Origin and diversity of the wild cottons (Gossypium hirsutum) of Mound Key, Florida.
Gossypium hirsutum
Domestication
Genetic diversity
Polyploid
Upland cotton
Wild relatives
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
18 Jun 2024
18 Jun 2024
Historique:
received:
21
03
2024
accepted:
13
06
2024
medline:
19
6
2024
pubmed:
19
6
2024
entrez:
18
6
2024
Statut:
epublish
Résumé
Elucidating genetic diversity within wild forms of modern crops is essential for understanding domestication and the possibilities of wild germplasm utilization. Gossypium hirsutum is a predominant source of natural plant fibers and the most widely cultivated cotton species. Wild forms of G. hirsutum are challenging to distinguish from feral derivatives, and truly wild populations are uncommon. Here we characterize a population from Mound Key Archaeological State Park, Florida using genome-wide SNPs extracted from 25 individuals over three sites. Our results reveal that this population is genetically dissimilar from other known wild, landrace, and domesticated cottons, and likely represents a pocket of previously unrecognized wild genetic diversity. The unexpected level of divergence between the Mound Key population and other wild cotton populations suggests that the species may harbor other remnant and genetically distinct populations that are geographically scattered in suitable habitats throughout the Caribbean. Our work thus has broader conservation genetic implications and suggests that further exploration of natural diversity in this species is warranted.
Identifiants
pubmed: 38890398
doi: 10.1038/s41598-024-64887-8
pii: 10.1038/s41598-024-64887-8
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
14046Subventions
Organisme : Cotton Incorporated (Cotton Inc.)
ID : 22-605
Organisme : United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)
ID : 58-6066-0-066
Informations de copyright
© 2024. The Author(s).
Références
Gepts, P. The contribution of genetic and genomic approaches to plant domestication studies. Curr. Opin. Plant Biol. 18, 51–59 (2014).
pubmed: 24631844
doi: 10.1016/j.pbi.2014.02.001
Purugganan, M. D. & Fuller, D. Q. The nature of selection during plant domestication. Nature 457, 843–848 (2009).
pubmed: 19212403
doi: 10.1038/nature07895
Brozynska, M., Furtado, A. & Henry, R. J. Genomics of crop wild relatives: Expanding the gene pool for crop improvement. Plant Biotechnol. J. 14, 1070–1085 (2016).
pubmed: 26311018
doi: 10.1111/pbi.12454
Hu, G. et al. Evolution and diversity of the cotton genome. In Cotton Precision Breeding (eds Rahman, M.-U. et al.) 25–78 (Springer International Publishing, 2021).
doi: 10.1007/978-3-030-64504-5_2
Wendel, J. F. & Grover, C. E. Taxonomy and evolution of the cotton genus, Gossypium. In Cotton 25–44 (American Society of Agronomy, Inc., Crop Science Society of America, Inc., and Soil Science Society of America, Inc., 2015).
Viot, C. R. & Wendel, J. F. Evolution of the cotton genus, Gossypium, and its domestication in the Americas. CRC Crit. Rev. Plant Sci. 42, 1–33 (2023).
doi: 10.1080/07352689.2022.2156061
Applequist, W. L., Cronn, R. & Wendel, J. F. Comparative development of fiber in wild and cultivated cotton. Evol. Dev. 3, 3–17 (2001).
pubmed: 11256432
doi: 10.1046/j.1525-142x.2001.00079.x
Brubaker, C. L. & Wendel, J. F. Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). Am. J. Bot. 81, 1309–1326 (1994).
doi: 10.1002/j.1537-2197.1994.tb11453.x
Wendel, J. F., Brubaker, C. L. & Percival, A. E. Genetic diversity in Gossypium hirsutum and the origin of upland cotton. Am. J. Bot. 79, 1291–1310 (1992).
doi: 10.1002/j.1537-2197.1992.tb13734.x
Wendel, J. F., Brubaker, C., Alvarez, I., Cronn, R. & Stewart, J. M. Evolution and natural history of the cotton genus. In Genetics and Genomics of Cotton (ed. Paterson, A. H.) 3–22 (Springer US, 2009).
doi: 10.1007/978-0-387-70810-2_1
Grover, C. E. et al. Genetic analysis of the transition from wild to domesticated cotton (Gossypium hirsutum L.). Genetics 10, 731–754 (2020).
Coppens d’eckenbrugge, G. & Lacape, J.-M. Distribution and differentiation of wild, feral, and cultivated populations of perennial upland cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean. PLoS ONE 9, e107458 (2014).
doi: 10.1371/journal.pone.0107458
Fryxel, P. A. The Natural History of the Cotton Tribe: Malvaceae, Tribe Gossypieae (Texas A & M University Press, 1981).
Alavez, V., Cuervo-Robayo, Á. P., Martínez-Meyer, E. & Wegier, A. Eco-geography of feral cotton: A missing piece in the puzzle of gene flow dynamics among members of Gossypium hirsutum primary gene pool. Front. Ecol. Evol. 9, 653271 (2021).
doi: 10.3389/fevo.2021.653271
Yuan, D. et al. Parallel and intertwining threads of domestication in allopolyploid cotton. Adv. Sci. 8, 2003634 (2021).
doi: 10.1002/advs.202003634
Thompson, V. D. Considering Urbanism at Mound Key (Caalus), the capital of the Calusa in the 16th Century, Southwest Florida, USA. J. Anthropol. Archaeol. 72, 101546 (2023).
doi: 10.1016/j.jaa.2023.101546
Marquardt, W. H., Krus, A. M. & Thompson, V. D. Rethinking the Estero Island Site: A possible satellite village of Mound Key. J. Anthropol. Archaeol. 58, 101145 (2020).
doi: 10.1016/j.jaa.2020.101145
Verma, K., Sharma, P., Tripathi, K., Yadav, R. & Singh, S. P. Recent advances in genetic improvement of cotton. In Genetic Engineering of Crop Plants for Food and Health Security Vol. 1 (eds Tiwari, S. & Koul, B.) 69–99 (Springer Nature Singapore, 2023).
doi: 10.1007/978-981-99-5034-8_4
Sweeney, M. & McCouch, S. The complex history of the domestication of rice. Ann. Bot. 100, 951–957 (2007).
pubmed: 17617555
pmcid: 2759204
doi: 10.1093/aob/mcm128
Doebley, J. The genetics of maize evolution. Annu. Rev. Genet. 38, 37–59 (2004).
pubmed: 15568971
doi: 10.1146/annurev.genet.38.072902.092425
Hutchinson, J. B. Intra-specific differentiation in Gossypium hirsutum. Heredity 5, 161–193 (1951).
doi: 10.1038/hdy.1951.19
Stephens, S. G. The effects of domestication on certain seed and fiber properties of perennial forms of cotton, Gossypium hirsutum L. Am. Nat. 99, 355–372 (1965).
doi: 10.1086/282377
Stephens, S. G. The potentiality for long range oceanic dispersal of cotton seeds. Am. Nat. 100, 199–210 (1966).
doi: 10.1086/282413
Wang, P. et al. Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense. Plant J. 110, 764–780 (2022).
pubmed: 35132720
doi: 10.1111/tpj.15702
Chen, Y. et al. Identification of introgressed alleles conferring high fiber quality derived from Gossypium barbadense L. In secondary mapping populations of G. Hirsutum L. Front. Plant Sci. 9, 1023 (2018).
pubmed: 30073008
pmcid: 6058274
doi: 10.3389/fpls.2018.01023
Nordborg, M. & Tavaré, S. Linkage disequilibrium: What history has to tell us. Trends Genet. 18, 83–90 (2002).
pubmed: 11818140
doi: 10.1016/S0168-9525(02)02557-X
De Groeve, J. et al. Global raster dataset on historical coastline positions and shelf sea extents since the Last Glacial Maximum. Glob. Ecol. Biogeogr. 31, 2162–2171 (2022).
pubmed: 36606261
pmcid: 9804564
doi: 10.1111/geb.13573
Noss, R. F. Between the devil and the deep blue sea: Florida’s unenviable position with respect to sea level rise. Clim. Change 107, 1–16 (2011).
doi: 10.1007/s10584-011-0109-6
Fulgione, A. et al. Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages. Nat. Commun. 13, 1–14 (2022).
doi: 10.1038/s41467-022-28800-z
Guo, J.-F. et al. Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana. J. Syst. Evol. 61, 143–156 (2023).
doi: 10.1111/jse.12821
Casier, M. et al. Genetic diversity and structure of endangered native yew Taxus baccata in remnant populations in Belgium. For. Ecol. Manage. 553, 121633 (2024).
doi: 10.1016/j.foreco.2023.121633
Dong, Y. et al. Salt-tolerance diversity in diploid and polyploid cotton (Gossypium) species. Plant J. 101, 1135–1151 (2020).
pubmed: 31642116
doi: 10.1111/tpj.14580
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
pubmed: 19451168
pmcid: 2705234
doi: 10.1093/bioinformatics/btp324
Kendig, K. I. et al. Sentieon DNAseq variant calling workflow demonstrates strong computational performance and accuracy. Front. Genet. 10, 736 (2019).
pubmed: 31481971
pmcid: 6710408
doi: 10.3389/fgene.2019.00736
Van der Auwera, G. A. et al. From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinform. 43, 11101–111033 (2013).
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
pubmed: 21653522
pmcid: 3137218
doi: 10.1093/bioinformatics/btr330
Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).
pubmed: 21903627
pmcid: 3198575
doi: 10.1093/bioinformatics/btr509
Neph, S. et al. BEDOPS: High-performance genomic feature operations. Bioinformatics 28, 1919–1920 (2012).
pubmed: 22576172
pmcid: 3389768
doi: 10.1093/bioinformatics/bts277
Purcell, S. et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
pubmed: 17701901
pmcid: 1950838
doi: 10.1086/519795
Frichot, E. & François, O. LEA: An R package for landscape and ecological association studies. Methods Ecol. Evol. 6, 925–929. https://doi.org/10.1111/2041-210X.12382 (2015).
doi: 10.1111/2041-210X.12382
Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
pubmed: 14734327
doi: 10.1093/bioinformatics/btg412
Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T.T.-Y. Ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).
doi: 10.1111/2041-210X.12628
Zhang, C., Dong, S.-S., Xu, J.-Y., He, W.-M. & Yang, T.-L. PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786–1788 (2019).
pubmed: 30321304
doi: 10.1093/bioinformatics/bty875
Korunes, K. L. & Samuk, K. PIXY: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Mol. Ecol. Resour. 21, 1359–1368 (2021).
pubmed: 33453139
pmcid: 8044049
doi: 10.1111/1755-0998.13326
Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: An R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938–2940 (2017).
pubmed: 28645171
pmcid: 5870712
doi: 10.1093/bioinformatics/btx364
Manichaikul, A. et al. Robust relationship inference in genome-wide association studies. Bioinformatics 26, 2867–2873 (2010).
pubmed: 20926424
pmcid: 3025716
doi: 10.1093/bioinformatics/btq559
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: Analysis of next generation sequencing data. BMC Bioinform. 15, 356 (2014).
doi: 10.1186/s12859-014-0356-4
Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595 (1989).
pubmed: 2513255
pmcid: 1203831
doi: 10.1093/genetics/123.3.585
Terhorst, J., Kamm, J. A. & Song, Y. S. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49, 303–309 (2017).
pubmed: 28024154
doi: 10.1038/ng.3748
Grover, C. E. et al. Comparative genomics of an unusual biogeographic disjunction in the cotton tribe (Gossypieae) yields insights into genome downsizing. Genome Biol. Evol. 9, 3328–3344 (2017).
pubmed: 29194487
pmcid: 5737505
doi: 10.1093/gbe/evx248
De La Torre, A. R., Li, Z., Van de Peer, Y. & Ingvarsson, P. K. Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. Mol. Biol. Evol. 34, 1363–1377 (2017).
pubmed: 28333233
doi: 10.1093/molbev/msx069
Kahle, D. & Wickham, H. Ggmap: Spatial visualization with ggplot2. R J. 5, 144 (2013).
doi: 10.32614/RJ-2013-014