Genomic diversity and the domestication history of cotton ( <i>Gossypium hirsutum</i> )

is the leading fiber crop globally, but its origin as a domesticated plant and patterns of diversity in the wild remain to be elucidated. Here, we use extensive sampling of wild populations and comparative genome sequence data to illuminate the scope and patterning of wild cotton diversity across its native range. Analyses confirm the hypothesis that the Yucatán Peninsula (México) is the center of domestication, from which the original perennial forms and later modern annualized cultivars were derived. Population structure and phylogenomic analyses indicate that northwestern Yucatán harbors greater genetic diversity relative to smaller, geographically dispersed populations in northeastern Yucatán and the Caribbean basin. Genetic load and transposable element burden also are the lowest in northwestern Yucatán relative to other regions, consistent with its greater diversity and reflecting the effects of historical genetic bottlenecks in other populations. Populations from Florida and elsewhere in the Caribbean basin maintain unique pockets of diversity. Analyses of selection suggest that cotton domestication entailed long-term accumulation of mutations with relatively minor phenotypic effects, as opposed to a more punctuated process involving major domestication genes. Our study quantifies the scope and scale of genomic diversity in wild cotton, the origin of the cultivated gene pool, and the likely ecological and anthropogenic processes that shaped extant diversity and modern geographic patterning.

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Publication Details

Journal
Proceedings of the National Academy of Sciences
Published
2026-05-18
DOI
https://doi.org/10.1073/pnas.2607107123
Primary Topic
Research in Cotton Cultivation
Type
article
Field-Weighted Citation Impact
0.00

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article

Genomic diversity and the domestication history of cotton ( Gossypium hirsutum )

Joshua A. Udall, Ted C. J. Turlings, Zenaida V. Magbanua, Marine Mamin et al.
Proceedings of the National Academy of Sciences
Research in Cotton Cultivation
article

Genomic diversity and the domestication history of cotton ( Gossypium hirsutum )

Joshua A. Udall, Ted C. J. Turlings, Zenaida V. Magbanua, Marine Mamin, Uriel Solís‐Rodríguez, Luis Abdala‐Roberts, Guanjing Hu, Weixuan Ning, John Z. Yu, Jonathan F. Wendel, Mark A. Arick, Alejandra Garnica‐Cabrera, Sandra Díaz-Cruz, Carlos Bustos-Segura, Mary V. Clancy, Olga Pechanova, Yeyson Briones-May, Chuan-Yu Hsu, Corrinne E. Grover, Daniel G. Peterson
article en

Abstract

is the leading fiber crop globally, but its origin as a domesticated plant and patterns of diversity in the wild remain to be elucidated. Here, we use extensive sampling of wild populations and comparative genome sequence data to illuminate the scope and patterning of wild cotton diversity across its native range. Analyses confirm the hypothesis that the Yucatán Peninsula (México) is the center of domestication, from which the original perennial forms and later modern annualized cultivars were derived. Population structure and phylogenomic analyses indicate that northwestern Yucatán harbors greater genetic diversity relative to smaller, geographically dispersed populations in northeastern Yucatán and the Caribbean basin. Genetic load and transposable element burden also are the lowest in northwestern Yucatán relative to other regions, consistent with its greater diversity and reflecting the effects of historical genetic bottlenecks in other populations. Populations from Florida and elsewhere in the Caribbean basin maintain unique pockets of diversity. Analyses of selection suggest that cotton domestication entailed long-term accumulation of mutations with relatively minor phenotypic effects, as opposed to a more punctuated process involving major domestication genes. Our study quantifies the scope and scale of genomic diversity in wild cotton, the origin of the cultivated gene pool, and the likely ecological and anthropogenic processes that shaped extant diversity and modern geographic patterning.

Proceedings of the National Academy of SciencesVol. 123(21)
Pennsylvania State University (US), United States Department of Agriculture (US), Iowa State University (US), Autonomous University of Yucatán (MX), Agricultural Genomics Institute at Shenzhen (CN), New York State College of Agriculture & Life Sciences (US), Cotton Research Institute (CN), Chinese Academy of Agricultural Sciences (CN), Biocom (US), Ministry of Agriculture and Rural Affairs (CN), University of Neuchâtel (CH), Universidad Nacional Autónoma de México (MX), Mississippi State University (US)
National Science Foundation, U.S. Department of Agriculture, Cotton Incorporated, Iowa State University, Agricultural Research Service
Life below water
Openalex Percentile: Top 7%
Research in Cotton Cultivation
DOIOpen Access PDFOpenAlex
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