AsianScientist (Jun. 13, 2017) – Researchers have identified over 500 genes that were epigenetically modified during the domestication of the cotton plant. Their findings, published in Genome Biology, pave the way for more resilient and productive cotton varieties.
In recent decades, scientists have discovered that many traits in living things are controlled not just by their genetics—what’s written in the code of their DNA—but also by processes outside their DNA that determine whether, when and how much the genes are expressed, known as epigenetics. This opens up the possibility of entirely new ways to breed plants and animals. By selectively turning gene expression on and off, breeders could create new varieties without altering the genes.
In this latest study, the researchers identified more than 500 genes that are epigenetically modified between wild cotton varieties and domesticated cotton, some of which are known to relate to agronomic and domestication traits. This information could aid selection for the kinds of traits that breeders want to alter, like fiber yield or resistance to drought, heat or pests. For example, varieties of wild cotton might harbor genes that help them respond better to drought, but have been epigenetically silenced in domesticated cotton.
“This understanding will allow us to supplement genetic breeding with epigenetic breeding,” said Professor Jeffery Chen, the D. J. Sibley Centennial Professor of Plant Molecular Genetics at the University of Texas at Austin. “Since we know now how epigenetic changes affect flowering and stress responses, you could reactivate stress-responsive genes in domesticated cotton.”
Cotton is the top fiber crop grown in the world, with more than 150 countries involved in cotton export and import. Annual business revenue stimulated by cotton in the US economy exceeds US$100 billion, making it America’s No. 1 value-added crop.
Chen and his colleagues at Texas A&M University and Nanjing Agricultural University in China produced a cotton methylome—a list of genes and genetic elements that have been switched on or off through a natural process called DNA methylation. This methylome covers the most widely grown form of cotton, known as Upland or American cotton; its cousin, Pima or Egyptian cotton; and their wild relatives, while showing how these plants changed over more than a million years.
“Knowing how the methylome changed during evolution and domestication will help bring this technology one step closer to reality,” said Chen.
The researchers discovered changes in DNA methylation occurred as wild varieties combined to form hybrids, the hybrids adapted to changes in their environment and finally, humans domesticated them. One key finding is that the change that allowed cotton to go from a plant adapted to grow only in the tropics to one that grows in many parts of the world was not a genetic change, but an epigenetic one.
Chen said modern breeders can modify gene methylation with chemicals or through modified gene-editing technologies such as CRISPR/Cas9. These methods could allow breeders to make targeted changes to a plant’s epigenome and create new breeds with improved traits. Epigenetic breeding could be applied not just to cotton but to many other major crops such as wheat, canola, coffee, potatoes, bananas and corn.
The article can be found at: Song et al. (2017) Epigenomic and Functional Analyses Reveal Roles of Epialleles in the Loss of Photoperiod Sensitivity During Domestication of Allotetraploid Cottons.
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Source: University of Texas at Austin; Photo: Chen Laboratory.
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