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Reduced height 8 (Rht8) is the main alternative to the GA-insensitive Rht alleles in hot and dry environments and reduces plant height without yield penalty. The potential of Rht8 in northern-European wheat breeding remains unclear. In the present study, near-isogenic lines contrasting for the Rht8/tall allele in the UK-adapted and photoperiod-sensitive variety Paragon were evaluated in trials with varying nitrogen fertiliser (N) treatments and water regimes across sites in the UK and Spain. Rht8 conferred a robust height reduction of 11% regardless of treatment and was more resistant to root-lodging at agronomically-relevant N levels. In the UK, the Rht8 NIL showed a 10% yield penalty due to concomitant reduction in grain number and spike number whereas grain weight and harvest index were not significantly different to the tall NIL. The yield penalty was abolished at low N and in irrigated conditions in the UK and Spain. This indicates the utility of Rht8 in reduced-input agriculture. Decreased spike length and constant spikelet number in Rht8 compacted spikes by 15% independent of environment. The genetic interval of Rht8 overlaps with the most recent mapping of the compactum gene on 2DS (Johnson et al., 2008) and future work with the markers found in this study is required to genetically dissect these loci. Rht8 had been previously fine-mapped to a 1.29 cM interval (Gasperini et al., 2012). Rht8 was further fine-mapped using an RNA-Seq enabled bulked segregant analysis method, as well as utilising SNP-platforms and emerging Triticeae genomic resources to identify molecular markers. Rht8 was reduced to a 1.015 cM genetic interval and syntenic intervals of 1.34 Mb on rice chromosome 4, 1.36 Mb on Brachypodium chromosome 5, 2.9 Mb on barley 2H and 4.25 Mb on Ae. tauschii 2D. Disruption to micro-collinearity was found with Brachypodium and rice, with better but imperfect collinearity with Ae. tauschii and barley. Rht8 was also anchored to a single IWGSC-2 POPSEQ bin and to a 2.3 cM region in the whole genome shotgun-ordered wheat scaffolds.

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No description available.

The regulation of leaf thickness in rice (Oryza sativa L.) S. Narawatthana One of the most important targets to improve crop yield is leaf photosynthetic capacity. Leaf thickness is one parameter closely associated with photosynthetic function and is strongly influenced by the level of irradiance. Generally, high light grown leaves are thicker, have higher light-saturated rates of photosynthesis, higher amounts of Rubisco and a higher chlorophyll a:b ratio than shade grown leaves. However, the developmental stage at which leaf thickness is set and how it is set are unclear. In this thesis I investigate the outcome on leaf thickness of changing irradiance level at specific points in the development of leaf 5 of rice plants via a series of transfer experiments from high light (HL) to low light (LL) at specific stages of leaf development. The results from these experiments show that the P2- to P4-stage of rice leaf development represents a developmental window during which final thickness can be altered via light regime. Analysis of photosynthetic capacity and gas exchange of the leaves from the transfer experiments indicated some correlation of leaf thickness with biochemical/physiological adaptation to the prevailing irradiance level. Interestingly, whilst HL induced the development of thicker rice leaves with a visibly larger mesophyll cell size, transferral of the leaves to LL conditions at any developmental stage led to a LL-acclimated photosynthetic response. To identify lead genes potentially involved in the growth response of young leaves to the prevailing light environment, I performed a microarray analysis of leaf primordia at P3-stage undergoing a leaf-thickness response to altered irradiance level. A number of lead genes were identified and a selection process based on independent expression analyses was performed to narrow the number of candidates for future functional analysis. An initial analysis of some of these genes is reported.

Producing enough food to sustainably meet the demands of a growing global population is one of the greatest challenges we face. In wheat, 8% of yield is lost to insect herbivores before harvest, so improving pest control would contribute significantly to food security. Given the negative effects of chemical insecticides, managing habitat to boost numbers of pest natural enemies offers a promising alternative. Recent studies highlight the importance of wider landscape context for natural enemy management, but there is uncertainty over which landscape characteristics are most important for different natural enemies, how this varies temporally, and which management strategies are worthwhile. In this thesis novel analytical approaches using random forests were used to explore temporal and inter-specific variation in the influence of landscape context on species of aphid and hymenopterous parasitoid in winter wheat fields in the UK, and to produce models predicting the abundance of aphids, parasitoids and syrphid larvae as functional groups. Aphid and parasitoid numbers responded strongly to the spatial configuration of vegetation parcels, both being more common in more fine-grained landscapes. Syrphid larvae were more abundant when arable land was rare within 1500 metres. Seasonal variation in landscape influence was more important than annual or inter-species differences for both aphids and parasitoids. Map-based simulations were then performed to predict the outcome of hypothetical land-use scenarios, using a novel method based on statistical models. Displacement of non-crop vegetation by arable land, alongside increased aggregation, produced consistently undesirable results. Estimates of the economic value of natural enemies to farmers were made, showing the potential to reduce yield loss and insecticide cost by at least £55 per hectare through beneficial habitat management. At high aphid densities, natural enemies were more valuable under insecticide free management. Future work and implications of these results are discussed in chapter 6.

The projected negative impacts of climate change threaten to endanger smallholder rain-fed maize production and therefore food security across Sub-Saharan Africa. It is widely advocated that the provision of improved, climate-tolerant maize seeds will overcome this problem by enabling agricultural adaptation to changing weather conditions. However, attempts to launch new agricultural technologies in Africa have rarely successfully transformed prospects for the most vulnerable, and historical uptake of improved maize has remained low in some countries, including Malawi, despite a strong political legacy of modern input promotion. This thesis investigates how social dimensions (such as asset ownership, cultural preferences and perceptions of climate risk) affect the potential for cultivar adoption to enable equitable adaptation to climate change amongst smallholder maize farmers in Malawi. National strategies for the diffusion of maize cultivars are explored and analysed with reference to agricultural innovation theory. Adoption outcomes are then assessed using household data from two case study areas selected on the basis of their contrasting climate vulnerability characteristics and productive potentials for maize. Lastly, perceptions of climate change amongst research participants are explored and considered in relation to a statistical analysis of historical rainfall and temperature data within the two research areas, Kasungu and Ngabu. The empirical findings reveal that whilst Malawi’s maize seed industry is modernising, changes do not necessarily benefit smallholders, and access to cultivars and information about them remains unequal. State agricultural policies lack regional contextual specificity and have contributed to heightened vulnerability in Ngabu (the less productive case study area). Stakeholders’ perceptions and attitudes about current and future climate change reveal incongruities and misconceptions. Widespread beliefs that seasons are shortening are driving preferences for short season hybrid cultivars, which increasingly flood the seed market, but statistical analysis of historical seasonal rainfall data reveals no clear seasonal trend in this direction. New diffusion strategies, increasing policy sensitivity for dealing with climate vulnerability in marginal areas, and better understanding and communication about climate variability and change will all be required if cultivar adoption is to enable successful and equitable adaptation for Malawian smallholders. These goals could be better supported if vulnerability reduction, rather than corporate growth, was made central to the development of Malawi’s agricultural innovation system. Practical methods by which this change might be achieved are discussed.

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Septoria leaf blotch, caused by the fungal pathogen Zymoseptoria tritici, is one of the most damaging diseases of wheat (Triticum aestivum), a crop plant of significant worldwide importance. Using the system of Virus-Induced Gene Silencing, to create transient knockdowns of target genes, a novel wheat gene, TaR1, was identified as playing a key role in the host response to this pathogen. Silencing this gene leads to the earlier onset of disease symptoms, but reduced reproduction of the causal pathogen. Sequence analysis, confocal microscopy and protein-protein interaction assays were used to determine that the protein TaR1 localises the nucleus, where its function involves the binding of histones. Precisely, TaR1 is able to bind the Histone 3 subunit, specifically methylated on Lysine 4. Through this action, the host defence response is delayed, and successful pathogen colonisation is promoted. It is hypothesised that this is an example of the pathogen ‘hi-jacking’ TaR1 from its original function, in order to complete its lifecycle.

Pre-harvest sprouting (PHS) and Pre-maturity amylase (PMA) are physiological defects in wheat grains that reduce their end-use quality. PHS is the precocious germination of grains before harvest while PMA is the accumulation of α-amylase in grains. Both traits are quantitative in their expression and are strongly influenced by the environment. In this project, I studied six Quantitative Trait Loci (QTL) located on chromosomes 1A, 2D, 3A (2 loci), 4A and 7B, which confer resistance to PHS or PMA in UK wheat varieties. The aims of this project were to validate and characterise the effects of these QTL, as well as to fine-map the QTL with the most significant effect. To achieve these aims, isogenic materials were developed to independently study these QTL effects. Physiological characterisation of these QTL showed that they exert their effects by affecting the dynamic of dormancy loss in grains, albeit at different stages of grain development and maturation. We also show that temperature during grain development and germination affect the expression of these QTL effects. In addition to the characterisation above, I also undertook the fine-mapping and positional cloning of the 4A QTL (named Phs), as this QTL showed the highest effect on PHS resistance of all the QTL studied. I took advantage of recent advances in wheat genomics, high-throughput genotyping and the syntenic relationship between wheat and other grasses, to delimit Phs to a less than 0.2 cM interval. Furthermore, examination of the physical map of this interval identified 17 genes with varied biological functions. High-resolution fine-mapping of the 0.2 cM interval in three independent and diverse populations further delimited Phs to a 10 kb genomic interval. Finally, I report on the comparative sequence analysis around this critical interval, and show the presence of some genomic lesions that could be critical for the Phs effect.