Genome Wide Alternative Polyadenylation and Gene Expression Studies in Forage Crops - Tall Fescue and Red Clover

Forage crops contribute significantly to the US economy by virtue of being major constituent of the ruminant animal diet. In recent years focus of forage crop research has shifted from ‘quantity’ to ‘quality’, such as cultivation in resource limited environments (e.g. drought) and improving nutritional quality (e.g.  protein content). Here we report genome-wide studies on two key forage crops, tall fescue (Lolium arundinaceum) and red clover (Trifolium pratense).

Tall fescue is a cool season perennial forage grass that forms symbiotic association with the fungus, Epichloe. Endophyte infected plants perform better in stressed conditions than non-infected plants. A genome-wide poly(A) site choice analysis was performed using tall fescue-endophyte symbiosis under drought stress to assess the impact of host-endophyte interaction on the global poly(A) site usage. Additionally, transcriptome analysis was conducted using poly(A) tags to investigate the role of this symbiosis in altering gene expression during drought stress in order to impart stress tolerance.

Red clover is the most important forage legume after alfalfa in the US. Genome-wide transcriptome analysis was carried out using different tissues of red clover. A de novo transcriptome was assembled and functionally annotated, followed by identification of distinct patterns of gene expression across different tissues and comparative transcriptome analysis with Arabidopsis and other legumes. Additionally, genome-wide poly(A) site choice usage was also investigated.

Altogether, we have provided genomic insight into the gene expression and its regulation via alternative polyadenylation in two key forage crops, which can serve as an important resource for future crop improvement initiatives.