 sequence and assemble the genome for the JGI.
“In addition, the unique structure of the cotton fiber makes it useful in bioremediation, and accelerated cotton crop improvement also promises to improve water efficiency and reduce pesticide use,” he added.
Cotton production contributes substantially to economies around the globe. The value of cotton fiber grown in the U.S. exceeds $6 billion per year. Cottonseed oil and meal byproducts adds another $1 billion annually.
More than 200,000 domestic jobs are related to cotton production and processing, with an aggregate influence of $35 billion on the annual U.S. gross domestic product.
Don Jones, director of agricultural and environmental research responsible for biotechnology research at Cotton Incorporated, said this Gossypium raimondii sequence will be the foundation for improving commercial cotton.
“This sequencing effort demonstrates that wise investment of grower and importer supplied funding produces cutting-edge research which benefits the entire cotton community. The accomplishment is a cornerstone that will enable us to more thoroughly understand the biology that leads to higher yield, improved fiber quality, and better stress tolerance while reducing inputs used in producing the crop,” Jones said.