Climatic variability, typified by erratic heavy-rainfall events, causes waterlogging in intensively irrigated crops and is exacerbated when crops are grown under warm temperature regimes on soils with poor internal drainage. Irrigated cotton is often grown in precisely these conditions around the world, exposing it to waterlogging-induced yield losses after substantial summer rainfall. This requires a deeper understanding of the basis of waterlogging tolerance and its relevance to cotton. The yield penalty depends on soil type, phenological stage and the cumulative period of root exposure to air-filled porosities below 10%. Events in the soil include O2 deficiency in the root zone, which changes the redox state of nutrients, making them unavailable (e.g. nitrogen) or potentially toxic (e.g. manganese) for plants. Furthermore, root-derived hormones that are transported through the xylem have long been associated with oxygen deficits. These belowground effects (impaired root growth, nutrient uptake and transport, hormonal signalling) have impacts in the shoots, interfering with canopy development, photosynthesis (Pn) and radiation use efficiency. Compared with the more waterlogging tolerant cereals, cotton does not have identified adaptations to waterlogging in the root zone, forming no conspicuous root aerenchyma and having low fermentative activity. These factors contribute substantially to the sensitivity of cotton to sustained periods of waterlogging. Despite significant advances in cotton production systems, limited efforts have been made to improve cotton performance in waterlogged soils. Management practices such as soil aeration, scheduling irrigation and fertiliser application are practiced to reduce waterlogging damage. However, little information is available on physiological responses of cotton to waterlogging. Cotton plants respond to a variety of stresses through a complex signalling network of hormones. Understanding the biosynthesis and regulation of these hormones (e.g. ethylene) in cotton tissue offers an opportunity to modulate cotton performance under stressful environments. The central research question was: can waterlogging-induced yield losses in cotton be minimised by modulating key physiological processes? This thesis aims to investigate the physiological mechanisms of waterlogging damage to cotton and devise targets for increased waterlogging tolerance. Since heavy rainfall events are often associated with cloudy conditions, restricting light availability to waterlogged (WL) cotton, it was hypothesised that shade would amplify yield losses in WL cotton. The initial field studies investigated how conditions of low incident light (i.e. shade) can modify the growth and yield of cotton crops experiencing waterlogging. The objective of these experiments was to study physiological mechanisms of waterlogging- and shade-induced damage to cotton. Either early or late in the reproductive phase, the crop was waterlogged (96 h and 120 h, in 2012-13 and 2013-14 cotton seasons, respectively) and/or shaded (6 d or 9 d in 2012-13 and 2013-14, respectively). Waterlogging at the early reproductive phase significantly reduced lint yield (17% averaged across both seasons) of cotton, although shade-induced yield losses (18%) were only significant in 2013-14. Shade significantly exacerbated yield losses under moderate waterlogging only, when the impact of waterlogging damage was modest (2013-14). More intense waterlogging impaired yield independently of light levels. Yield reductions in stressed cotton were mainly the consequence of accelerated fruit abscission and fewer fruiting nodes produced. Plants had lower leaf nitrogen levels and photosynthetic rates after waterlogging and/or shade treatments and produced fewer fruiting nodes, while stress-induced ethylene most likely acted by stimulating fruit abscission. Although, long-term shade increased specific leaf area (30%), leaf N (20%) and stomatal conductance (5%) immediately following 5 d of WL, it did not restore shoot growth, node formation or lint yield because of suppressed photosynthetic performance and carbohydrate supply. Thus, it can be concluded that interaction between waterlogging and shade depends on the intensity of individual stress. After observing limited effects of shade to a severely WL cotton crops, further studies were focused on exploring the physiological mechanisms of waterlogging damage alone in more detail. Due to indeterminate growth of cotton, it was hypothesised that different canopy layers would respond variably to soil waterlogging. Field experiments were conducted with the objective of understanding how waterlogging influences growth and yield of cotton across canopy layers. The crop was waterlogged at early (WLearly, 77 d after planting [DAP]) and late reproductive phases (WLlate, 101 DAP) for 120 h. Plants were tagged, and data from different canopy layers (bottom eight (MSN1-8), middle five (MSN9-13), and upper main stem nodes (MSN14+) were collected one day (post-WL) and 7 d after termination of waterlogging (post-recovery). Both waterlogging events significantly reduced post-WL dry biomass, leaf N and fruit development on MSN1-8. In addition, WLearly significantly reduced photosynthesis and increased total soluble sugars in MSN1-8 and MSN14+ leaves, although MSN14+ leaves restored photosynthesis, N level and sugars at recovery. These results suggested that WL plants could maintain photosynthesis in the upper leaves, possibly by transporting N from the lower leaves. Seed cotton yield reduction (22%) under WLearly was mainly the result of fruit loss from the first fruiting position of the upper and lowest sympodial fruiting branches (FB1-5 and FB11+), and WL plants continued to produce additional fruits on 2nd and 3rd position located on FB1-5. Despite the recovery in growth through improved photosynthesis and leaf N concentration, there was no yield recovery on FB11+ suggesting that plants used additional assimilates for the growth of established fruits. No significant yield reduction in response to WLlate suggested that the established cotton bolls were less sensitive to abscission across all canopy layers. Variable response of different canopy layers to soil waterlogging indicated the need of studying the effect of any stress on the whole canopy rather than top Field experiments clearly demonstrated that accelerated abscission of young fruits in WL cotton is the major cause of yield reduction, and the process is potentially regulated by ethylene. Thus, it was hypothesised that waterlogging damage to cotton can be minimised by blocking ethylene production. Glasshouse and field experiments were conducted with an objective to optimise application rates (0, 50, 100 and 150 [active ingredient, ai] ha-1) and time (pre- and post-waterlogging) of an anti-ethylene agent, aminoethoxyvinylglycine (AVG) for WL cotton. The glasshouse study suggested that AVG (ReTain®, 100-150 g [ai] ha-1) applied 24 h prior to waterlogging can increase growth and fruit retention of WL and non-waterlogged (NWL) cotton. The positive effects of AVG were further validated in two years of field studies. The crop was exposed to WLearly and WLlate. The data from field experiments suggested that AVG (125 g [ai] ha-1) applied at the early reproductive phase of cotton can significantly increase cotton yield under WL (13%, averaged across two years) and NWL (9%, averaged across two years) environments. Yield increase in AVG-treated cotton was associated with increased boll numbers, boll weight and fruit retention. On the other hand, no further improvement in cotton yield under higher AVG concentration (150 g [ai] ha-1) indicated the saturation of AVG on ethylene inhibition. Thus, appropriate AVG concentration and application timing may help to overcome waterlogging-induced yield losses in cotton production systems. The role of ethylene in regulating cotton yield was further explored in glasshouse experiments conducted at Macquarie University, Australia. The objective of the first glasshouse experiment was to investigate the relationships between ethylene accumulation and waterlogging sensitivity of two cotton cultivars, Sicot 71BRF (moderately waterlogging tolerant) and LA 887 (waterlogging sensitive). It was hypothesised that elevated ethylene accumulation in cotton tissues is responsible for waterlogging damage to cotton. The plants were grown in a clay-loam soil, and exposed to waterlogging at early reproductive phase (53 DAP). One d prior to waterlogging, the shoots were sprayed with AVG (830 ppm≈ AVG 125 g [ai] ha-1). Continuous waterlogging for 2 weeks accelerated the shedding of leaves and fruits. As the duration of waterlogging increased, shoot growth rate, biomass accumulation, Pn and gs were all reduced. Growth of LA 887 was more severely impaired than Sicot 71BRF, with a decline in leaf Pn and gs after just 4 h of waterlogging. Waterlogging inhibited allocation of N to the youngest fully expanded leaves, Pn and biomass accumulation, while it accelerated ethylene production promoting leaf and fruit abscission. AVG blocked the ethylene accumulation in leaves and subsequently improved leaf growth, N acquisition and photosynthetic parameters. In addition, AVG enhanced fruit production of both cotton cultivars under WL and NWL conditions. Higher ethylene production in cotton was linked with fruit abscission, implying that AVG-induced ethylene inhibition could potentially limit yield losses in WL cotton. Since yield losses in WL cotton were strongly associated with photosynthesis inhibition and accelerated ethylene production, it was hypothesised that waterlogging damage can be mitigated by modulating ethylene and carbon metabolism in cotton. The second glasshouse experiment at the Macquarie University investigated the role of ethylene as a major yield limiting factor for WL cotton. The objective of this experiment was to investigate the response to waterlogging tolerance by manipulating carbon and ethylene metabolism. Two cotton genotypes, varying in lint production and sensitivity to ethylene, namely Empire, a fully linted cotton cultivar and 5B, a lintless mutant line (lintless), were compared in a glasshouse study. At the peak reproductive phase (66 DAP), plants were exposed to waterlogging for 9 d and allowed to recover for 7 d after termination of waterlogging. Ethylene synthesis was inhibited by spraying AVG (830 ppm) one day prior to waterlogging and carbon dioxide enrichment (eCO2) was applied at the start of reproductive growth. The effect of these treatments on fruit production and distribution was studied in both cotton genotypes. By the end of the experiment, lintless plants produced significantly more fruits compared with Empire under all treatment conditions. In addition, the growth and fruiting pattern of the two cotton genotypes varied significantly in response to waterlogging, AVG and eCO2. Waterlogging significantly increased the release of ethylene from different tissues of both cotton genotypes, although fruit production was significantly inhibited only in Empire. Consistently, AVG significantly reduced waterlogging-induced abscission of fruits, mainly in Empire, by suppressing ethylene synthesis. Elevated CO2 promoted plant growth and fruit production in both genotypes, and was more effective in lintless than in Empire plants. Limited damage to fruits in lintless, despite increased production of ethylene during waterlogging, suggested that fruit abscission was generally associated with ethylene action, and that lintless was ethylene insensitive. The lintless produced more fruits than Empire, providing additional sinks that enhanced the response to CO2 enrichment. By contrast, eCO2 induced ethylene production in reproductive organs of the ethylene-sensitive Empire plants and subsequently affected fruit abscission, counteracting the positive effects of CO2 enrichment on reproductive development. These experiments provide conclusive evidence that increased ethylene biosynthesis in cotton plants and photosynthetic inhibition are the major reasons for yield reduction in cotton exposed to WL environments. The data contribute to the understanding of mechanisms through which waterlogging induces yield losses in cotton and suggest techniques for ameliorating this damage. Future studies should focus on characterisation of ethylene-responsive genes and their regulation in cotton with a prospect of increasing stress tolerance. This thesis elucidates the physiological mechanisms underlying the responses of cotton to soil waterlogging. WL cotton plants exhibited an ability to maintain yield in the top layers of canopy by remobilising nutrients. Photosynthetic inhibition and abscission of young fruits were the major reasons of waterlogging-induced yield losses in cotton, which can be minimised by suppressing ethylene or enhancing carbon metabolism
