Project Summaries

11-861  Project Manager: D. C. Jones


Jonathan Wendel, Iowa State University

The modern genomics era has revealed the prevalence of genome doubling, i.e. polyploidy, during plant evolution. This phenomenon has wide ranging genetic, epigenetic, and genomic consequences whose actions have been widely documented in cotton and other polyploid species, but whose mechanistic underpinnings and functional consequences are poorly understood. The goal of this project is to explore the effects of genome merger and doubling on genomic architecture and to evaluate the fate of duplicated pathways and networks in a polyploid plant. Specifically, we seek to (1) use comparative genomic sequencing to reveal the fine scale colinearity and architectural differences between the polyploid genome of upland cotton and its two model diploid progenitors, (2) assess the usefulness of the G. raimondii genome, whose genome sequence is complete, for targeting traits of interest and for future sequencing of the G. hirsutum genome, (3) begin to unravel the complexities and consequences of pathway duplication on associated genes, and (4) begin to understand how those changes are experienced over an entire gene network in response to human-guided selection for a specific trait (flowering time), which occurred in parallel in the two cultivated polyploid species, G. hirsutum and G. barbadense. In the last twelve months of this project, we tabulated the final results of the comparative BAC sequencing project and completed the analyses of synteny among the genomes sequenced. We have generated the figures and tables necessary for publication, which we anticipate submitting for publication later this year. These analyses provide new information on the comparative genome evolution among diploid and polyploid cotton genomes. They also provide information about the utility and limitations in using the newly published G. raimondii genome sequence to target traits of interest in the polyploid species or as a reference for a future polyploid genome sequence. Additionally, we utilized the newly released G. raimondii to bioinformatically obtain the cotton homologs of the flowering time and have initiated a new sequence capture bait design based on those predication. In addition, we assessed the utility of Illumina in future sequence capture experiments, whose low cost and deep coverage will make it an asset in future sequence capture experiments. Once completed, this component project will provide useful insight into the function of duplicated networks and pathways in polyploid cotton, generating important information for future crop improvement.

A Cotton Incorporated Fellow, Dr. Corrinne Grover, was supported on this project.


Project Year: 2012

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