Abstract
Lolium perenne L. (perennial ryegrass) is the leading forage crop in New Zealand, sustaining much of the agricultural sector. Ryegrass heading (the transition from vegetative to reproductive growth) is a major trait that influences agricultural productivity: heading decreases yield, reducing milk production; heading requirements limit the number of generations per year, increasing breeding time; variation in heading date impacts seed production and farm management.
Ryegrass is an outbred, highly heterogeneous species. Heading is controlled by genetic variation in genes regulated by environmental factors such as vernalization (a prolonged cold period) and photoperiod (day length). Within the industry, there is a desire to develop cultivars of ryegrass with specialized heading phenotypes based on different allelic combinations. This thesis explores genetic variation in ryegrass genes associated with heading regulation.
The first goal of this thesis was to characterize a non-heading phenotype found in the New Zealand ryegrass cultivar Array as there is interest in developing a non-heading ryegrass cultivar to maintain yields throughout summer. A proportion of cv. Array plants did not head in the field, and it was hypothesised this was due to a homozygous recessive mutation. Sequencing of target genes and genome-wide genotyping-by-sequencing (GBS) did not reveal any homozygous mutations just in the non-heading plants, although these analyses were limited by high levels of heterozygosity. Gene expression analysis of key genes that regulate heading suggested that vernalization was not being perceived differently in non-heading Array plants compared to heading Array plants. Heading phenotypes from the following summer then indicated that the environment was playing a larger role in heading regulation than genetic variation was. This aligns with the understanding that ryegrass heading is a complex trait controlled by both environmental and genetic factors.
The second goal of this thesis was to develop a method to genotype target genes in inbred ryegrass plants using genome-wide GBS data. Heading is regulated by many known genes, but the influence that genetic variants within these genes have on heading phenotypes is largely unknown. Therefore, the ability to easily determine alleles of target genes will be important for understanding how genetic variants relate to heading phenotypes for breeding specialised cultivars. Additionally, an available inbred population was ideal for genotyping as there were two alleles per gene. A method was developed that identifies genetic markers close to target genes from GBS data and uses these markers to genotype plants. The genotypes of related individual plants were combined to determine which target genes had been fixed in previous generations, which was confirmed with a PCR-based genotyping assay. A correlation between heading phenotype and the genotype combination of two genes in the photoperiod pathway was possibly identified.
This research has highlighted that ryegrass heading is a complex trait, controlled by multiple genetic and environmental factors. It has added data to the growing understanding of ryegrass heading for future breeding applications.