Abstract
Perennial ryegrass (Lolium perenne L.) is a grass species that is widely sown on dairy and sheep farms in temperate agricultural regions, including New Zealand, owing to its persistence and capacity to produce high amounts of herbage that is rich in nutrients and metabolizable energy. However, the transition from the vegetative to the reproductive growth phase results in a significant decrease in the digestibility and metabolizable energy content of ryegrass-based farm pastures, resulting in reduced animal performance, overall farm productivity, and economic gains. To address this, past breeding efforts have aimed to delay the onset of the reproductive phase transition (floral transition) and/or timing of floral head emergence (heading date). However late heading poses certain challenges for commercial seed production. In comparison to well-studied plant species, such as Arabidopsis, Brachypodium, rice, and wheat, the genetics of floral transition and timing of heading emergence in ryegrass is not well understood. The main objectives of this doctoral research were (i) to advance understanding of the genetics of floral transition and heading date in ryegrass and (ii) to explore strategies for creating a ryegrass cultivar that does not produce floral heads on farms in New Zealand and is, therefore, able to maintain high levels of metabolizable energy, yet can be induced to produce floral heads for seed production.
As a first step, a scalable pipeline using Oxford Nanopore long-read amplicon sequencing was developed for routine haplotype analysis in perennial ryegrass populations. Following the successful establishment of this pipeline, several F2 populations generated from crosses between various New Zealand commercial cultivars and European ecotypes were screened for heading response. These populations were found to segregate for extremely late heading (≥ +35 days) over several seasons. A survey of the key genes acting downstream in the vernalization and photoperiod flowering pathways in these populations using the established protocol revealed high genetic and haplotype diversity in these genes, as well as an association between heading date and the CO and FT3 loci. Furthermore, a comparison of sequence variation and various heading phenotypes led to the identification of mid-season and extra late haplotypes of CO and FT3 in these populations. Moreover, extremely late flowering plants could be induced to produce floral heads earlier by altering the duration of daylength, indicating that extra late heading was a photoperiod duration-dependent response. Additionally, the use of Nanopore cDNA sequencing on the transcriptomes of mid-season and extremely late plants uncovered novel floral regulators in ryegrass that belonged to the COL, FLZ and LNK gene families putatively associated with the extra late heading trait. The information and resources developed in this thesis have further advanced the current understanding of mechanisms controlling heading in ryegrass and have laid the groundwork towards the breeding of an elite non-heading perennial ryegrass.