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
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Date
2020
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Massey University
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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.
Description
Figure 1.1 (=Clay & Schardl, 2002 Fig 2) was removed for copyright reasons. Figure 1.2 (=Schardl et al., 2013c Fig 1) is reused under a Creative Commons Attribution 3.0 (CC BY 3.0) license. https://creativecommons.org/licenses/by/3.0/
Keywords
Epichloë, Endophytic fungi, Genetics, Lolium perenne, Breeding, Fungal molecular biology