Abstract
Lolium perenne (perennial ryegrass) is the primary pasture crop supporting New Zealand’s agricultural industry. Limited genetic gains have been made with current breeding strategies compared to other grass crops such as rice and maize, which have benefited from the use of complementary inbred parental lines to generate vigorous and uniform hybrid offspring. One of the largest constraints on producing hybrid cultivars in L. perenne is self-incompatibility. This prevents the production of inbred lines and limits the ability to both purge deleterious alleles and fix agronomically advantageous traits in breeding populations. The ability to overcome self-incompatibility, either naturally or through engineering, would be a desirable trait for NZ’s agricultural industry. One naturally occurring mutation that can overcome the self-incompatibility mechanism has been identified as a mutant allele termed the SF-locus. This locus has been identified in several populations and has been mapped to a region on chromosome 5.
To increase genetic gain in NZ L. perenne, this project aimed to introgress the SF-locus from a European, self-compatible population, into a New Zealand elite L. perenne cultivar and subsequently develop an inbred line that could be used to select for desirable traits. This was conducted through the development of a breeding plan that initially crossed the two populations and was followed by two subsequent rounds of inbreeding. The success of the breeding programme was assessed genomically to determine population structure. The genomic information was also used to investigate the allelic proportions and degree of inbreeding, at the completion of the breeding programme, which indicated that inbreeding increased with each generation of selfing.
Genetic markers specific to the SF-locus in the NZ self-compatible population were developed utilising genomic resources. The markers located the SF-locus to a ~1.6 Mb region, and were used to genotype the inbred offspring produced through the breeding process. The development of genetic markers specific to the NZ elite population was required to identify plants containing the SF-locus reliably and accurately. Identifying these markers means the SF-locus can be tracked after introgression into elite NZ L. perenne breeding populations, producing inbred lines with agronomically advantageous traits specific to NZ.
Identifying the genetic region containing the SF-locus also enabled the investigation of candidate causal genes. Prior research on potential causal genes was based on syntenic regions and functional predictions. As the SF-locus is pollen-expressed, transcriptomic analysis on pollen from both self-compatible and self-incompatible plants was assessed to determine differential expression. This provided a set of putative causal genes that were functionally annotated. A hypothetical model of how the L. perenne SI system could be overcome by the SF-locus was developed based on the results of the analyses.