As the first barrier to the external environment, the epicuticular waxes have a number of key roles in plant physiology. Although the wheat wild progenitors display a diversity of epicuticular wax phenotypes, the glaucous (visible wax) phenotype dominates cultivated varieties. However, the UK winter wheat variety Shamrock is unusual in that it exhibits a non-glaucous phenotype, conferred by the wild emmer gene Inhibitor of Wax 1 (Iw1). UK field trials with Shamrock associated a yield advantage of 4.15% with Iw1. This PhD tests the hypothesis that Iw1 imparts an advantage for wheat yield and physiology in the UK. Crossing Shamrock with six glaucous UK winter wheat varieties (Malacca, Alchemy, Hereward, Xi19, Robigus and Einstein) created non-glaucous near isogenic lines (NILs) with Iw1. NILs were grown at multiple field trial locations in the east of England over four years. A long-term shade trial reducing incoming light by 40 and 60% was also carried out in 2014. Yield, and various physiological components including water use efficiency (WUE) and spectral properties, were measured. Iw1 reduced flag leaf photosynthetically active radiation (PAR) reflectance by 15-40% and canopy reflectance by 12-20% (p<0.05). Despite this, Iw1 did not affect flag leaf PAR absorbance or canopy temperature, and conferred no advantage under long-term shading. Furthermore, there was no difference between NILs in photoinhibition following an extended period of high light stress. Iw1 did not affect WUE or yield. However, non-glaucous Hereward and Alchemy NILs yielded 4.96±1.15% (p<0.001) and 2.59±1.01% (p=0.045) more than their glaucous counterparts, although this advantage did not map to Iw1. Iw1 offered no advantage to UK winter wheat under normal UK growing conditions, nor under long-term shading. However, the yield advantage associated with the Iw1 introgression in Hereward and Alchemy is significant within a backdrop of plateauing wheat yields and worth pursuing.

In this thesis I address the question: does breeding to improve nitrogen use efficiency of winter wheat, Triticum aestivum, increase its susceptibility to infestation by cereal aphids? Laboratory and greenhouse experiments were used to monitor population performance of the aphids Sitobion avenae and Metopolophium dirhodum on double haploid genotypes of a Savannah cross Rialto (SavRia) wheat population. The genotypes varied in nitrogen use efficiency and its two components: nitrogen uptake efficiency and nitrogen utilisation efficiency. A quantitative trait loci analysis, using 94 genotypes grown under greenhouse and laboratory conditions, identified genetic markers associated with individual performance and population measures of S. avenae and M. dirhodum. Twelve markers across chromosomes on the SavRia genetic map were statistically associated with nine of the fourteen aphid performance traits measured. Nine wheat genotypes, representing the range of nitrogen use efficiencies, were used to analyse how aphid development rate, fecundity and intrinsic rate of increase, varied between genotype and whether settling behaviour and preference between genotypes, reflected differences in performance. Significant differences in performance of S. avenae between different genotypes were found but performance was not correlated with plant nitrogen uptake. In a randomised split plot experiment in the field, six SavRia genotypes and both parental varieties were grown under three application rates of nitrogen fertiliser. Significant variation between genotypes and between different nitrogen application rates was observed for eight plant traits, including both nitrogen uptake and utilisation efficiencies. Density of S. avenae differed significantly between genotypes with significant genotype x nitrogen application rate interactions. Aphid densities were not significantly correlated to either components of nitrogen use efficiency. I conclude that this study does not support the hypothesis that increasing nitrogen use efficiency, or either of its primary components, increases the susceptibility of winter wheat to infestation by cereal aphids.

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Wheat is one of the most economically important crop species in the world. It provides twenty percent of calories to a global population of seven billion people. However, genetic research of wheat is complicated as the genome is very large, full of repetitive sequences and comprised of three similar sub-genomes. During the course of this project, the genetic resources available for wheat drastically improved. The abundance of genome-specific SNP markers increased considerably, and 2014 saw the release of a chromosome-based draft sequence of the hexaploid wheat genome. The wealth of publicly-available SNP genotype information was exploited, to identify statistical associations between SNP markers and agronomically important traits, using two experimental populations: the Avalon x Cadenza doubled haploid mapping population, and the NIAB elite Multi-parent Advanced Generation Intercross (MAGIC) population. Genomewide association, and QTL analyses identified regions of interest on chromosomes 3D, 4B 4D, 5A, 5B and 6A. These regions contained SNPs which had an association with either grain yield; grain weight; grain width; grain length; grain surface area; or a combination of these traits. Furthermore, regions of chromosomes IB, 2A, 5B, 5D and 6A were of particular interest as they not only contained SNPs with a statistical association with a trait, they contained a transcript that had differential expression between plants with high and low thousand grain weight. These results suggest that although genetic diversity is limited, there is still potential for the identification of yield-increasing genes within elite wheat. Due to the lack of sequence information for wheat, few of the sequences of interest were annotated with gene or protein function. However, a set of putative candidate genes have been identified in both populations, which appear to be involved in plant growth and development. Of particular interest to the wheat breeding industry is the range of elite material studied. Over 80% of allelic diversity seen in elite UK wheat was captured by the two experimental populations, which, in total, represented 10 elite varieties. Therefore, there is a high chance that the SNPs identified in these populations are segregating in elite breeding material. Furthermore, a variety of hexaploid, tetraploid and diploid wheat material, including elite varieties; wheat relatives; and wild landraces have previously been screened with the majority of the SNPs used in this analysis. The SNP data is publicly available, making the results of this study immediately available for validation or introduction into breeding programmes.

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