Cotton’s roots trace to Yucatan Peninsula, where wild gene pool runs deepest

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There’s nothing like this in nature, Jonathan Wendel said as he showed a visitor in his Bessey Hall office the long white puffs billowing from a cotton boll – the protective flower capsule of the plant cultivated by humans for thousands of years. In the wild, cotton bolls are far smaller and hold darker, coarser and shorter fibers.

Wild cotton, on left, has short, brown, and coarse fibers, while modern domesticated cotton has white, fine and abundant fibers. A new study led by Iowa State University scientists identified the northwestern Yucatan Peninsula in Mexico as the original source of domesticated cotton. Image credit: Corrinne Grover/Iowa State University

How did we get from there to here? Wendel, a distinguished professor of ecology, evolution and organismal biology at Iowa State University, has been asking that question for decades.

“This is my 40th year on faculty, and I came here with this project in mind. And it took 40 years to develop the resources, tools and technologies to solve the problem,” he said.

Wendel and a team of 19 co-authors outlined an answer in a paper published last month in the Proceedings of the National Academy of Sciences, showing that newly collected wild plant samples and advanced analysis of genomic sequencing data confirm modern cotton was domesticated from a diverse population native to Mexico’s Yucatan Peninsula.

Tracing the lineage of cotton gives scientists a better understanding of how plants evolve. But given the plant’s significance as a crop – cotton remains the most common source of natural textiles, by far – there are also direct practical benefits. Knowing where cotton came from is a genetic treasure map, pointing where to look for valuable traits such as disease resistance or salt tolerance that were lost along the way as farmers bred for other qualities.

“When humans domesticate a plant, you pick from a big population and everything else is left behind. Do that for 1,000 generations, and you have a very narrow genetic base,” Wendel said. “So we’re very interested in that wild genetic diversity. We want to know what’s still out there.”

Collections years in the making
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Pinpointing modern cotton’s home in the Yucatan was not a surprise. Earlier studies by Wendel, a prominent expert in cotton genetics, used less precise methods to suggest the peninsula curling to the north in southeastern Mexico was a likely origin of the plant’s domestication – a process that began about 5,000 years ago.

The advent of quick, affordable genome sequencing put a more definitive determination within reach, if Wendel and his colleagues could gather a wide enough sampling of wild specimens. He’s been collecting wild cotton his whole career, scouring herbarium shelves and Caribbean coastlines for variants.

“If everything you’re looking at has crazy new variation, you clearly haven’t reached saturation. But if the next 10 things look like the last thing you picked and everything’s forming a nice tight cluster, well, why bother to keep doubling up?” Wendel said.

Cotton plants steadily gathered over the years were important contributions to the study, but systematic collection in known wild populations was the linchpin. Corrinne Grover, an Iowa State research scientist and assistant adjunct professor in ecology, evolution and organismal biology, led new specimen sequencing and analysis of the complex data.

“Our collaborators did an amazing job sampling across the Yucatan strategically, and once we had that sequencing data it was very clear that’s where it came from,” she said.

Researchers compared hundreds of cotton genomes in different ways to validate their findings, including quantifying the differences between individual genomes and mapping which are most similar. That analysis linked domestic cotton genomes most closely to the specimens from the northwest corner of Yucatan, Grover said.

“Essentially, we’re building huge data-powered genealogies of these plants, just like you could with people,” Wendel said.

Mining old plants for new benefits
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After cultivated cotton spread out of northwestern Yucatan, it went on to dominate the worldwide population, crowding out other varieties independently domesticated in South America, Africa and India. The species native to Mexico – Gossypium hirsutum, also called upland cotton – accounts for about 90% of cotton plants today, a takeover researchers say was based on gradual improvement as opposed to dramatic mutations.

The diversity left behind in the wild during thousands of years of selective human breeding is most concentrated in cotton’s ancestral home because domestication creates a genetic bottleneck, narrowing the gene pool in successive generations. The genomes of two random wild cotton plants from northwestern Yucatan have on average twice as many genetic differences as two random modern cultivars, researchers found.

“As it turns out, cultivated cotton was poured out of a very small genetic bottleneck,” Wendel said.

The benefits of that diversity are obvious when you walk through a greenhouse where both domestic and wild cotton are growing, Grover said. The shorter, more compact domestic plants have fluffier bolls, but their wild brethren are often in better health overall.

“We know there are genetic traits in wild populations that could be useful if we can figure out what they are and get them into domesticated cotton,” she said. “Now we have all this data from the Yucatan, and it’s ready to be mined.”

Citation
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The paper Genomic diversity and the domestication history of cotton Gossypium hirsutum was published in Proceedings of the National Academy of Sciences

Genomic diversity and the domestication history of cotton (Gossypium hirsutum) Weixuan Ning, Mark A. Arick, II, Joshua A. Udall, Chuan-Yu Hsu, Luis Abdala-Roberts, Uriel Solís-Rodríguez, Yeyson Briones-May, Zenaida V. Magbanua, Olga Pechanova, Carlos Bustos-Segura, Mary V. Clancy, Sandra Díaz-Cruz, Alejandra Garnica-Cabrera, Marine Mamin, John Z. Yu, Ted C. J. Turlings, Guanjing Hu, Daniel G. Peterson, Corrinne E. Grover, corrinne@iastate.edu, and Jonathan F. Wendel jfw@iastate.edu Authors Info & Affiliations Contributed by Jonathan F. Wendel; received February 26, 2026; accepted April 20, 2026; reviewed by Brandon S. Gaut and Michael D. Purugganan May 18, 2026 123 (21) e2607107123 https://doi.org/10.1073/pnas.2607107123

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