Unpredictable flooding is a major constraint to rice production. It can occur at any growth stage. The effect of simulated flooding post-anthesis on yield and subsequent seed quality of pot-grown rice (Oryza sativa L.) plants was investigated in glasshouses and controlled-environment growth cabinets. Submergence post-anthesis (9-40 DAA) for 3 or 5 days reduced seed weight of japonica rice cv. Gleva, with considerable pre-harvest sprouting (up to 53%). The latter was greater the later in seed development and maturation that flooding occurred. Sprouted seed had poor ability to survive desiccation or germinate normally upon rehydration, whereas the effects of flooding on the subsequent air-dry seed storage longevity (p50) of the non-sprouted seed fraction was negligible. The indica rice cvs IR64 and IR64Sub1 (introgression of submergence tolerance gene Submergence1A-1) were both far more tolerant to flooding post-anthesis than cv. Gleva: four days’ submergence of these two near-isogenic cultivars at 10-40 DAA resulted less than 1% sprouted seeds. The presence of the Sub1A-1 allele in cv. IR64Sub1 was verified by gel electrophoresis and DNA sequencing. It had no harmful effect on loss in seed viability during storage compared with IR64 in both control and flooded environments. Moreover, the germinability and changes in dormancy during seed development and maturation were very similar to IR64. The efficiency of using chemical spray to increase seed dormancy was investigated in the pre-harvest sprouting susceptible rice cv. Gleva. Foliar application of molybdenum at 100 mg L-1 reduced sprouted seeds by 15-21% following 4 days’ submergence at 20-30 DAA. Analyses confirmed that the treatment did result in molybdenum uptake by the plants, and also tended to increase seed abscisic acid concentration. The latter was reduced by submergence and declined exponentially during grain ripening. The selection of submergence-tolerant varieties was more successful than application of molybdenum in reducing pre-harvest sprouting.

In specific mammalian cells, the Ten-Eleven Translocation (TET) enzymes which are family members of 2-oxoglutarate (2-OG)-and Fe (II)-dependent dioxygenase (2ODD) are responsible for the modification of 5-mC to generate oxidised products such as 5-hmC, 5-caC and 5-fC, which are involved in oxidative demethylation. In rice, some reports have also revealed that 5-hmC was also present but the enzyme(s) responsible for oxidising 5-mC has not been identified. Here, possible Tet gene homologues in rice were identified by using various databases. There are 18 genes having a 2ODD domain most similar to TETs. Moreover, additional significant information such as the relatedness of protein sequence, protein interaction, nuclear localisation prediction, mutant analysis as well as gene annotation was obtained. Next, the spatial and temporal expression patterns of these genes were analysed within seedling root, mature leaf, young leaf and young panicle by analysing data from both microarray and qPCR. It was found that Os01g0546900 had highest expression in young leaf and six genes showed highest expression in mature leaf, whereas the remaining genes showed low expression in various organs. Finally, selected contrasting cultivars of rice were used to examine the expression of three genes of 2ODD and SLENDER RICE 1 (SLR1) under flooding and drought in order to evaluate the molecular aspects of Submergence 1A (Sub1A) regulation. The results showed that the Sub1A gene of tolerant rice was highly expressed under submergence but was not expressed under drought. Os03g0803500, Os07g0194500 and Os09g0489200, and SLR1 did not show any significant difference in expression in submerged and dehydrated plants of both IR64 and IR64.S1, nor in Japonica varieties which were used as susceptible check. To conclude, this finding indicates that Os03g0803500, Os07g0194500, Os09g0489200 and SLR1 may not have a correlation with Sub1A under flooding and drought stress.

Global climate change has been forecast to result in significant alterations to current temperature and precipitation patterns in cereal growing regions worldwide. The increased occurrence of elevated temperature stress at anthesis is likely to result in significant yield losses in wheat (Triticum aestivum L.). The ability of plant tissue to depress its temperature has been reported in relation to the canopy but recent work has demonstrated that spike temperature depression (STD) can be assessed in controlled environments (CE). The findings from two consecutive years of potbased CE experiments, a field-based experiment under polytunnel cover and a rhizobox-based experiment, in which the thermal dynamics of the spike and flag leaf under contrasting conditions of elevated temperature and water-deficit stress at anthesis, are reported. Flag leaf temperature depression (FLTD) was significantly greater than STD at anthesis. The data do not demonstrate an increased cooling capacity of the spike in the early stages of anthesis but rather in the latter stages, a phenomenon hypothesized to be primarily associated with the onset of senescence in the canopy. The inconsistent relationship observed between FLTD/STD at anthesis and grain yield (GY) does not currently elucidate whether a failure to depress tissue temperature at anthesis is associated with a yield penalty. The effect of experimental design on the physiological response to abiotic stress at anthesis was explored. The plant-wide distribution of photoassimilates at mid-anthesis was examined. Starch and water-soluble carbohydrate content in the flag leaf, peduncle and glumes was not found to correlate to GY. Further examination of the effects that abiotic stress at anthesis have on the photoassimilate distribution and GY need to take place in field-grown wheat.

No description available.

Pollen formation is considered ‘the Achilles tendon of reproductive development’. Therefore, special attention must be directed towards making sure that pollen is sufficiently robust, in order to cope with future climatic changes. One such anticipated future change in climate is increasing global temperature. Wheat is a very important crop for global food security, but wheat pollen development has been shown particularly sensitive to temperature stress. Therefore, work is needed to increase the environmental resilience of wheat pollen. In this thesis, attempts were made to not only find modern wheat varieties that had an increased tolerance to heat stress during pollen development, but also to clarify which stage(s) of wheat pollen development were the most sensitive to heat stress. Additionally, experimentation was conducted in order to assess the effect of heat stress on anther/pollen related gene expression, and the effect that inter-ear viable pollen movement had on yield restoration. In spite of it being shown that there were varieties that sustained significantly less grain losses, due to a heat stress event, and that a reduced level of pollen damage played a key role in this, it was apparent that this was not an example of tolerance, but instead an example of avoidance. Additionally, unlike previous reports, the developmental stage around pollen mother cell meiosis was not found to be the most significantly affected by heat stress, either in relation to grain number or microspore/pollen wellbeing. Instead, this designation was given to the latter stages of pollen wall development. Heat stress, during pollen development, had a profound effect on the expression levels/patterns of six anther/pollen related genes. This research has established a firm platform, in numerous different areas, for the future exploration of possibilities for reducing the effects of abiotic stress on wheat pollen development, and therefore directly increase yield resilience.

In recent years the amount of genomic resources of wheat has increased to the point where manual analysis is unfeasible. The aim of this PhD was to develop bioinformatics tools that help answer biological questions relevant to research and breeding by addressing the complexities associated with the wheat genome. I took advantage of resources which became publicly available as the analyses were carried out and I developed new approaches, strategies and tools to help accelerate wheat research. Chapter 1 reviews the genomic resources used for the thesis, placing them in historic context with the work and analyses performed. Chapter 2 describes the development of PolyMarker, a bioinformatics pipeline to design genome-specific primers in a timely and effective manner. Examples of different applications of PolyMarker are also included. Chapter 3 describes the analysis of an F2 population to generate a genetic map for Yr15, a gene that provides resistance to yellow rust. The SNP calling was done from bulked segregating samples, sequenced with RNASeq as a method of reduced representation. Chapter 4 describes expVIP, a tool to integrate RNA-Seq experiments in a relational database. Data from different studies can be visualised simultaneously, enabling comparisons between them. Lastly, in Chapter 5 all the data types used for the analysis on each of the previous chapters is integrated into a relational database. The discussion further explores how genetic maps, SNP markers, novel SNPs, gene annotations, gene assemblies and gene expression can be used simultaneously in research and breeding programs. All the tools and pipelines described in this thesis are open source and are available on: https://github.com/homonecloco.

Grain yield potential in wheat is a complex trait controlled by sub-traits like grain number, grain size, and assimilate partitioning. To achieve further understanding of grain yield potential, this thesis combines physiological and genetic dissection of wheat development. In particular, how the length of developmental phases can be optimized in favour of increased partitioning of assimilates to the spike, in order to reduce abortion rates of florets. The physiological section of the thesis (Chapter 2 and 3) comprises the in depth study of the CIMCOG panel (CIMMYT Core Germplasm). In this section the variation in patterns of floret and phenological development was determined, ascertaining how these differences affect the number of fertile florets. The differences in floret development were clear in the intermediate florets (floret primordia 3, 4, and 5 from the rachis). Floret survival was found to be positively related to the length of the period of floret development. Also fruiting efficiency, using the frontier concept, show a positive relationship with the stem elongation period. The genetic section (Chapter 4 and 5) involves the use of quantitative trait locus (QTL) analysis with a segregating population to determine the chromosomal locations affecting key developmental traits. A Buster x Charger doubled haploid population provided a crucial contrast between similar genetic background and differences in length of phenological phases. The results show that a QTL on chromosome 7A has an effect on the time to terminal spikelet phase, i.e. the onset of stem elongation, and QTL affecting time to heading was found on chromosomes 2D and 4A. Furthermore, this population also varies in lodging resistance. A major QTL was found on chromosome 2D affecting height and providing lodging resistance. These studies provide the basis to optimise wheat developmental patterns and, therefore, maximize spike fertility.

Zinc (Zn) is an essential micronutrient in plants but becomes toxic when present in excess, with nutritional extremes leading to agricultural yield losses. Homeostatic mechanisms are in place to control cellular Zn levels with transcription factors and membrane transport proteins playing vital roles. In Arabidopsis thaliana, two F-group bZIP transcription factors, bZIP19 and bZIP23, are proposed to sense and respond to Zn deficiency by regulating the expression of particular Zn membrane transporters, ZIPs (ZRT/IRT-like proteins). In this thesis, four unique bzip19 bzip23 knockout mutants with different combinations of T-DNA insertion sites were generated and shown to be hypersensitive to Zn-deficiency. To understand the role of F-group bZIPs in the economically important crop Hordeum vulgare (barley), HvbZIP1, 10, 56, 57, 58, and 61 were cloned and characterized to various extents. HvbZIP56, HvbZIP57, HvbZIP62 but not HvbZIP1 partially rescue the hypersensitive phenotype of the A. thaliana bzip19-4 bzip23-2 mutant. HvbZIP56 was localised to the cytoplasm and nucleus when expressed in A. thaliana and tobacco. Promoter analysis demonstrates that barley ZIP transporters that are up-regulated under Zn deficiency contain cis Zn-deficiency response elements (ZDREs), similarly to A. thaliana. Overall, these results indicate that the mechanisms operating in controlling Zn levels in barley are conserved. Two transporters, AtHMA3 (a P1B-2-type ATPase) and AtMTP1 (a Metal tolerance protein) have been implicated in sequestering Zn in Arabidopsis vacuoles to alleviate Zn toxicity. In this study, only the mtp1 mutant and not the hma3 mutant showed hypersensitivity to high Zn levels. HvHMA3 (a barley P1B-2-ATPase) when expressed in mtp1 rescued this hypersensitivity indicating a role in Zn transport, although this could not be confirmed by expression in S. cerevisiae. This study represents a significant step forward in understanding the mechanisms controlling Zn responses in cereal crops, and will aid in developing strategies for crop improvement.

Wheat is one of the major grain crops worldwide and provides approximately 20% of the total caloric and protein input for the world’s population. An increase in crop yields is required to meet the demands of the increasing world population in a challenging scenario of less predictable climatic conditions and sustainability requirements. There is an urgent need to develop crop plants that are more productive per land area and yield more stable outputs, without having to increase inputs of fertilizer or water. The canopy light-driven carbon uptake through photosynthesis is the primary determinant of plant biomass and yield. In this context, it is crucial to understand crop physiology and plant behaviour, with a focus on carbon balance, in contrasting environments, as well as to map the interactions between traits that drive wheat yields. Exploiting new methods of enhancing yield through successful strategies observed in other organisms can be used to achieve positive results for crop improvement. The impact of contrasting environments in wheat development and yield was studied in a panel of elite wheat cultivars over 3 seasons in UK. Late sowing and lower rainfall decreased the duration of grain development, impacting on grain yields. Yield stability was related to the crop resilience to shorter grain development periods and was partially explained by genetic similarities between cultivars or by the presence of genes related to crop development. The interaction between traits recognized as potential yield drivers and their stability and correlation to yield were studied in a double-haploid wheat mapping population. Traits correlated to light interception and use, and biomass allocation were strong yield drivers. Different lines adopt different strategies, based on these traits, to achieve high yields. The possible effect of the insertion of the ictB gene, related to carbon concentration in the chloroplast in cyanobacteria and to improved yields in plants, was studied in genetically modified wheat plants. No improvement was observed for photosynthetic traits or yield in the transgenic plants when compared to control plants, although unforeseen experimental problems could have hidden the expected phenotype. The achievements of this research contribute to improve the knowledge of wheat yield formation, its correlation to the carbon uptake process and stability in different climatic conditions. It may lead to a better understanding of new potential strategies to be applied in the breeding of genotypes for higher and more stable yields.

No description available.