Dr. Joshua Udall in the Department of Plant and Wildlife Sciences has worked with graduate student Justin T. Page and undergraduate students Zach S. Liechty, Rich H. Alexander, and Kimberly Clemons, as well as researchers at Texas A&M University and University of California-Davis, on an article in PLOS Genetics about tetraploid cotton. The author summary is provided below, and the complete open-access article is available at this link: http://dx.plos.org/10.1371/journal.pgen.1006012. This research has been funded by Cotton Inc. and the NSF Plant Genome Research Program. He has also received an additional NSF grant for $3 million to continue this research.
The polyploid genome of domesticated cotton contains two different copies of most genes because its genome is duplicated. Instead of 13 chromosomes like its wild relatives, domesticated cotton has 26 chromosomes (13 AT chromosomes and 13 DT chromosomes). Differences in the gene copies may hold keys to the genetic improvement of cotton. In fact, it has been thought that the two copies in the cotton genome interact in an unexpected way called gene conversion. In regular diploid genomes, gene conversion occurs when the maternal copy is used to ‘fix’ or ‘overwrite’ the paternal copy (or vice versa) during cell division. In cotton, this mechanism of conversion has been used to explain small DNA changes between genomes over evolutionary time. However, we do not see any evidence for conversion events in our new, large sequencing datasets. Our datasets and methods are much more robust than previous reports. Correction of the idea that “extensive homoeologous gene conversion is common in cotton” is important because 1) the cotton genome is used as a model for plant genome research and 2) efforts to induce homoeologous gene conversion in cotton breeding would be unsuccessful. In addition, this report discovers a large set of single-base changes (SNPs) among cotton varieties and makes them available to the research community for public use.
Citation: Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, et al. (2016) DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. PLoS Genet 12(5): e1006012. doi:10.1371/journal.pgen.1006012