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ARS Home » Southeast Area » Florence, South Carolina » Coastal Plain Soil, Water and Plant Conservation Research » Research » Publications at this Location » Publication #410354
Research Project: Advancing Cotton Genetics and Innovative Cropping Systems for Improved Quality and Production

Location: Coastal Plain Soil, Water and Plant Conservation Research

Title: Genome resources for three modern cotton lines guide future breeding efforts

Author
item SREEDASYAM, A. - Hudsonalpha Institute For Biotechnology
item LOVELL, J. T. - Hudsonalpha Institute For Biotechnology
item MAMIDI, S. - Hudsonalpha Institute For Biotechnology
item KHANAL, S. - Hudsonalpha Institute For Biotechnology
item JENKINS, J. W. - Hudsonalpha Institute For Biotechnology
item PLOTT, C. - Joint Genome Institute
item KEMPTON, B. B. - Joint Genome Institute
item LI, Z. - Joint Genome Institute
item SHU, S. - Joint Genome Institute
item CARLSON, J. - Joint Genome Institute
item GOODSTEIN, D. - Joint Genome Institute
item SANTIAGO, L. D. - University Of Texas
item KIRKBRIDE, R. C. - University Of Texas
item CALLEJA, S. - University Of Arizona
item Campbell, Benjamin - Todd
item KOEBERNICK, J. C. - University Of Auburn
item DEVER, J. K. - Texas A&M Agrilife
item Scheffler, Jodi
item PAULI, D. - University Of Arizona
item Jenkins, Johnie
item McCarty, Jack
item WILLIAMS, M. - Hudsonalpha Institute For Biotechnology
item BOSTON, L. - Hudsonalpha Institute For Biotechnology
item WEBBER, J. - Hudsonalpha Institute For Biotechnology
item Udall, Joshua - Josh
item CHEN, Z. J. - University Of Texas
item BOURLAND, F. - University Of Arkansas
item STILLER, W. N. - Csiro, Australian Cotton Research Institute, Narrabri
item SAAKI, C. A. - Clemson University
item GRIMWOLD, J. - Hudsonalpha Institute For Biotechnology
item CHEE, P. W. - University Of Georgia
item JONES, D. C. - Cotton, Inc
item SCHMUTZ, J. - Hudsonalpha Institute For Biotechnology

Submitted to: Nature Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2024
Publication Date: 5/30/2024
Citation: Sreedasyam, A., Lovell, J., Mamidi, S., Khanal, S., Jenkins, J., Plott, C., Kempton, B., Li, Z., Shu, S., Carlson, J., Goodstein, D., Santiago, L., Kirkbride, R., Calleja, S., Campbell, B.T., Koebernick, J., Dever, J., Scheffler, J.A., Pauli, D., Jenkins, J.N., Mccarty Jr, J.C., Williams, M., Boston, L., Webber, J., Udall, J.A., Chen, Z., Bourland, F., Stiller, W., Saaki, C., Grimwold, J., Chee, P., Jones, D., Schmutz, J. 2024. Genome resources for three modern cotton lines guide future breeding efforts. Nature Plants. https://doi.org/10.1038/s41477-024-01713-z.
DOI: https://doi.org/10.1038/s41477-024-01713-z

Interpretive Summary: Cotton (Gossypium hirsutum L.) is the most important renewable fiber crop worldwide; however, cotton yield and fiber quality exhibit high variability, influenced by genotype-specific traits and the intricate interplay among cultivars, management practices, and environmental conditions. Future yield gains may decline due to a narrow founding gene pool that has been further impoverished by modern plant breeding practices. A solution to the challenge of limited genetic diversity may come from precision breeding and biotechnological designs; however, such technologically advanced breeding toolboxes require accurate cultivar-specific sequence data. We provide a foundation for breeding advances through the generation and detailed exploration of high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’, ‘CSX8308’) and a major update to the existing ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, we observed regions of significant sequence and structural variation among the four genomes, some of which correspond with ancient and ongoing genomic introgressions (from the related ‘Pima’ G. barbadense cotton), gene regulatory, and phenotypic trait divergence. Crucially, differentially expressed genes across fiber developmental time courses were enriched in biological processes related to fiber production, which may underlie the unique fiber quality traits of modern cotton cultivars. These genomes and comparative analyses provide a foundation that will facilitate future genetic efforts to further enhance yield and sustainability of global cotton production.

Technical Abstract: Cotton is the most important renewable fiber crop worldwide; however, cotton yield and fiber quality exhibit high variability, influenced by genotype-specific traits and the intricate interplay among cultivars, management practices, and environmental conditions. Future yield gains may decline due to a narrow founding gene pool that has been further impoverished by modern plant breeding practices. A solution to the challenge of limited genetic diversity may come from precision breeding and biotechnological designs; however, such technologically advanced breeding toolboxes require accurate cultivar-specific sequence data. We provide a foundation for breeding advances through the generation and detailed exploration of high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’, ‘CSX8308’) and a major update to the existing ‘TM-1’ cotton genetic standard reference. Results suggest chromosome regions of significant sequence and structural variation among the four cultivars some of which correspond with ancient and ongoing genomic introgressions from Pima cotton) corresponding to unique fiber quality traits in modern cotton cultivars. These results provide a foundation that will facilitate future genetic efforts to further enhance yield and sustainability of global cotton production.