Why Study Cotton Genes?

Traits are products of genes. When researchers understand which genes are involved in shaping which traits in cotton, they can use that information to make new types of plants that are easier to grow, resistant to challenges like drought and pests, and easier on the environment.

Examples of traits that can make a better cotton crop:

  • High yield of fiber
  • High quality fiber (e.g., longer, stronger; depends on use)
  • Resistant to drought
  • Resistant to pests
  • Resistant to diseases
  • Tolerates salt
  • Less need for fertilizer
  • Less need for pesticides
  • Easy to grow in multiple environments

Related content

For a refresher on traits, DNA, genes, and more visit our Basic Genetics page


Dr. Joshua Udall

studies cotton genomics at Brigham Young University
Photo Credit: Mark A. Philbrick/BYU

Characteristics begin with genes


Many of the differences among individuals come from variations in genes.

Domesticated cotton has certain characteristics, or traits, that make it more useful than its wild relatives. For example, compared to its wild relatives, domesticated cotton grows more fiber, its fibers are longer, and they more easily separated from their seeds. All of these traits were developed from naturally occurring genetic variations in the wild ancestors of cotton.

Just like humans vary in their traits—like height, hair color, and lots of other things—so do other species. Many of these variations are genetically programmed, arising from small differences in genes from one individual to the next. During the process of domestication, the individuals with the most-desirable traits are set aside so that they can become the parents of the next generation. The hope is that the same traits will pass, through genes, from parent to offspring.

Related content

Uses & Types of Cotton

Domestication decreases genetic diversity

The process of domestication develops favorable traits—but it also introduces "bottlenecks," where large amounts of genetic diversity are lost. The individuals that are harvested and not used to make the next generation don't get to pass on their genetic variations.

This lack of genetic diversity becomes important when conditions change—say a new disease comes along, or a shift in the weather causes a drought, or someone wants to start growing cotton in a new environment. Before domestication, the wild starting population may have had genetic variations that could have helped individuals survive these challenges. But if the challenges were not a factor during the domestication process, those variations could easily have been lost.

genetic bottleneck

Wild populations tend to have a lot of genetic diversity. The process of domestication leads to a population that has favorable traits, but is also much less genetic diversity.

Wild populations are reservoirs of genetic diversity


Repeated cycles of irrigation and evaporation have caused salt and other minerals to build up, leaving huge swaths of land unusable for farming. Salt and drought resistant plants could help make this land useful again. (Photo Credit: USDA)

The good news for cotton is that there are many wild populations alive in the world today. Because they haven't gone through recent genetic bottlenecks, these wild populations have far more genetic diversity than their domesticated cousins. Within that diversity are many gene variants that have the potential to make new types of cotton with even better characteristics.

The need for crop improvement is real and immediate. Cotton farmers are continually faced with new challenges. In 2011, for example, a record-setting drought caused Texas cotton farmers to lose more than half of their crop. Over the next two years, cotton production was not much better.

As global temperatures increase, forecasters predict that many farming regions will see even more extended periods of drought. Additionally, drought-stressed plants are more vulnerable to pests like spider mites and thrips. Wild cotton relatives may have gene variations that make them resistant to these and other challenges.

Which genes control which traits?

Researchers are studying various cotton genomes to try to identify specific gene variations that influence favorable traits. Below are some of the questions researchers are trying to answer:

  • What gene variations allow Pima cotton to produce fiber that is so long and strong?
  • What gene variations allow upland cotton to produce fiber in such great abundance?
  • Why are tetraploid cotton species (AADD, including Pima and upland cotton) better crop plants than any of their diploid relatives (AA or DD)?
  • What gene variations make some types of wild cotton resistant to farm pests like insects and bacterial and fungal infections?

The general approach researchers are using to answer these questions is to sequence the genomes of multiple wild and domesticated forms of cotton. Sequencing involves reading an organism's DNA code—long strings of the bases A, C, G and T. They can then compare the DNA code from different types of cotton to identify the genetic differences that may underlie desirable traits.

dna on paper

A genome is a complete set of all of the genes than an organism has. It is made up of very, very long chains of DNA "letters." In tetraploid cotton, the genome is about 2.4 billion letters long!

Let's say we have found the genes. Now what?

In the past, crop improvement was done through the long, slow process of "traditional" breeding.

But when researchers know which gene variations influence a useful trait, they can use newer, faster methods to develop a better cotton plant: marker-assisted breeding or transgenic technology.

To learn more about these methods, visit Crop Improvement Methods.

baby cotton


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Byrne, P. & Richardson, K. (2005?). Marker-Assisted Selection (online lesson). Plant & Soil Sciences eLibrary. Retrieved December 7, 2016, from https://passel.unl.edu/pages/informationmodule.php?idinformationmodule=1087488148&topicorder=1&maxto=10&minto=1

Flowers, T. J. (2004). Improving crop salt tolerance. Journal of Experimental Botany, 55(396), 307-319. doi: 10.1093/jxb/erh003

Guo-Liang Jiang (2013). Molecular Markers and Marker-Assisted Breeding. In Andersen, S. B. (Ed.) Plants, Plant Breeding from Laboratories to Fields. InTech. doi: 10.5772/52583. Available from: http://www.intechopen.com/books/plant-breeding-from-laboratories-to-fields/molecular-markers-and-marker-assisted-breeding-in-plants

Yamaguchi, T. & Blumwald, E. (2005). Developing salt-tolerant crop plants: challenges and opportunities. Trends in Plant Science, 10(12), 615-620. doi: 10.1016/j.tplants.2005.10.002

Zielinski, S. (October 28, 2014). Earth's soil is getting too salty for crops to grow. Smithsonian.com. Available from http://www.smithsonianmag.com/science-nature/earths-soil-getting-too-salty-crops-grow-180953163/?no-ist

APA format:

Genetic Science Learning Center. (2010, December 9) Why Study Cotton Genes?. Retrieved December 14, 2017, from http://learn.genetics.utah.edu/content/cotton/genes/

CSE format:

Why Study Cotton Genes? [Internet]. Salt Lake City (UT): Genetic Science Learning Center; 2010 [cited 2017 Dec 14] Available from http://learn.genetics.utah.edu/content/cotton/genes/

Chicago format:

Genetic Science Learning Center. "Why Study Cotton Genes?." Learn.Genetics. December 9, 2010. Accessed December 14, 2017. http://learn.genetics.utah.edu/content/cotton/genes/.