Scientists are Breeding Better Genes to Help Cotton Survive Climate Change

Cotton-derived products can be found in a variety of everyday items, including blue jeans, bedsheets, paper, candles, and peanut butter. Cotton is a $7 billion annual crop grown in 17 states from Virginia to California in the United States. Today, however, it is in jeopardy.

Cotton plants from the world's top three producers, India, China, and the United States, all grow, flower, and produce cotton fibre in very similar ways. This is due to their genetic similarity.

This can be beneficial because breeders choose the best-performing plants and crossbreed them to produce better cotton with each generation. If one variety produces the best-quality fibre at the best price, growers will plant only that variety. However, after many years of this cycle, cultivated cotton begins to look the same: high-yielding and easy to harvest with machines, but woefully unprepared to combat disease, drought, or insect-borne pathogens.

Because breeding works with what exists, and what exists all looks the same, it may not be enough to combat the low genetic diversity of the cultivated cotton genome. Furthermore, genetic modification may not be a viable option for producing cotton that is useful to farmers because getting engineered crops approved is costly and time-consuming. My research focuses on potential solutions that exist at the crossroads of these tools.

In an ideal world, scientists could alter just a few key components of the cotton genome to make plants more resistant to pests, bacteria, fungi, and water scarcity. Even so, the plants would continue to produce high-quality cotton fibre. This approach is not novel. Approximately 88 percent of cotton grown in the United States has been genetically modified to resist caterpillar pests, which are costly and difficult to control with traditional insecticides. However, as new problems arise, new solutions will be required, necessitating more complex changes to the genome.

Recent advances in plant tissue culture and regeneration enable the development of an entire new plant from a few cells. Scientists can use good genes from other organisms to replace defective ones in cotton, resulting in cotton plants that contain all of the resistance genes as well as all of the agriculturally valuable genes. The issue is that obtaining regulatory approval for a genetically modified crop to enter the market takes a long time, often 8 to 10 years. And it's usually pricey.

However, genetic engineering is not the only option. Researchers now have access to massive amounts of data on all living things. Scientists have sequenced the entire genomes of many organisms and annotated many of them to show where the genes and regulatory sequences are located. Various sequence comparison tools enable scientists to compare one gene or genome to another and quickly identify all of the differences.

Plants have very large genomes with a lot of repetitive sequences, making them difficult to unpack. However, in 2020, a group of scientists changed the game in cotton genetics by releasing five updated and annotated genomes—two from cultivated species and three from wild species.

With the wild genomes assembled, researchers can begin using their valuable genes to try to improve cultivated cotton varieties by breeding them together and looking for those genes in the offspring. This method combines traditional plant breeding with in-depth knowledge of the cotton genome. We now know which genes are required to make cultivated cotton more disease and drought-resistant. We also know where to avoid modifying important agricultural genes.

These genomes also allow for the development of new screening tools for characterizing interspecific hybrids, which are the offspring of two cotton plants from different species. Prior to this information, there were two primary types of hybrid characterization. Both relied on single nucleotide polymorphisms, or SNPs, which are differences between species in a single base pair, the individual building blocks that comprise DNA. Even small-genome plants have millions of base pairs.

SNPs work well when you know where they are in the genome, there are no mutations that change the SNPs, and there are a lot of them. Cotton has a small number of SNPs that have been identified and verified in specific regions of the genome. Characterizing cotton hybrids solely based on SNPs would thus provide insufficient information about the genetic composition of those hybrids.

These new genomes pave the way for hybrid screening based on sequencing, which I've incorporated into my work. SNPs are still used as a starting point in this approach, but scientists can also sequence the surrounding DNA. This helps to fill in gaps and occasionally discover new, previously unknown SNPs. Sequence-based screening enables scientists to create more accurate and robust maps of hybrid genomes. Determining which parts of the genome are from which parent can help breeders decide which plants to cross to create better, more productive cotton in each generation.

Climate change is raising global average temperatures, and some important cotton-producing regions, such as the United States' Southwest, are becoming drier. Cotton is already a heat-tolerant crop—our research plots can thrive in temperatures as high as 102 degrees Fahrenheit—but one cotton plant requires approximately 10 gallons of water over the course of a four-month growing season to reach its maximum yield potential.

Researchers have begun to look for cultivated cotton that can withstand drought at the seedling stage, as well as hybrid and genetically modified lines. Scientists are optimistic that they will be able to develop drought-resistant plants. My goal, like that of many other cotton breeders worldwide, is to create more sustainable and genetically diverse cotton so that this critical crop can thrive in a changing world.