ISU Comparative Genomics and Genome Size Evolution

Project Information



We recently initiated a large genome resequencing project (led by Josh Udall, with Daojun Yuan and Thiru Ramaraj) funded by the National Science Foundation Plant Genome Program.  In this project, we are addressing biological questions of broad relevance to polyploid plant genomes, while at the same time generating detailed information on genomic and phylogeographic patterns of diversity in wild and domesticated cotton, advancing our capacity to utilize an expanded gene pool for cotton improvement.


The two cultivated allopolyploid cottons, Gossypium hirsutum and G. barbadense, represent a remarkable example of parallel independent domestication, both involving dramatic morphological transformations under selection from wild perennial plants to annualized row crops. We combine deep resequencing of 643 newly sampled accessions spanning the wild-todomesticated continuum of both species, and their allopolyploid relatives, with existing data to resolve species relationships and elucidate multiple aspects of their parallel domestication. We confirm that wild G. hirsutum and G. barbadense were initially domesticated in the Yucatan Peninsula and NW South America, respectively, and subsequently spread under domestication over 4,000 - 8,000 years to encompass most of the American tropics. We present a robust phylogenomic analysis of infraspecific relationships in each species, quantify genetic diversity in both, and describe genetic bottlenecks associated with domestication and subsequent diffusion. As these species became sympatric over the last several millennia, pervasive genome-wide bidirectional introgression occurred, often with striking asymmetries involving the two coresident genomes of these allopolyploids. Diversity scans revealed genomic regions and genes unknowingly targeted during domestication and additional subgenomic asymmetries. These analyses provide a comprehensive depiction of the origin, divergence, and adaptation of cotton, and serve as a rich resource for cotton improvement.