Assessing the potential of genomic selection to improve yield and persistence in white clover : a thesis presented in the partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Plant Biology at Massey University, Manawatu, New Zealand. EMBARGOED until 30 April 2022.

Abstract

White clover (Trifolium repens L.) is an economically important forage legume in temperate pastures, providing quality fodder and plant-available nitrogen. However, its potential has not been fully exploited due to unpredictable herbage yield and poor vegetative persistence in pasture. Identification of genotypes that combine traits essential for yield and vegetative persistence, like dry matter yield and stolon density, are key objectives in breeding programmes. Long breeding cycles, high genome complexity and difficult-to-phenotype traits, usually assessed at late growth stages, are major constraints to conventional phenotypic selection in white clover breeding. In cultivar development programmes, elite individuals must be accurately identified and selected before crossing to generate superior progeny. Genomic selection is becoming a preferred method for increasing the rate of genetic gain by enabling early identification and selection of superior individuals, based on their genomic estimated breeding values (GEBVs), which can be generated without the need for phenotyping. Genomic selection is usually performed using a statistical model developed using genotypic and phenotypic information derived from a training population. In forage breeding, as parental breeding values are estimated by progeny testing, phenotypic data used in genomic prediction models is obtained from half-sib progeny. Recent single nucleotide polymorphism (SNP) genotyping methods like genotyping by sequencing (GBS) which generate a large volume of SNP marker information at low cost, have made genomic selection possible for species such as white clover. The main objective of this thesis was to explore the potential of genomic selection to improve important traits in white clover breeding. Our results indicate, for the first time, an integrated phenotypic and genomic selection approach to be superior to conventional phenotypic selection at increasing genetic gain for a simple trait in white clover. This demonstrates the potential of genomic selection to be used in enhancing white clover breeding programmes for quantitative trait improvement.--Shortened abstract