Genes, Jeans and Genomes: Exploring the Mysteries of Polyploidy In Cotton.

Increasingly powerful technologies are being used to study the ecology and evolution of polyploids, resulting in dramatic discoveries of novel genomic interactions and processes. Gossypium includes classic allopolyploids arising from a biological reunion 1-2 MYA of divergent diploids from different hemispheres. This serendipitous merger generated a spectrum of genomic responses, including gene silencing, intergenomic gene conversion, and genome-wide disruption and modification of ancestral expression patterns. We are studying transcriptional, genomic and proteomic changes in synthetic and natural Gossypium allopolyploids using several complementary approaches. Allopolyploid formation induces massive alteration in gene expression and complex transcriptomic responses, including genomic expression dominance and bias, transgressive expression, and novel cytonuclear interactions. Allopolyploidization entails significant homoeolog expression modulation that is temporally partitioned into alterations arising immediately as a consequence of genomic merger and secondarily as a result of long-term evolutionary transformations in duplicate gene expression, the latter reflecting long-term evolutionary forces such as duplicate gene neofunctionalization and subfunctionalization. We are exploring gene expression during cotton fiber development and evolution, taking advantage of a well-established phylogenetic framework and the unique opportunity offered by the existence of multiple, parallel domestications of different wild progenitors by aboriginal peoples in both Africa-Asia and Mesoamerica. The fiber transcriptome is extraordinarily complex and has been massively altered by domestication. Homoeolog expression varies even at the level of development and maturation of a single cell, and domestication has increased expression bias in fibers towards the D-genome. Ongoing experiments are designed to evaluate the functional consequences of gene duplication in cotton and the possibility of novel gene recruitment following genome doubling. This work provides insights into the genetic and network architecture underlying the evolution of morphology, as well as several evolutionary dimensions of a prominent mode of plant speciation.