Screening of potential donors for anaerobic stress tolerance during germination in rice.

The rising cost of transplanting rice has made direct seeding an affordable alternative for rice establishment, particularly in Africa. However, direct seeding, while cost-effective, faces crop establishment challenges due to flooding. Uncontrolled water, driven by erratic rains in low-lying areas or uneven fields, limit germination. Rice possesses the unique ability of anaerobic germination, enabling it to sprout and emerge in oxygen-deprived conditions. Understanding rice's response to anaerobic stress during germination is crucial for resilience breeding. Africa, although relying on direct seeding, has made limited progress in addressing flooding during germination compared to Asia. Anaerobic stress tolerance ensures successful crop emergence even in oxygen-limited environments and can help suppress weeds, a significant challenge in direct-seeded rice cultivation. This study aims to contribute by screening for potential rice donors exhibiting anaerobic stress tolerance. We screened 200 rice genotypes at Sokoine University of Agriculture (SUA) in Morogoro, Tanzania, primarily focusing on landraces with untapped potential. Using an alpha lattice design, we conducted two anaerobic experiments in September and October 2022, adding 7 cm of standing water immediately after dry seeding for flooded and maintaining a 2 cm water level after germination in the control for duration of 21 days. We identified potential donors based on selection index computed from genomic estimated breeding values (GEBVs) using eight variables: germination at 14 DAS, germination at 21 DAS, seedling height at 14 DAS, seedling height at 21 DAS, shoot dry matter at 21 DAS, root dry matter at 21 DAS, culm diameter at 21 DAS, and root length at 21DAS. Ten genotypes emerged as the most promising, exhibiting at least 70% germination in floodwater at 21 DAS and greater selection indices. These genotypes were like: Afaa Mwanza 1/159, Rojomena 271/10, Kubwa Jinga, Wahiwahi, Magongo ya Wayungu, Mpaka wa Bibi, Mwangaza, Tarabinzona, IB126-Bug 2013A, and Kanamalia with respective percentages of 75, 74, 71, 86, 75, 80, 71, 80, 70, and 73. These findings contribute to global efforts to mitigate the impacts of flooding during germination. These donors, will be potential to enrich the gene pool for anaerobic germination, providing valuable resources for breeding for flooding tolerance.

A meta-analysis of plant tissue O2 dynamics.

Adequate tissue O2 supply is crucial for plant function. We aimed to identify the environmental conditions and plant characteristics that affect plant tissue O2 status. We extracted data and performed meta-analysis on >1500 published tissue O2 measurements from 112 species. Tissue O2 status ranged from anoxic conditions in roots to >53kPa in submerged, photosynthesising shoots. Using information-theoretic model selection, we identified 'submergence', 'light', 'tissue type' as well as 'light×submergence' interaction as significant drivers of tissue O2 status. Median O2 status were especially low (Solanum tuberosum ) tubers and root nodules. Mean shoot and root O2 were ~25% higher in light than in dark when shoots had atmospheric contact. However, light showed a significant interaction with submergence on plant O2 , with a submergence-induced 44% increase in light, compared with a 42% decline in dark, relative to plants with atmospheric contact. During submergence, ambient water column O2 and shoot tissue O2 correlated stronger in darkness than in light conditions. Although use of miniaturised Clark-type O2 electrodes has enhanced understanding of plant O2 dynamics, application of non-invasive methods in plants is still lacking behind its widespread use in mammalian tissues.

Responses of key root traits in the genus Oryza to soil flooding mimicked by stagnant, deoxygenated nutrient solution.

Excess water can induce flooding stress resulting in yield loss, even in wetland crops such as rice (Oryza). However, traits from species of wild Oryza have already been used to improve tolerance to abiotic stress in cultivated rice. This study aimed to establish root responses to sudden soil flooding among eight wild relatives of rice with different habitat preferences benchmarked against three genotypes of O. sativa. Plants were raised hydroponically, mimicking drained or flooded soils, to assess the plasticity of adventitious roots. Traits included were apparent permeance (PA) to O2 of the outer part of the roots, radial water loss, tissue porosity, apoplastic barriers in the exodermis, and root anatomical traits. These were analysed using a plasticity index and hierarchical clustering based on principal component analysis. For example, O. brachyantha, a wetland species, possessed very low tissue porosity compared with other wetland species, whereas dryland species O. latifolia and O. granulata exhibited significantly lower plasticity compared with wetland species and clustered in their own group. Most species clustered according to growing conditions based on PA, radial water loss, root porosity, and key anatomical traits, indicating strong anatomical and physiological responses to sudden soil flooding.

Physiology, gene expression, and metabolome of two wheat cultivars with contrasting submergence tolerance.

Responses of wheat (Triticum aestivum) to complete submergence are not well understood as research has focused on waterlogging (soil flooding). The aim of this study was to characterize the responses of 2 wheat cultivars differing vastly in submergence tolerance to test if submergence tolerance was linked to shoot carbohydrate consumption as seen in rice. Eighteen-day-old wheat cultivars Frument (intolerant) and Jackson (tolerant) grown in soil were completely submerged for up to 19 days while assessing responses in physiology, gene expression, and shoot metabolome. Results revealed 50% mortality after 9.3 and 15.9 days of submergence in intolerant Frument and tolerant Jackson, respectively, and significantly higher growth in Jackson during recovery. Frument displayed faster leaf degradation as evident from leaf tissue porosity, chlorophylla , and metabolomic fingerprinting. Surprisingly, shoot soluble carbohydrates, starch, and individual sugars declined to similarly low levels in both cultivars by day 5, showing that cultivar Jackson tolerated longer periods of low shoot carbohydrate levels than Frument. Moreover, intolerant Frument showed higher levels of phytol and the lipid peroxidation marker malondialdehyde relative to tolerant Jackson. Consequently, we propose to further investigate the role of ethylene sensitivity and deprivation of reactive O2 species in submerged wheat.

Leaf gas films contribute to rice (Oryza sativa) submergence tolerance during saline floods.

Floods and salinization of agricultural land adversely impact global rice production. We investigated whether gas films on leaves of submerged rice delay salt entry during saline submergence. Two-week-old plants with leaf gas films (+GF) or with gas films experimentally removed (-GF) were submerged in artificial floodwater with 0 or 50 mm NaCl for up to 16 d. Gas films were present >9 d on GF plants after which gas films were diminished. Tissue ion analysis (Na+ , Cl- and K+ ) showed that gas films caused some delay of Na+ entry, as leaf Na+ concentration was 36-42% higher in -GF leaves than +GF leaves on days 1-5. However, significant net uptakes of Na+ and Cl- , and K+ net loss, occurred despite the presence of gas films, indicating the likely presence of some leaf-to-floodwater contact, so that the gas layer must not have completely separated the leaf surfaces from the water. Natural loss and removal of gas films resulted in severe declines in growth, underwater photosynthesis, chlorophylla and tissue porosity. Submergence was more detrimental to leaf PN and growth than the additional effect of 50 mm NaCl, as salt did not significantly affect underwater PN at 200 µm CO2 nor growth.

Leaf gas film retention during submergence of 14 cultivars of wheat (Triticum aestivum).

Flooding of fields after sudden rainfall events can result in crops being completely submerged. Some terrestrial plants, including wheat (Triticum aestivum L.), possess superhydrophobic leaf surfaces that retain a thin gas film when submerged, and the gas films enhance gas exchange with the floodwater. However, the leaves lose their hydrophobicity during submergence, and the gas films subsequently disappear. We tested gas film retention time of 14 different wheat cultivars and found that wheat could retain the gas films for a minimum of 2 days, whereas the wild wetland grass Glyceria fluitans (L.) R.Br. had thicker gas films and could retain its gas films for a minimum of 4 days. Scanning electron microscopy showed that the wheat cultivars and G. fluitans possessed high densities of epicuticular wax platelets, which could explain their superhydrophobicity. However, G. fluitans also had papillae that contributed to higher hydrophobicity during the initial submergence and could explain why G. fluitans retained gas films for a longer period of time. The loss of gas films was associated with the leaves being covered by an unidentified substance. We suggest that leaf gas film is a relevant trait to use as a selection criterion to improve the flood tolerance of crops that become temporarily submerged.

Flood tolerance of wheat - the importance of leaf gas films during complete submergence.

Submergence invokes a range of stressors to plants with impeded gas exchange between tissues and floodwater being the greatest challenge. Many terrestrial plants including wheat (Triticum aestivum L.), possess superhydrophobic leaf cuticles that retain a thin gas film when submerged, and the gas films enhance gas exchange with the floodwater. However, leaf hydrophobicity is lost during submergence and the gas films disappear accordingly. Here, we completely submerged wheat (with or without gas films) for up to 14 days and found that plants with gas films survived significantly longer (13 days) than plants without (10 days). Plants with gas films also had less dead tissue following a period of recovery. However, this study also revealed that reflections by gas films resulted in a higher light compensation point for underwater net photosynthesis for leaves with gas films compared with leaves without (IC=52 vs 35µmol photons m-2 s-1 with or without gas films, respectively). Still, already at ~5% of full sunlight the beneficial effect of gas films overcame the negative under ecologically relevant CO2 concentrations. Our study showed that dryland crops also benefit from leaf gas films during submergence and that this trait should be incorporated to improve flood tolerance of wheat.

Mechanisms of waterlogging tolerance in wheat--a review of root and shoot physiology.

We review the detrimental effects of waterlogging on physiology, growth and yield of wheat. We highlight traits contributing to waterlogging tolerance and genetic diversity in wheat. Death of seminal roots and restriction of adventitious root length due to O2 deficiency result in low root:shoot ratio. Genotypes differ in seminal root anoxia tolerance, but mechanisms remain to be established; ethanol production rates do not explain anoxia tolerance. Root tip survival is short-term, and thereafter, seminal root re-growth upon re-aeration is limited. Genotypes differ in adventitious root numbers and in aerenchyma formation within these roots, resulting in varying waterlogging tolerances. Root extension is restricted by capacity for internal O2 movement to the apex. Sub-optimal O2 restricts root N uptake and translocation to the shoots, with N deficiency causing reduced shoot growth and grain yield. Although photosynthesis declines, sugars typically accumulate in shoots of waterlogged plants. Mn or Fe toxicity might occur in shoots of wheat on strongly acidic soils, but probably not more widely. Future breeding for waterlogging tolerance should focus on root internal aeration and better N-use efficiency; exploiting the genetic diversity in wheat for these and other traits should enable improvement of waterlogging tolerance.

LocTree3 prediction of localization.

The prediction of protein sub-cellular localization is an important step toward elucidating protein function. For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria and in three for archaea. The method outputs a score that reflects the reliability of each prediction. LocTree2 has performed on par with or better than any other state-of-the-art method. Here, we report the availability of LocTree3 as a public web server. The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. Assessed on sequence-unique data, LocTree3 reached an 18-state accuracy Q18=80±3% for eukaryotes and a six-state accuracy Q6=89±4% for bacteria. The server accepts submissions ranging from single protein sequences to entire proteomes. Response time of the unloaded server is about 90 s for a 300-residue eukaryotic protein and a few hours for an entire eukaryotic proteome not considering the generation of the alignments. For over 1000 entirely sequenced organisms, the predictions are directly available as downloads. The web server is available at http://www.rostlab.org/services/loctree3.

Partial versus complete submergence: snorkelling aids root aeration in Rumex palustris but not in R. acetosa.

The root and shoot tissues of flood-tolerant wetland plants are highly porous to enable internal gas phase diffusion of O2 during waterlogging or submergence. In the case of only partial submergence (snorkelling), the atmosphere can act as source of O2 . The aim of this study was to assess the effect of waterlogging, partial submergence and complete submergence in the dark as well as in light on O2 partial pressure (pO2 ) in roots of Rumex palustris (flood tolerant) and R. acetosa (flood intolerant). We used O2 microelectrodes to measure pO2 of adventitious roots during manipulations of the water level around the shoot. Root pO2 in both species declined significantly upon submergence but remained oxic also when shoots were completely submerged in the dark (0.8 and 4.6 kPa in R. acetosa and R. palustris, respectively). The snorkelling effect was substantial in R. palustris only. Submergence in light had less impact on root pO2 and the effect of snorkelling was also minor. Hence, the benefits of light (underwater photosynthesis) and air contact (snorkelling) upon growth and survival in submerged wetland plants can now be linked to enhanced internal aeration.