Genetic signatures in a perennial ryegrass (Lolium perenne) population following recurrent selection for compatibility with an endophyte (Epichloë spp.) from tall fescue : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Breeding at Massey University, Palmerston North, New Zealand

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Perennial ryegrass or Lolium perenne L. (Poaceae) is the most extensively grown forage especially in the temperate regions of the world, including New Zealand. The development of forage cultivars is important to New Zealand since the livestock industry depends on perennial ryegrass for its nutrition needs. Among forage breeding objectives, persistence is particularly complex. It refers to the stability of dry matter yield over time. It is economically important because reseeding and cultivation can be capital-intensive. Persistence is partly modulated by the interaction of perennial ryegrass with Epichloë spp. as these fungal endophytes confer insect resistance for a more stable yield. Genetic factors in the host influence fungal biomass, alkaloid concentration, and endophyte vertical transmission frequency. The symbiotic relationship is therefore exploited in perennial ryegrass breeding. Thus, the objective of this study is to investigate a perennial ryegrass breeding population under recurrent selection (RS) for compatibility with an endophyte sourced from tall fescue. Specifically, this study aims to (1) investigate the transmission of the Epichloë sp. FaTG-3 strain AR501 in the breeding population PGG04, and (2) to examine how genetic variation changes during RS in terms of population differentiation. Since the selection program targets endophyte compatibility, signatures of selection that may be associated with the grass-endophyte interaction were also determined. It was hypothesized that: there will be a reduction of diversity, and an excess of rare alleles. Furthermore, it was hypothesized that loci under positive selection will have higher fixation index (FST), and their genotypes will be more correlated with the components of PCA- based population structure analysis compared to neutral loci. The presence of AR501 was examined in seeds, in the growing tillers, and by microsatellite genotyping for both the early and late generations of PGG04. The seed squash assay revealed that more than 90% of PGG04 seeds harboured the endophyte, regardless of the generation. Viable endophyte detection using tissue-print immunoblotting showed an increase in infection from ca. 5% to 33% between the early and late generations. Thus, the results suggest that positive selection for endophyte compatibility increased the proportion of viable endophyte in the population. This study provides evidence supporting host genetic control of the association in grass-endophyte interaction, and that this can be exploited in plant breeding programs. Changes in the genetic variation of PGG04 was investigated by comparing GBS data of the early and late generations. Results showed that selection enriched the late generation with rare alleles (0.02 - 0.08) compared with the early generation. Also, selection reduced expected heterozygosity from 0.3069 in PGG04-C2 to 0.3033 in PGG04-C6. Further, selection changed the population structure based on UPGMA dendrogram, PCA, and the model-based clustering method implemented in STRUCTURE. A few single nucleotide polymorphisms (SNPs) have relatively larger contribution to the population structure changes hence, they have relatively high FST, and their genotypes correlated with principal components. Logistic regression of these SNPs with infection data identified nine SNPs to be associated with the trait. Depending on the allele frequency, these SNPs can increase the odds of favourable infection by more than five times. Annotation of these SNPs identified S7_160751877 to be tagging an ABCG transporter gene. Since some ABC transporters mediate plant-microbe interactions, it is possible that the identified SNPs are tagging a gene involved in the host genetic control of grass-endophyte interaction.
Table 1.1 and Figure 2.1 are re-used with permission.
Lolium perenne, Epichloë spp., perennial ryegrass-endophyte interaction, transmission, genotyping-by-sequencing, selection signature, recurrent selection, FST, PCA, ABCG transporters