Flooding Tolerance Research Articles

Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice

BackgroundDue to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice.ResultsIn the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation.ConclusionThis study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.

Genetic Diversity of Rice Genotypes Screened under Normal and Flash Flooded Condition

The present investigation was undertaken to explore the extent of diversity in 30 rice genotypes under normal (E1) and flash flooded conditions (E2) during samba, 2020. Analysis of variance divulged significant variability with respect to all the nine traits viz., days to 50% flowering, plant height, number of productive tillers per plant, panicle length, number of grains per panicle, 1000 grain weight, grain length, grain breadth and grain yield per plant under study. Mahalanobis D2 values and non- hierarchical Euclidean cluster analysis categorized into seven clusters in E1 and three clusters in E2. The maximum intra cluster D2 was obtained in cluster V (80.618) in E1 and III (1626.542) in E2 and farthest inter cluster distance between III and cluster VI (129.797) in E1, cluster II and III (2743.060) in E2. The clusters VI and II exerted superior mean performance in E1 and cluster III and II had in E2. The characters viz., number of grains per panicles, panicle length, number of productive tillers per plant, grain breadth along with grain yield per plant were the major contributors for genetic divergence in E1. In the flash flood tolerance environment E2, the traits of plant height, grain breadth, and grain yield per plant contributed more toward the genetic divergence. Based on genetic diversity and performance of the genotypes Poongar, seeraga samba, CR 1009 sub1 and Swarna sub 1 are the superior parents for flash flood tolerance. Hence, these genotypes could be lucidly utilized for the flash flood genetic improvement program.

Salt Water Exposure Exacerbates the Negative Response of Phragmites australis Haplotypes to Sea-Level Rise.

The response of coastal wetlands to sea-level rise (SLR) largely depends on the tolerance of individual plant species to inundation stress and, in brackish and freshwater wetlands, exposure to higher salinities. Phragmites australis is a cosmopolitan wetland reed that grows in saline to freshwater marshes. P. australis has many genetically distinct haplotypes, some of which are invasive and the focus of considerable research and management. However, the relative response of P. australis haplotypes to SLR is not well known, despite the importance of predicting future distribution changes and understanding its role in marsh response and resilience to SLR. Here, we use a marsh organ experiment to test how factors associated with sea level rise-inundation and seawater exposure-affect the porewater chemistry and growth response of three P. australis haplotypes along the northern Gulf of Mexico coast. We planted three P. australis lineages (Delta, European, and Gulf) into marsh organs at five different elevations in channels at two locations, representing a low (Mississippi River Birdsfoot delta; 0-13 ppt) and high exposure to salinity (Mermentau basin; 6-18 ppt) for two growing seasons. Haplotypes responded differently to flooding and site conditions; the Delta haplotype was more resilient to high salinity, while the Gulf type was less susceptible to flood stress in the freshwater site. Survivorship across haplotypes after two growing seasons was 42% lower at the brackish site than at the freshwater site, associated with high salinity and sulfide concentrations. Flooding greater than 19% of the time led to lower survival across both sites linked to high concentrations of acetic acid in the porewater. Increased flood duration was negatively correlated with live aboveground biomass in the high-salinity site (χ2 = 10.37, p = 0.001), while no such relationship was detected in the low-salinity site, indicating that flood tolerance is greater under freshwater conditions. These results show that the vulnerability of all haplotypes of P. australis to rising sea levels depends on exposure to saline water and that a combination of flooding and salinity may help control invasive haplotypes.

Phytohormone and energy metabolism of rice germination and coleoptile growth during submergence by RNA-seq and LC-MS/MS analysis

Rice is one of the main food crops to guarantee the world's food security. Although rice is a semi-aquatic crop, long-term flooding stress can also inhibit growth and reduce yield and quality. Especially during the germination period, the germination rate of rice was inhibited by flooding stress, which resulted in the low emergence rate. Therefore, in this study, rice lines or cultivars with flood tolerance (C11) and flood sensitivity (KY60) were screened, and analyzed the response mechanisms during seed germination at different time points of waterlogging stress through transcriptome and metabolome sequencing. Compared with C11, waterlogging stress significantly inhibited the germination and coleoptile growth of KY60. Certain pathways, including plant hormones, energy metabolism, and carbohydrate metabolism, were identified as significantly involved in the flooding stress response in rice. The plant hormone-related DEGs (IAA, SAUR, ARF, LOX) and metabolites (IAA, JA, GA, and SA) were identified to up-regulate gene expression levels and significantly up-accumulate phytohormone content in C11 to resist waterlogging stress. However, the ABA signaling pathway-related genes (ZHD, PLY) and ABA content were decreased in C11 under submerged conditions. It is beneficial for C11 to promote seed germination and coleoptile elongation under flooding conditions. A total of 150 DEGs (AMY, PGLR) and 58 related compounds were identified as involved in the energy metabolism and carbohydrate metabolism of rice after flooding stress. Candidate key genes and metabolite compounds were identified by combined RNA-Seq and LC-MS/MS correlation network analysis. This study provided insights to explore the flood-tolerance mechanism of rice and laid the foundation for the cultivation of new varieties of flood-tolerance rice.

Effects of Flooding and Shade on Survival, Growth, and Leaf Gas Exchange of Bottomland Tree Species across the Great Lakes Region (USA)

Forested wetlands are common ecosystems within the Great Lakes region (Michigan, Minnesota, and Wisconsin), USA. Projected increases in extreme flooding events and shifting disturbance regimes create challenges for tree regeneration. Forest managers are considering the use of enrichment planting to increase tree species diversity, but limited information is available that quantifies the interactions between the flooding and shade tolerances of candidate tree species. We used a microcosm experiment to manipulate shade and flooding conditions to determine the effects on early survival, growth, and leaf gas exchange of 23 different tree species that vary in shade and flood tolerance. Seedlings were planted in pots and placed in 227 L tanks that were randomly assigned to light reduction (full sun, 40% and 70% reduced sunlight) and flood treatments (water levels of 0, 14, or 27 cm below the soil surface). In general, flooding treatments had a greater influence on seedling growth and leaf gas exchange rates than light reduction treatments. Of the species studied, bald cypress (Taxodium distichum (L.) Rich.) was the most flood-tolerant, but American sycamore (Platanus occidentalis L.) and river birch (Betula nigra L.) were also highly tolerant of flooding conditions throughout the entire growing season. The flood tolerances of the remaining species varied, but none were tolerant of water table depths within 14 cm of the soil surface for the entire growing season. Most species did not respond to the shade treatments in terms of early growth, survival, and leaf gas exchange. When considering species for planting in forested wetlands, matching the flood tolerance of candidate species to local site hydrology is an important step.

The evaluation of wetland reconstruction with nature-based solutions for eco-economic sustainable development

Nature-based solutions (NBS) are effective approaches for solving ecological and economic problems related to wetland reconstruction, while emergy and exergy are well suited for evaluating reconstructed eco-economic systems. In this paper, we executed a wetland reconstruction project involving a mulberry-fir woodland and dike-pond complex (MFWDPC) with NBS in the water-level fluctuation zone of the Three Gorges Reservoir (TGR), China. We evaluated the coupling mode of this eco-economic system by using emergy and exergy theories. After wetland reconstruction, the emergy density that entered the MFWDPC was 1.48E + 18 sej yr−1 hm−2, in which the naturally renewable flow accounted for 96.31 % of the emergy inflows, and the emergy sustainability index (ESI) for the eco-economic system was 708.88. The exergy and specific exergy were 2.41E + 14 j yr−1 and 2.08E + 08 j yr−1 kg−1, respectively, and the emergy/exergy ratio was 1.55E + 03 for the MFWDPC. In addition, mulberry trees with strong flooding tolerance provided good economic benefits due to the use of these plants in reconstructed eco-economic systems. Our study of NBS for wetland reconstruction helps in understanding the synergistic symbiosis between ecosystems and economic systems, thereby promoting the reconstruction of degraded wetlands in China and other regions.

Registration of USDA‐N6006 soybean germplasm combining high yield, flood tolerance, and elevated oil content

AbstractUSDA‐N6006 soybean [Glycine max (L.) Merr.] (Reg. no. GP‐527, PI 704140) is a conventional F4–derived early maturity group (MG) VI germplasm jointly released by USDA‐ARS and North Carolina Agricultural Research Service in 2023. USDA‐N6006 is the first MG VI, publicly released germplasm that combines flood tolerance with high‐yield lodging resistance, and elevated seed oil. Over 19 environments of the MG VI USDA Southern Uniform Soybean Trials (2017–2018), seed yield of USDA‐N6006 (3393 kg ha−1) was similar to high‐yielding lodging‐resistant check cultivars ‘NC‐Dunphy’ (3427 kg ha−1) and ‘NC‐Dilday’ (3475 kg ha−1). It matured 1 day earlier than NC‐Dunphy and exhibited similar lodging scores. Over 5 years of testing in North Carolina (2016–2019), USDA‐N6006 exhibited very robust flood tolerance. Mean flooding scores were numerically or statistically (p < 0.05) superior to the four flood‐tolerant controls at both V4 and R1 growth stages. USDA‐N6006 was not intentionally bred to be flood tolerant and identified as such only through an extensive screening of “in house” USDA breeding lines. USDA‐N6006 and most of its antecedents are unique in that they are derived from unreleased breeding lines developed at the flood prone Tidewater Research station in North Carolina. Inadvertent selection for flood tolerance may have been a part of the USDA's long‐term breeding effort to improve yield. Seed oil content of USDA‐N6006 (237 g kg−1) was similar to that of elevated seed oil cultivar NC‐Dilday, but significantly higher than NC‐Dunphy (228 g kg−1) in the Uniform Trials. Seed protein content and estimated meal protein contents of USDA‐N6006 (389 g kg−1 and 46.4%, respectively) were similar to that of NC‐Dunphy. USDA‐N6006 should be excellent parental stock for applied breeding in the southern United States.

Millmeter-wave irradiation regulates mRNA-expression and the ubiquitin-proteasome system in wheat exposed to flooding stress

The irradiation with millimeter-wave (MMW) of wheat seeds promotes root growth under flooding stress; however, its role is not completely clarified. Nuclear proteomics was performed, to reveal the role of MMW irradiation in enhancing flooding tolerance. The purity of nuclear fractions purified from roots was verified. Histone, which is a protein marker for nuclear-purification efficiency, was enriched; and cytosolic ascorbate peroxidase was reduced in the nuclear fraction. The principal-component analysis of proteome displayed that the irradiation of seeds affected nuclear proteins in roots grown under flooding stress. Proteins detected using proteomic analysis were verified using immunoblot analysis. Histone H3 accumulated under flooding stress; however, it decreased to the control level by irradiation. Whereas the ubiquitin accumulated in roots grown under stress when seeds were irradiated. These results suggest that MMW irradiation improves wheat-root growth under flooding stress through the regulation of mRNA-expression level and the ubiquitin-proteasome system. SignificanceTo reveal the role of millimeter-wave irradiation in enhancing flooding tolerance in wheat, nuclear proteomics was performed. The principal-component analysis of proteome displayed that irradiation of seeds affected nuclear proteins in roots grown under flooding stress. Proteins detected using proteomic analysis were verified using immunoblot analysis. Histone H3 accumulated under flooding stress; however, it decreased to the control level with irradiation. Whereas the ubiquitin accumulated in roots grown under stress when seeds were irradiated. These results suggest that millimeter-wave irradiation improves wheat-root growth under flooding stress through the regulation of mRNA-expression level and the ubiquitin-proteasome system.

Registration of R16‐45 as a flood‐tolerant, high‐yielding soybean germplasm line

AbstractR16‐45 (Reg. no. GP‐526, PI 704118) is a high‐yielding soybean [Glycine max (L.) Merr.] breeding line with flood tolerance at early reproductive stages released as germplasm by the Arkansas Agricultural Experiment Station in 2023. It is an F2 selection from the cross between the flood‐tolerant breeding line R07‐6669 and the high‐yielding Arkansas cultivar ‘UA 5612’. R16‐45 is a conventional (non‐genetically modified) soybean with a relative maturity of 5.6. Plants have determinate growth habit, white flower color, and buff hilum color. It has gray pubescence, tan pod wall at maturity, and yellow cotyledons with a dull yellow seed coat. R16‐45 showed high yield potential and broad adaptability across 17 environments in Arkansas and other southern states, with an average of 4145 kg ha−1 (95.3% of the checks’ mean). Six years of field evaluations for flooding tolerance showed that R16‐45 is consistently tolerant to 8‐to‐10‐day flooding stress at the R1/R2 growth stages (average flood damage score of 3.6, compared with 6.0 from the reference checks). In addition, R16‐45 is resistant to stem canker. Given substantial yield losses associated with flooding stress and stem canker, R16‐45 is a valuable germplasm source for public and private soybean breeding programs attempting to incorporate novel genetic diversity into their breeding pipeline.

Biochemical Analysis to Understand the Flooding Tolerance of Mutant Soybean Irradiated with Gamma Rays.

Flooding stress, which reduces plant growth and seed yield, is a serious problem for soybean. To improve the productivity of flooded soybean, flooding-tolerant soybean was produced by gamma-ray irradiation. Three-day-old wild-type and mutant-line plants were flooded for 2 days. Protein, RNA, and genomic DNA were then analyzed based on oppositely changed proteins between the wild type and the mutant line under flooding stress. They were associated with cell organization, RNA metabolism, and protein degradation according to proteomic analysis. Immunoblot analysis confirmed that the accumulation of beta-tubulin/beta-actin increased in the wild type under flooding stress and recovered to the control level in the mutant line; however, alpha-tubulin increased in both the wild type and the mutant line under stress. Ubiquitin was accumulated and genomic DNA was degraded by flooding stress in the wild type; however, they were almost the same as control levels in the mutant line. On the other hand, the gene expression level of RNase H and 60S ribosomal protein did not change in either the wild type or the mutant line under flooding stress. Furthermore, chlorophyll a/b decreased and increased in the wild type and the mutant line, respectively, under flooding stress. These results suggest that the regulation of cell organization and protein degradation might be an important factor in the acquisition of flooding tolerance in soybean.

Responses of the maize rhizosphere soil environment to drought-flood abrupt alternation stress.

Changes in the soil environment in the root zone will affect the growth, development and resistance of plants. The mechanism underlying the effect of drought and flood stress on rhizosphere bacterial diversity, soil metabolites and soil enzyme activity is not clear and needs further study. To analyze the dynamic changes in bacteria, metabolites and enzyme activities in the rhizosphere soil of maize under different drought-flood abrupt alternation (DFAA) stresses, the barrel test method was used to set up the 'sporadic light rain' to flooding (referring to trace rainfall to heavy rain) (DFAA1) group, 'continuous drought' to flooding (DFAA2) group and normal irrigation (CK) group from the jointing to the tassel flowering stage of maize. The results showed that Actinobacteria was the most dominant phylum in the two DFAA groups during the drought period and the rewatering period, and Proteobacteria was the most dominant phylum during the flooding period and the harvest period. The alpha diversity index of rhizosphere bacteria in the DFAA2 group during the flooding period was significantly lower than that in other stages, and the relative abundance of Chloroflexi was higher. The correlation analysis between the differential genera and soil metabolites of the two DFAA groups showed that the relative abundance of Paenibacillus in the DFAA1 group was higher during the drought period, and it was significantly positively correlated with the bioactive lipid metabolites. The differential SJA-15 bacterium was enriched in the DFAA2 group during the flooding period and were strongly correlated with biogenic amine metabolites. The relative abundances of Arthrobacter, Alphaproteobacteria and Brevibacillus in the DFAA2 group were higher compared with DFAA1 group from rewatering to harvest and were significantly positively correlated with hydrocarbon compounds and steroid hormone metabolites. The acid phosphatase activity of the DFAA1 group was significantly higher than that of the DFAA2 group during the flooding period. The study suggests that there is a yield compensation phenomenon in the conversion of 'continuous drought' to flooding compared with 'sporadic light rain', which is related to the improvement in the flooding tolerance of maize by the dominant bacteria Chloroflexi, bacterium SJA-15 and biogenic amine metabolites. These rhizosphere bacteria and soil metabolites may have the potential function of helping plants adapt to the DFAA environment. The study revealed the response of the maize rhizosphere soil environment to DFAA stress and provided new ideas for exploring the potential mechanism of crop yield compensation under DFAA.

Comparative flooding tolerance of Typha latifolia and Phalaris arundinacea in wetland restoration: Insights from photosynthetic CO2 response curves, photobiology and biomass allocation

Tall helophytes such as Typha latifolia and Phalaris arundinacea often rapidly colonise after rewetting of former agricultural soil and are therefore often the first plants to contribute to the soil carbon pool. In this study we carried out a mesocosm experiment where these two species grew at three different water levels relative to the soil surface (−15 cm, 0 cm, +15 cm). After eight weeks' growth, measurements of photosynthetic CO2-response curves, stomatal conductance and chlorophyll fluorescence of photosystem II were carried out to detect flooding stress. After 10 weeks’ growth, the plants were harvested and biomass production, biomass allocation and specific leaf area were determined. T. latifolia had a higher and more stable photosynthetic performance across all water level treatments, which resulted in an overall higher aboveground and belowground production than P. arundinacea. In contrast, Vcmax and Jmax decreased by 41 % and 42 %, respectively from drained to flooded conditions with signs of flooding stress as impairment of the photosynthetic apparatus. Moreover, increasing water level resulted in maintenance of aboveground organs for P. arundinacea but a decrease in allocation to belowground organs. P. arundinacea did not invest in a higher specific leaf area to counter the decreased photosynthesis under flooding. From −15 cm to 0 cm water levels, P. arundinacea showed a 68 % reduction in belowground biomass, which has negative implication for carbon retention immediately after rewetting. In contrast, recolonization of T. latifolia is likely to be a suitable contributor to the soil carbon pool due to its stable physiology and high above- and belowground biomass production at all water depths, and also likely under natural water level fluctuations. We showed that even though both species are generally considered wetland plants, they are likely to support considerably different photosynthetic carbon assimilation and soil carbon sequestration rates.

Recent progress in understanding the cellular and genetic basis of plant responses to low oxygen holds promise for developing flood-resilient crops.

With recent progress in active research on flooding and hypoxia/anoxia tolerance in native and agricultural crop plants, vast knowledge has been gained on both individual tolerance mechanisms and the general mechanisms of flooding tolerance in plants. Research on carbohydrate consumption, ethanolic and lactic acid fermentation, and their regulation under stress conditions has been accompanied by investigations on aerenchyma development and the emergence of the radial oxygen loss barrier in some plant species under flooded conditions. The discovery of the oxygen-sensing mechanism in plants and unravelling the intricacies of this mechanism have boosted this very international research effort. Recent studies have highlighted the importance of oxygen availability as a signalling component during plant development. The latest developments in determining actual oxygen concentrations using minute probes and molecular sensors in tissues and even within cells have provided new insights into the intracellular effects of flooding. The information amassed during recent years has been used in the breeding of new flood-tolerant crop cultivars. With the wealth of metabolic, anatomical, and genetic information, novel holistic approaches can be used to enhance crop species and their productivity under increasing stress conditions due to climate change and the subsequent changes in the environment.

Group VII ethylene response factors forming distinct regulatory loops mediate submergence responses.

Group VII ethylene response factors (ERFVIIs), whose stability is oxygen concentration-dependent, play key roles in regulating hypoxia response genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) during submergence. To understand the evolution of flooding tolerance in cereal crops, we evaluated whether Brachypodium distachyon ERFVII genes (BdERFVIIs) are related to submergence tolerance. We found that three BdERFVIIs, BdERF108, BdERF018, and BdERF961, form a feedback regulatory loop to mediate downstream responses. BdERF108 and BdERF018 activated the expression of BdERF961 and PHYTOGLOBIN 1 (PGB1), which promoted nitric oxide turnover and preserved ERFVII protein stability. The activation of PGB1 was subsequently counteracted by increased BdERF961 accumulation through negative feedback regulation. Interestingly, we found that OsERF67, the orthologue of BdERF961 in rice, activated PHYTOGLOBIN (OsHB2) expression and formed distinct regulatory loops during submergence. Overall, the divergent regulatory mechanisms exhibited by orthologs collectively offer perspectives for the development of submergence-tolerant crops.

Field practice of Scirpus mariqueter restoration in the bird habitats of Chongming Dongtan Wetland, China

The coastal saltmarshes in China have been seriously degraded and artificial restoration strategies have become one of the primary measures to protect the coastal habitats. In this study, we investigated efficient restoration techniques for native saltmarsh plants in vacant habitats within the project area of the Ecological Control of Spartina alterniflora and Improvement of Birds Habitats in the Shanghai Chongming Dongtan Bird National Nature Reserve in the Yangtze Estuary. Through field and pilot experiments, we analyzed the effects of propagule types and transplanting methods on the restoration efficiency of Scirpus mariqueter, a dominant saltmarsh species in the Yangtze Estuary. We further evaluated the cost and efficiency of various restoration strategies. Our results indicated that: 1) The corm seedlings of S. mariqueter had higher flood tolerance, and were suitable for use in the habitats with higher environmental heterogeneity. 2) Across the four treatments for S. mariqueter restoration, the most economically efficient treatment was to transplant low-density corm seedlings without sediment, with an investment cost of approximately ￥10100 per hectare. The costs were ￥41100, ￥30000, and ￥120100 per hectare for high-density without sediment, low-density with sediment, and high-density with sediment restoration, respectively. 3) After nearly 5-yr efforts, the S. mariqueter community of Plot C3 in project area had achieved a coverage of over 60%, marking a relatively successful large-scale field restoration. This study could provide the foundation and support for large-scale coastal saltmarsh restoration projects.

Integrating Non-photochemical Quenching (NPQ) Measurements for Identifying Flood-Tolerant Soybean Genotypes in the Era of Climate Change

Climate change has negatively affected agriculture worldwide, including soybean production. Studies have shown that rising temperatures and extreme weather events like droughts and floods significantly reduce soybean yields. Developing flood-tolerant soybean genotypes is crucial for ensuring food security. Conventional breeding programs are limited by laborious and imprecise visual rating methods for flooding tolerance identification. High-throughput platforms for plant phenotyping using imaging techniques offer potential solutions, but they lack information on underlying physiological mechanisms. Non-photochemical quenching (NPQ) is a molecular adaptation in photosynthesis that dissipates excess light energy, protecting plants from damage. This study aimed to integrate NPQ measurements into high-throughput phenotyping procedures to identify flooding-tolerant soybean genotypes. The study evaluated 160 soybean genotypes for flooding tolerance, identifying those with higher grain yield potential. Subsequently, ten genotypes were selected for monitoring NPQ responses under flooded conditions. Results showed that genotypes with higher grain yields also exhibited superior NPQ performance, suggesting a positive correlation between flooding tolerance and energy dissipation capacity. Among these genotypes, 58I60 RSF IPRO, 64HO130 I2X and BRS 525 displayed superior potential and could be further exploited in breeding efforts, considering their grain yield capacity, plant leaf area, and photoprotective capacity under flooding conditions. These findings suggest that integrating NPQ measurements into high-throughput phenotyping platforms can aid in identifying flood-tolerant soybean genotypes for breeding programs, leading to more resilient crops in the face of climate change. Further field studies are warranted to validate these hypotheses and improve crop models for future climate scenarios.

Comparative Transcriptome Analysis Reveals the Molecular Mechanism of Salt Combined with Flooding Tolerance in Hybrid Willow (Salix matsudana × alba)

Plants in coastal areas often face the combined stress of salt and flooding, which can cause severe damage. The impact of multiple stresses on plant growth and survival is greater than that of individual stresses. However, the molecular responses of hybrid willow (Salix matsudana × alba) to the combination of salt and flooding have not been well understood. In this study, we conducted a comparative transcriptome analysis to investigate the molecular mechanism underlying the tolerance of hybrid willow to salt-flooding. Seedings were, respectively, treated with 200 mM NaCl and flooded with water or 200 mM NaCl solution for 3 d, 10 d, and 17 d. We identified 1842, 3350, and 2259 differentially expressed genes (DEGs) regulated by hybrid willow under single salt stress, single flooding stress, and combined salt and flooding stress, respectively. Many DEGs detected in single salt- and flooding-treated plants were expressed differentially after the combined salt and flooding. Most of the shared transcripts exhibited similar fold changes in common molecular responses such as detoxification of reactive oxygen species (ROS) and signaling pathways related to calcium, phytohormones, and protein kinases, which were also observed in plants exposed to each stress individually. Additionally, a large number of specific DEGs were identified under salt-flooding stress, primarily associated with cell wall remodeling, osmotic adjustments, stress signaling, primary metabolism, and ROS scavenging. KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation indicated that hybrid willow leaves responded to salt-flooding stress mainly through phytohormone signaling and MAPK signaling pathways. Overall, this study provides new insights into the molecular mechanisms underlying the response of Salix species to multiple stresses and identifies potential candidate genes for enhancing the performance of hybrid willows.

Variability to flooding tolerance in barnyardgrass and early flooding benefits on weed management and rice grain yield

Barnyardgrass (Echinochloa crus-galli (L.) Beauv.) is one of the most problematic weed species in paddy fields. The recent large-scale evolution of herbicide resistance in this species requires the adoption of integrated methods of weed control. The present study aimed to determine the interaction of water depth, flooding irrigation onset, and pre-emergent herbicides on the control of barnyardgrass populations and to identify the variability and the putative genes involved in the regulation of flooding tolerance in this species. We identified tolerant, moderately tolerant, and flood-sensitive barnyardgrass populations through water depth-response experiments in a greenhouse. The relative expression of genes related to flooding tolerance were evaluated to confirm the flooding tolerance variability. A field experiment was conducted during the summer seasons of 2020/21 and 2021/22 to assess the interaction of the flooding onset, water depth, and pre-emergent herbicides on populations with different flood tolerances and herbicide resistance mechanisms. Water depths of 7.5 cm and 12.5 cm and plant height were selected for the diagnosis of flood tolerance. After 28 days under flooding, the 7.5 cm depth reduced plant height by an average of 26.82%. Of the 45 populations evaluated, 43 overcame the water depth of 7.5 cm, and four surpassed 12.5 cm. The relative expression of alcohol dehydrogenase 1 (ADH1), alcohol dehydrogenase 2 (ADH2), pyruvate decarboxylase (PDC1), aldehyde dehydrogenase (ALDH), and sucrose synthase 3 (SUS3) was between eight and sixteen times higher for the flood-tolerant population than for the sensitive one. In the field study, the anticipation of flooding to the two-leaves (V2) stage of rice resulted in an increase of up to 55.6% in the control of all populations evaluated compared with conventional irrigation at the four-leaves (V4) stage, including those resistant to herbicides. The grain yield was increased by approximately 11.4% with flooding onset in the V2 stage compared to the V4 stage. Barnyardgrass control and rice grain yield were not affected by water depths of 5 cm or 15 cm. The early flooding, in the V2 stage, increased rice grain yield and favored barnyardgrass control. However, variability in flood tolerance was identified in barnyardgrass populations, which may jeopardize the effect of early flooding for weed control in rice crops. The results we obtained add information on the basic knowledge of flooding tolerance in barnyardgrass and to the integrated weed management for dry direct-seeded rice.

Development and Characterization of Rice Lines Carrying both Sub1 and Anaerobic Germination Tolerance: SUB1A does not Inhibit AG [RESEARCH NOTE

Accelerated coleoptile elongation in flooded soils allowed seedling shoots to reach the water surface to maintain gas exchange and CO2 fixation. Rice genotypes with tolerance of flooding during germination (anaerobic germination, AG) exhibited fast coleoptile elongation as an escape mechanism. On the other hand, tolerance of complete submergence during the vegetative stage, conferred by SUB1A, involved growth retardation to conserve energy for maintenance metabolism, with resumption of growth upon de-submergence. Combining genes controlling flood tolerance at these two stages with contrasting mechanisms was necessary in flood-prone areas for protection during germination under direct seeding and during vegetative stage. Breeding lines combining AG + Sub1 were used to determine the timing of the expression of SUB1A and elucidate its impact when combined with tolerance of flooding during seed germination and to evaluate seedling performance under complete submergence. Time-points for SUB1A expression in IR64-Sub1 and AG + Sub1 lines germinated under hypoxia or submerged for 30 h at vegetative stage showed that during flooding treatment, SUB1A and SUB1C expression was inhibited in young seedlings (< 6 d old) in IR64-Sub1 and at 2 and 4 d of seedling growth under hypoxia in AG + Sub1 materials. SUB1A was weakly expressed in AG + Sub1 starting at seedling age of 6 d following 1 d of complete submergence, indicating that expression of SUB1A may be stage-specific. Physiological tests showed higher percentage of survival of AG + Sub1 lines under hypoxia, comparable to that of AG tolerant check and significantly different from intolerant check IR42, indicating that the presence of SUB1A does not affect tolerance of flooding during germination. When seedlings were completely submerged, Sub1 expression was not inhibited by the presence of AG and tolerant genotypes showed suppressed elongation that was significantly different from intolerant check IR42. Despite their contrasting mechanisms of tolerance, combining AG with Sub1 provides multiple flooding tolerance from early crop establishment using direct seeding through to the vegetative stages.

Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice.

Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.