An international consortium with representatives from most of the world’s major cotton-producing countries, led by Regents Professor Andrew Paterson of the University of Georgia and including Candace Haigler, a North Carolina State University professor of crop science and plant biology, has described the first ‘gold-standard’ genome sequence for cotton. Published today in Nature, this is the culmination of a more than 20-year effort in the analysis of cotton genes, chromosomes and their evolution.
The cotton genome sequence will be invaluable both on the farm and in the biotechnology laboratory. 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 ‘polyploid’ 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 could be 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 peanut.
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.
The ‘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. Partnership with the Mississippi State University’s Institute for Genomics, Biocomputing & Biotechnology and the USDA-ARS, augmented the scope and impact of the research by allowing production of ‘draft’ sequences of a model for the other (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 complete genome sequence of ancestral G. raimondii and the ‘draft’ sequences of commercial cotton and other related species will empower our ongoing research in ‘functional genomics,’ or the search for particular genes controlling cotton-fiber quality,” Haigler says.
Haigler and another co-author, Alison Roberts from the University of Rhode Island, classified the G. raimondii genes encoding cellulose synthases and related enzymes required for plant cell wall synthesis. Cotton fiber strength comes from its thick secondary cell wall composed of nearly pure cellulose, which is also the world’s most abundant renewable polymer because of the essential role of cellulose fibrils in plant structure.
Uncovering the genetic control of cellulose synthesis could lead to the improvement of cotton fibers, as well as other plant fibers such as those in wood and biomass crops targeted towards biofuels production, Haigler adds.
“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,” said Jeremy Schmutz, head of the Department of Energy’s Joint Genome Institute 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.
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 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 U.S. gross domestic product and an estimated annual $500 billion worldwide.
Don Jones, director of agricultural research at Cotton Incorporated, said this G. raimondii gold standard sequence will be the foundation for further sequencing of commercially important upland cotton, G. 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.”
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