(THE CONVERSATION) Cotton-derived products appear in many items that people use daily, including jeans, sheets, paper, candles, and peanut butter. In the United States, cotton is a US$7 billion annual crop grown in 17 states, from Virginia to Southern California. Today, however, it is in danger.
Cotton plants from fields in India, China and the United States – the world’s top three producers – all grow, flower and produce cotton lint in very similar ways. This is because they are genetically very similar.
This can be a good thing since breeders select the best performing plants and cross them to produce better cotton with each generation. If a variety produces the highest quality fiber that sells for the best price, growers will plant that type exclusively. But after many years of this cycle, the cotton grown begins to look the same: high yielding and easy for farmers to harvest using machinery, but extremely ill-prepared to fight disease, drought or pathogens. transmitted by insects.
Breeding alone may not be enough to combat the low genetic diversity of the cultivated cotton genome, because breeding works with what exists, and what exists looks alike. And genetic modification may not be a realistic option for creating useful cotton for farmers, because getting modified crops approved is expensive and heavily regulated. My research focuses on possible solutions that lie at the intersection of these tools.
How to Retool Cotton
In a perfect world, scientists could modify a few key components of the cotton genome to make plants more resistant to stresses such as pests, bacteria, fungi and water limitations. And the factories would still produce high quality cotton fiber.
This strategy is not new. About 88% of cotton grown in the United States has been genetically modified to resist pest caterpillars, which are expensive and difficult to manage with traditional insecticides. But as new problems emerge, new solutions will be needed that will require more complex genome edits.
Recent advances in plant tissue cultivation and regeneration make it possible to develop an entirely new plant from a few cells. Scientists can use good genes from other organisms to replace defective ones in cotton, producing cotton plants with all the resistance genes and all the useful genes in agriculture.
The problem is that obtaining regulatory approval for the marketing of a genetically modified crop is a long process, often eight to ten years. And it’s usually expensive.
But genetic modification is not the only option. Researchers today have access to a gigantic amount of data on all living beings. Scientists have sequenced the entire genomes of many organisms and annotated many of these genomes to show where genes and regulatory sequences are located. Various sequence comparison tools allow scientists to align one gene or genome against another and quickly determine where all the differences lie.
Plants have very large genomes with many repeating sequences, which makes them very difficult to unpack. However, a team of researchers has changed the game for cotton genetics in 2020 by releasing five updated and annotated genomes – two from cultivated species and three from wild species.
The assembly of wild genomes makes it possible to start using their valuable genes to try to improve cultivated varieties of cotton by crossing them together and looking for these genes in the offspring. This approach combines traditional plant breeding with detailed information about the cotton genome.
We now know what genes we need to make cultivated cotton more resistant to disease and drought. And we also know where to avoid modifying important agricultural genes.
Analysis of cotton hybrids
These genomes also make it possible to develop new screening tools to characterize interspecific hybrids, descendants of two cotton plants of different species. Before this information was available, there were two main forms of hybrid characterization. Both were based on single nucleotide polymorphisms, or SNPs – differences between species in a single base pair, the individual building blocks that make up DNA. Even plants with small genomes have millions of base pairs.
SNPs work well if you know exactly where they are in the genome if there are no mutations that modify the SNPs and if there are a lot of them. Although cotton has SNPs that have been identified and verified in specific regions of the genome, they are few and far between. Thus, characterizing cotton hybrids by focusing exclusively on SNPs would result in incomplete information on the genetic composition of these hybrids.
These new genomes open the door to the development of sequencing-based hybrid screening, which I have incorporated into my work. In this approach, scientists still use SNPs as a starting point, but they can also sequence surrounding DNA. This helps fill in gaps and sometimes discover new, previously undocumented SNPs.
Sequence-based screening helps scientists create more informed and robust maps of hybrid genomes. Determining which parts of the genome come from which parent can give breeders a better idea of which plants to cross to then create better and more productive cotton with each generation.
What cotton needs to thrive
As the world’s population increases to the projected 9.8 billion by 2050, the demand for all agricultural products will also increase. But making cotton plants more productive is not the only goal of genetic improvement.
Climate change is increasing average global temperatures and some important cotton-growing regions like the southwestern United States are getting drier. Cotton is already a crop accustomed to heat – our research plots can thrive in temperatures as high as 102 degrees Fahrenheit (39 C) – but a cotton plant requires about 10 gallons (38 liters) of water over the course of a ‘a four-month growing season to reach its maximum yield potential.
Researchers began to search for cultivated cotton plants that could tolerate drought at the seedling stage, but also in hybrid lines and genetically modified lines. Scientists are optimistic about the possibility of developing more drought-resistant plants. Along with many other cotton breeders around the world, my goal is to create more sustainable and genetically diverse cotton so that this essential crop can thrive in a changing world.