IOWA STATE UNIVERSITY
Elucidating the causes and consequences of polyploid evolution is central to understanding the origin and diversification of most lineages of eukaryotes. Polyploids experience the combined challenge and potential of having two or more genomes together in the same nucleus.
For survival of a polyploid individual, a balance must be reached between the potential benefits of extra heterozygosity and biochemical diversity and the cost of carrying and expressing multiple genomes. However, most of what we know about the genetic and genomic consequences of polyploidy is derived from the study of crops, synthetic polyploids, and models. To understand how polyploidy shapes genome evolution and gene function in nature, we must extend from a few models and synthetics to naturally occurring polyploids.
Tragopogon is a useful model for the study of recent and recurrent allopolyploidy in nature. Two new allotetraploid species (T. mirus and T. miscellus) each formed multiple times following the introduction of three diploids from Europe to the U.S. during the early 1900s. Meiotic studies and analyses of allozymes and microsatellites demonstrate clearly that these are disomic allopolyploids. Using genomic approaches, we will address questions fundamental to an increased understanding of the genetic and genomic consequences of polyploidy.
a. Via examination of several hundred loci distributed throughout the genome, is homoeolog loss more common than expression change, as our initial gene-by-gene approach (~30 genes) suggests?
b. Does evolution repeat itself?part I? Do the same patterns of true expression change and homoeolog loss occur in natural populations of T. mirus and T. miscellus of separate origin?
c. How fast do homoeolog loss and true expression change occur in synthetic polyploids?
d. Does evolution repeat itself?part II? Have the same changes observed in natural populations occurred in the multiple synthetic lines of T. mirus and T. miscellus?
e. Are genes that are lost or silenced spread across the genome, or are they clustered?
Rather than slowly building a wall of genetic data for Tragopogon one brick at a time, we propose to use a genomics approach to build a wall all at once, querying thousands of genes. We will use 454 FLX-Titanium sequencing to sample transcriptomes of the diploid Tragopogon parents for computational identification of SNPs for analyses of gene loss and altered gene expression in the allotetraploids and for genetic map construction. Deep Illumina sequencing of tetraploid individuals will identify ?differentially expressed genes?, i.e. those genes that appear to deviate from the null hypothesis of additive expression of parental copies in the allotetraploids. These genes will be used to design Sequenom assays to test for gene loss vs. expression differences, and for changes in allele number (due to duplication or homoeologous translocation) in both natural populations of separate origin of T. mirus and T. miscellus and synthetic lines of each species. Preliminary 454 and Illumina
data support the application of this computational genomics approach to an evolutionary model.
Broader Impacts. Tragopogon provides the unique opportunity to investigate the genetic and genomic changes that occur across a continuum from F1 hybrids, synthetic allopolyploids, independently formed natural populations of T. mirus and T. miscellus that are 60-80 years postformation, to older Eurasian polyploids. Through analysis of hundreds of loci, we will assess the
relative frequency of gene loss and gene expression changes in natural populations of the two allotetraploid species and in synthetic allotetraploids and determine whether evolution repeats itself and if underlying ?rules? govern genomic interactions in polyploids. The proposed methodology has not been applied to non-model species and is particularly promising for genomic work on species for which limited genetic and genomic resource