Bioinformatic detection of genetic changes in the fungal endophyte Epichloë festucae AR37 during adaptation to a new perennial ryegrass host : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Microbial Genetics at Massey University, Palmerston North, New Zealand

Abstract

Mutualistic association with the fungus Epichloë festucae var lolii improves the resistance to abiotic stress and herbivory of perennial ryegrass (Lolium perenne). Breeders are interested in moving select E. festucae strains between ryegrass cultivars. In one such attempt E. festucae strain AR37 was transferred from its original ryegrass host to two new ryegrass cultivars. Performance of the resulting novel associations was improved over several years in a breeding program. We wanted to determine if genetic changes in AR37 contributed to this enhanced performance and, if so, identify the nature of these changes. The Epichloë endophyte indeed changed during adaptation to both new host cultivars. We demonstrated this by comparing the genome sequence of AR37 in its original host with pooled “AR37 population genomes” from the two novel associations at the end of the breeding program. These comparisons revealed mutations associated with ~ 150 genes. Frequency of mutations in endophytes increased with the number of seed cycles their new host has gone through. A wide variety of genes including those encoding for certain binding proteins e.g. acting binding, zinc ion binding, DNA-binding, and calcium binding as well as genes encoding for proteins that form signal recognition particles and involved in intracellular signal transduction were amongst those affected by mutations. These genes and their products can play an important role in establishing symbiotic association with the host cultivar. These results indicate that an array of endophyte genes may be involved in establishing a successful association with the new host cultivar. I conclude that (i) the Epichloë genome undergoes functionally relevant alterations as the endophyte adapts to new cultivars and (ii) monitoring the genes encoding the proteins involved, may facilitate breeding programs aimed at improving the performance of new endophyte ryegrass associations.