Structural Variation of Diploid and Polyploid Plant Genomes

Brigham Young University, Provo UT

Investigators

Abstract

PI: Joshua A. Udall (Brigham Young University) CoPIs: Thiruvarangan Ramaraj (National Center for Genomic Resources) and Louisa A. Stark (University of Utah) Cotton has one of the narrowest germplasm pools of any domesticated plant. Although crosses between G. barbadense and G. hirsutum can be made, introgression in either direction has been difficult. Identification of structural rearrangements between the two polyploids will provide the basic information that can be used to develop an improved method of chromosome and trait introgression between the two species for crop improvement. With regard to outreach and training, the project will incorporate physical mapping concepts and plant genomes into the award winning educational websites "Learn.Genetics" and "Teach.Genetics" developed by the University of Utah. These sites will contain learning and teaching content for the concepts of genome sequencing, physical mapping, and polyploidy of plant genomes. In addition to the training of students and postdoctoral fellows, a research experience that includes physical map analysis will be provided at Brigham Young University for biology and genetics high school teachers. Structural rearrangements of plant genomes contribute to speciation and phenotypic variability. Traditionally, structural rearrangements are identified through extensive comparative sequencing of plant genomes. In this project, structural variation will be investigated in diploid and polyploid genomes using physical maps. Because generating a physical map for a single species is expensive and time-consuming, strategies to compare physical maps between multiple species within a phylogenetic framework have not been developed. Specific objectives are to: 1) assess and validate the use of next generation optical mapping technology to rapidly create physical maps of four different species of diploid and polyploid cotton; 2) create additional physical maps that represent the genome diversity in the approximate 40 different species of the cotton family; and, 3) use these maps to develop novel comparative mapping strategies to place structural rearrangements identified in a phylogenetic context. All project outcomes will be made available to the public through a project website. Sequence data will be accessible through long-term repositories such as Genbank, the NCBI's SRA, and Phytozome. Data will also be available long-term through CottonGen (http://www.cottongen.org/), a community genomics, genetics and breeding database for cotton.