Advanced phenomics- and genomics-based tools for molecular breeding of Ryegrass (Lolium spp.)

Submission note: A thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy to the School of Applied Systems Biology, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora.

Perennial ryegrass and Italian ryegrass are the most important temperate forage grasses for world pastoral agriculture. However, small levels of genetic gain, estimated at c. 0.25- 0.6% per annum, have been achieved by conventional ryegrass breeding programs. This genetic gain has been limited by a number of factors, such as an obligate outbreeding reproductive habit, a broad range of agronomically important traits but limited phenotypic assessment technologies, long breeding cycles, and inability to exploit heterosis. This thesis explores a number of innovative strategies and methodologies for enhancement of commercial ryegrass breeding. In the first instance, development of genomics and bioinformatics tools to enable the most effective establishment and maintenance of breeding nurseries, allowing capture and characterisation of useful genetic diversity. Secondly, development of high-throughput semi-automated low-cost phenotypic measurement protocols for forage quality traits, to enable the breeding of ryegrass with superior nutrient profiles matching the requirements of grazing ruminants, ultimately improving animal production, but also contributing to farm-system nutrient-use efficiency and reduced environmental impacts. Thirdly, conduct of a candidate gene-based association mapping study for such herbage quality traits, to initiate implementation of genomics-assisted breeding of ryegrass, while also providing a valuable insight into the most suitable pathways for application of genomic selection. Fourthly, presentation and exploration of a novel breeding design and methodology for commercial F1 hybrid ryegrass production, in order to enable breeders to capture, retain and exploit heterosis in their cultivars. Finally, development of a second-generation genotyping tool and associated bioinformatic procedures for identification and discrimination between ryegrass varieties, providing protection of breeder’s proprietary germplasm as well as quality assurance and quality control (QA/QC) within breeding programs. These advances offer improvements to commercial ryegrass breeding from the initial stages of breeding nursery establishment, through to phenotypic assessment, selection and breeding design, and finally to cultivar protection and QA/QC.