Genetic variation for alternative splicing in polyploid wheat

Advisor:
Lewis Lukens (Plant Agriculture)

Many animal and plant species are polyploids, and polyploids are over-represented among domesticated species. One remarkable polyploid is wheat, Triticum aestivum, which as a hexaploid, has three genomes in the haploid cell and immense 16 billion nucleotides, compared to the 3 billion nucleotides human genome. An outstanding question is how gene expression in polyploids such as wheat genetically varies. For example, do genes that are present in three copies generate more splice isoform diversity than genes that are present in one or two copies? Do those genes whose sequences rapidly evolve such as disease resistance and stress responsive genes also have a large amount of genetic variation for splice site usage? To answer these questions, we have sequenced over 30 million paired end cDNA fragments using RNASeq from over 350 wheat lines. This project will use this data to investigate if isoform diversity is similar regardless of gene copy number and to determine if genetic variation is higher amongst certain types of genes. The project will primarily use R Bioconductor applications for analyses. The work will gain insights on the genetic changes that have led to wheat diversity and improvement.