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Genomes Assembled from Five Cotton Species Could Lead to Better Varieties

Genomes Assembled from Five Cotton Species Could Lead to Better Varieties
Researchers assembled the genomes of five cotton varieties, revealing their evolutionary history and new insights for breeding. Flower images by Atsumi Ando (UT Austin) and field of cotton by James Frelichowskin (USDA-ARS, College Station).

Cotton producers in Texas, elsewhere in the US and around the world are looking for new varieties that can better withstand droughts, pests and pathogens, yet yield higher-quality fibers for the textile industry.

To help accelerate the breeding and improvement of cotton varieties, researchers from The University of Texas at Austin, HudsonAlpha Institute for Biotechnology, Texas A&M University and elsewhere teamed up to produce the reference-grade genomes of all five species, including two cultivated cottons. Their results were published today in the journal Nature Genetics.

Cultivated cottons are tetraploid, which means each has four sets of chromosomes: two from a 'mother' from Africa (Old World) and two from a 'father' from the Americas (New World). The 'unification' took place in the New World about one and half million years ago and produced five species. In the last 8,000 years, two of them were domesticated independently into Upland (or American) and Pima (or Egyptian) cottons that account for 95% and 5% of cotton production worldwide, respectively. Three wild relatives diversified in Hawaii, Brazil and the Galapagos Islands. The complexity of polyploid genomes makes it difficult for putting sequencing pieces together.

The team sequenced, assembled and compared the genomes of wild and domesticated varieties. They discovered genetic and epigenetic differences associated with a range of traits including seed production, environmental adaptations, fiber quality and disease resistance. "Epigenetics" refers to changes in traits that aren't caused by a change in a genetic sequence, but by changes in the way genes are expressed.

The work, which expands on the genome sequence of Upland cotton published by the team in 2015, was led by Z. Jeffrey Chen, the D. J. Sibley Centennial Professor in Plant Molecular Genetics at UT Austin. The research team also includes Jane Grimwood and Jeremy Schmutz of HudsonAlpha.

Key Findings

They found that overall, the gene content differences between the domesticated and wild species are limited, but the genes related to disease resistance are very different between the five species.

"Modifying those genes may help improve cotton production in response to climate change and pest emergence," Chen said.

Another key finding is that when humans domesticated cotton and selected for certain agronomic traits, those traits were caused by epigenetic changes, rather than genetic changes. This finding builds on pioneering work published in 2017 that identified other epigenetic changes across various cotton species. The team found RNA modification can affect gene expression in fibers.

An exciting finding is that polyploidy, having more than two sets of chromosomes, in cotton suppresses DNA recombination, a process that shuffles genetic material from two parents into new combinations in their offspring. This low recombination leads to low genetic diversity for crop breeding. The low genetic recombination can be overcome by hybridizing a cultivated cotton with wild species.

Chen said breeders could use wild species and/or modify genes and genomes with chemicals or through 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.

"These findings also open a new direction for exploring epigenetic variation to facilitate epigenetic breeding and engineering for this important crop." Chen said, "They should help develop new tools to modify gene expression to improve fiber yield, quality and other traits."

Part of the research was conducted using the computing resources of UT Austin's Texas Advanced Computing Center, Iowa State University Research Information Technology Unit, and Bioinformatics Center at Nanjing Agricultural University.

Global Impact

Cotton is the top fiber crop grown in the world; over 150 countries are involved in cotton export and import. The U.S. is a leading exporter of cotton, and annual business revenue stimulated by cotton in the U.S. economy exceeds $100 billion, making cotton America's number one value-added crop. Texas grows more cotton than any state, producing nearly 40 percent of the nation's supply.

"Globally, cotton is the premier natural fiber crop of the world, a major oilseed crop, and important feed crop." said David Stelly, "Advances in these scientific areas are likely to increase the breadth, effectiveness and efficiency of the development of new cultivars that help humanity and the environment."

"This work reaches the long-sought goal of comparing the polyploid genomes of cotton to its wild relatives," said Kelly Dawe, program director of the Plant Genome Research Program at the National Science Foundation. "These studies provide important new insights into the evolution and function of genes that form cotton fibers, one of the world's most interesting and important plant products."

Other institutions involved in the research include: Nanjing Agricultural University (China); the U.S. Department of Agriculture-Agricultural Research Service; Zhejiang A&F University (China); Clemson University; Iowa State University; The U.S. Department of Energy Joint Genome Institute; Mississippi State University; Alcorn State University; and Cotton Incorporated, a not-for-profit company working with cotton scientists, the textile industry, and consumers.

This work is supported by grants from the U.S. National Science Foundation, U.S. Department of Agriculture and Cotton Incorporated. The work conducted by the U.S. Department of Energy (DOE) Joint Genome Institute is supported by the Office of Science of the DOE. The work is also supported by grants from National Natural Science Foundation of China, Jiangsu Collaborative Innovation Center for Modern Crop Production, and Natural Science Foundation of Zhejiang Province, China.

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Saturday, 11 July 2020

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