Location: Coastal Plain Soil, Water and Plant Conservation Research
Title: Genome resources for three modern cotton lines guide future breeding effortsAuthor
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SREEDASYAM, A. - Hudsonalpha Institute For Biotechnology |
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LOVELL, J. T. - Hudsonalpha Institute For Biotechnology |
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MAMIDI, S. - Hudsonalpha Institute For Biotechnology |
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KHANAL, S. - Hudsonalpha Institute For Biotechnology |
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JENKINS, J. W. - Hudsonalpha Institute For Biotechnology |
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PLOTT, C. - Joint Genome Institute |
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KEMPTON, B. B. - Joint Genome Institute |
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LI, Z. - Joint Genome Institute |
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SHU, S. - Joint Genome Institute |
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CARLSON, J. - Joint Genome Institute |
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GOODSTEIN, D. - Joint Genome Institute |
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SANTIAGO, L. D. - University Of Texas |
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KIRKBRIDE, R. C. - University Of Texas |
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CALLEJA, S. - University Of Arizona |
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Campbell, Benjamin - Todd |
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KOEBERNICK, J. C. - University Of Auburn |
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DEVER, J. K. - Texas A&M Agrilife |
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Scheffler, Jodi |
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PAULI, D. - University Of Arizona |
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Jenkins, Johnie |
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McCarty, Jack |
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WILLIAMS, M. - Hudsonalpha Institute For Biotechnology |
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BOSTON, L. - Hudsonalpha Institute For Biotechnology |
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WEBBER, J. - Hudsonalpha Institute For Biotechnology |
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Udall, Joshua - Josh |
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CHEN, Z. J. - University Of Texas |
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BOURLAND, F. - University Of Arkansas |
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STILLER, W. N. - Csiro, Australian Cotton Research Institute, Narrabri |
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SAAKI, C. A. - Clemson University |
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GRIMWOLD, J. - Hudsonalpha Institute For Biotechnology |
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CHEE, P. W. - University Of Georgia |
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JONES, D. C. - Cotton, Inc |
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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. |