Co-Authors:
Hu, G., Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, United States
Hovav, R., Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
Grover, C.E., Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, United States
Faigenboim-Doron, A., Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
Kadmon, N., Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
Page, J.T., Biology Department, Brigham Young University, Provo, United States
Udall, J.A., Biology Department, Brigham Young University, Provo, United States
Wendel, J.F., Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, United States
Abstract:
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight.We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication. Network comparisons among species indicate that topologies are altered in addition to gene expression profiles, indicating that changes in transcriptomic coexpression relationships play a role in the developmental architecture of cotton seed development. The global network topology of allopolyploids, especially fordomesticatedG. hirsutum, resembles the network of the A-genome diploid more than that of the D-genome parent, despite its D-like phenotype in oil content. Expression modifications associated with allopolyploidy include coexpression leveldominance and transgressive expression, suggesting that the transcriptomic architecture in polyploids is to some extent a modular combination of that of its progenitor genomes. Among allopolyploids, intermodular relationships are more preserved between two different wild allopolyploid species than they are between wild and domesticated forms of a cultivated cotton, and regulatory connections of oil synthesis-related pathways are denser andmore closely clustered in domesticated vs. wild G. hirsutum. These results demonstrate substantial modification of genic coexpression under domestication. Our work demonstrates how network inference informs our understanding of the transcriptomic architecture of phenotypic variation associated with temporal scales ranging from thousands (domestication) tomillions (speciation) of years, and by polyploidy. © The Author 2016.
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