A new major-effect QTL for waterlogging tolerance in wild barley (H. spontaneum)

Genome-wide identification of potassium channels in maize showed evolutionary patterns and variable functional responses to abiotic stresses

Potassium (K) channels are essential components of plant biology, mediating not only K ion (K+) homeostasis but also regulating several physiological processes and stress tolerance. In the current investigation, we identified 27 K+ channels in maize and deciphered the evolution and divergence pattern with four monocots and five dicot species. Chromosomal localization and expansion of K+ channel genes showed uneven distribution and were independent of genome size. The dispersed duplication is the major force in expanding K+ channels in the target genomes. The mean Ka/Ks ratio of <0.5 in paralogs and orthologs indicates horizontal and vertical expansions of K+ channel genes under strong purifying selection. The one-to-one K+ channel orthologs were prominent among the closely related species, with higher synteny between maize and the rest of the monocots. Comprehensive K+ channels promoter analysis revealed various cis-regulatory elements mediating stress tolerance with the predominance of MYB and STRE binding sites. The regulatory network showed AP2-EREBP TFs, miR164 and miR399 are prominent regulatory elements of K+ channels. The qRT-PCR analysis of K+ channels and regulatory miRNAs showed significant expressions in response to drought and waterlogging stresses. The present study expanded the knowledge on K+ channels in maize and will serve as a basis for an in-depth functional analysis.

Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley (Hordeum vulgare L.)

Barley (Hordeum vulgare L.) is used in malt production for brewing applications. Barley malting involves a process of controlled germination that modifies the grain by activating enzymes to solubilize starch and proteins for brewing. Initially, the grain is submerged in water to raise grain moisture, requiring large volumes of water. Achieving grain modification at reduced moisture levels can contribute to the sustainability of malting practices. This study combined proteomics, bioinformatics, and biochemical phenotypic analysis of two malting barley genotypes with observed differences in water uptake and modification efficiency. We sought to reveal the molecular mechanisms at play during controlled germination and explore the roles of protein groups at 24 h intervals across the first 72 h. Overall, 3,485 protein groups were identified with 793 significant differentially abundant (DAP) within and between genotypes, involved in various biological processes, including protein synthesis, carbohydrate metabolism, and hydrolysis. Functional integration into metabolic pathways, such as glycolysis, pyruvate, starch and sucrose metabolism, revealed a metabolic rerouting due to low oxygen enforced by submergence during controlled germination. This SWATH-MS study provides a comprehensive proteome reference, delivering new insights into the molecular mechanisms underlying the impacts of low oxygen during controlled germination. It is concluded that continued efficient modification of malting barley subjected to submergence is largely due to the capacity to reroute energy to maintain vital processes, particularly protein synthesis.

Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response

Waterlogging leads to major crop losses globally, particularly for waterlogging-sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related quantitative trait loci have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called "core hypoxia response genes," thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study "predisposition" to waterlogging tolerance or sensitivity in barley.

Ethylene enhanced waterlogging tolerance by changing root architecture and inducing aerenchyma formation in maize seedlings

Waterlogging negatively affects maize growth and yield. In this study, we found that ethylene played a vital role in plant adaptation to waterlogging. ET promotes better growth in seedlings under waterlogging conditions by altering root architecture and increasing lateral root formation by 42.1%. What's more, plants with high endogenous ethylene levels exhibited reduced sensitivity to waterlogging stress. ET also induced the formation of aerenchyma, a specialized tissue that facilitates gas exchange, in a different pattern compared to aerenchyma formed under waterlogging. Aerenchyma induced by ET was mainly located in the medial cortex of the roots and was not prone to decay. ethylene inhibited root elongation under normal conditions, but this inhibition was not alleviated under waterlogging stress. Upon activation of the ET signaling pathway, the transcription factor EREB90 promoted aerenchyma formation by enhancing the programmed cell death process. Overexpression of EREB90 resulted in increased waterlogging tolerance compared to wild type plants. Our findings suggest that pre-treatment of maize seedlings with ET before waterlogging stress can trigger the programmed cell death process and induce aerenchyma formation, thus improving waterlogging resistance.

Transcriptome analysis of barley (Hordeum vulgare L.) under waterlogging stress, and overexpression of the HvADH4 gene confers waterlogging tolerance in transgenic Arabidopsis

BACKGROUND

Waterlogging is one of the major abiotic stresses in barley and greatly reduces grain yield and quality. To explore the mechanism controlling waterlogging tolerance in barley, physiological, anatomical and transcriptional analyses were performed in two contrasting barley varieties, viz. Franklin (susceptible) and TX9425 (tolerant).

RESULTS

Compared to Franklin, TX9425 had more adventitious roots and aerenchymas and higher antioxidant enzyme activities. A total of 3064 and 5693 differentially expressed genes (DEGs) were identified in TX9425 after 24 h and 72 h of waterlogging treatment, respectively, while 2297 and 8462 DEGs were identified in Franklin. The results suggested that TX9425 was less affected by waterlogging stress after 72 h of treatment. The DEGs were enriched mainly in energy metabolism, hormone regulation, reactive oxygen species (ROS) scavenging, and cell wall-modifying enzymes. Alcohol dehydrogenase (ADH) plays an important role in response to waterlogging stress. We found that HvADH4 was significantly upregulated under waterlogging stress in TX9425. Transgenic Arabidopsis overexpressing HvADH4 displayed higher activity of antioxidant enzymes and was more tolerant to waterlogging than the wild type (WT).

CONCLUSIONS

The current results provide valuable information that will be of great value for the exploration of new candidate genes for molecular breeding of waterlogging tolerance in barley.

Genome-wide association scan and transcriptome analysis reveal candidate genes for waterlogging tolerance in cultivated barley

Waterlogging is the primary abiotic factor that destabilizes the yield and quality of barley (Hordeum vulgare L.). However, the genetic basis of waterlogging tolerance remains poorly understood. In this study, we conducted a genome-wide association study (GWAS) by involving 106,131 single-nucleotide polymorphisms (SNPs) with a waterlogging score (WLS) of 250 barley accessions in two years. Out of 72 SNPs that were found to be associated with WLS, 34 were detected in at least two environments. We further performed the transcriptome analysis in root samples from TX9425 (waterlogging tolerant) and Franklin (waterlogging sensitive), resulting in the identification of 5,693 and 8,462 differentially expressed genes (DEGs) in these genotypes, respectively. The identified DEGs included various transcription factor (TF) genes, primarily including AP2/ERF, bZIP and MYB. By combining GWAS and RNA-seq, we identified 27 candidate genes associated with waterlogging, of which three TFs (HvDnaJ, HvMADS and HvERF1) were detected in multiple treatments. Moreover, by overexpressing barley HvERF1 in Arabidopsis, the transgenic lines were detected with enhanced waterlogging tolerance. Altogether, our results provide new insights into the genetic mechanisms of waterlogging, which have implications in the molecular breeding of waterlogging-tolerant barley varieties.

Multi-omics revolution to promote plant breeding efficiency

Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.

Concurrent waterlogging and anthracnose-twister disease in rainy-season onions (Allium cepa): Impact and management

Waterlogging and anthracnose-twister disease are significant obstacles in rainy-season onion cultivation. As a shallow-rooted crop, onions are highly sensitive to waterlogging. Wherever rainy-season onion cultivation has been undertaken, the anthracnose-twister disease complex is also widespread across the world in addition to waterlogging. Waterlogging is the major predisposing factor for anthracnose and other fungal diseases. However, studies on the combined stress impact on onions have been ignored. In the present review, we have presented an overview of the anthracnose-twister disease, the waterlogging effect on host physiology, host-pathogen interaction under waterlogging stress, and appropriate management strategies to mitigate the combined stress effects. Crucial soil and crop management strategies can help cope with the negative impact of concurrent stresses. Raised bed planting with drip irrigation, the use of plant bio-regulators along with nutrient management, and need-based fungicide sprays would be the most reliable and feasible management options. The most comprehensive solution to withstand combined stress impacts would be a genetic improvement of commercial onion cultivars.

Foliar Application of Spermidine Alleviates Waterlogging-Induced Damages to Maize Seedlings by Enhancing Antioxidative Capacity, Modulating Polyamines and Ethylene Biosynthesis

Waterlogging is a major threat to maize production worldwide. The exogenous application of spermidine is well known to enhance plant tolerance to abiotic stresses. The role of exogenous spermidine application in waterlogging tolerance in maize was investigated in this study. Two maize varieties (a waterlogging-tolerant variety: Xundan 20 (XD20) and a waterlogging-sensitive variety: Denghai 662 (DH662)) were subjected to waterlogging stress at the seedling stage, and then foliar spraying of 0.75 mM spermidine or purified water. Findings demonstrated lower chlorophyll content, reduced growth indices, considerable increase in superoxide anion (O2-) generation rate, and H2O2/malondialdehyde accumulation in the two maize varieties under waterlogging stress compared to the control treatment. However, the tolerance variety performed better than the sensitive one. Foliar application of spermidine significantly increased antioxidant enzyme activities under waterlogging stress. In addition, the application of spermidine increased polyamine levels and led to the reduction of ethylene levels under waterlogging. Consequences of spermidine application were most apparent for the waterlogging-sensitive cultivar DH662 under waterlogging than the waterlogging-tolerant variety XD20.

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.

Expression dynamics of metabolites in diploid and triploid watermelon in response to flooding

Watermelon (Citrullus lanatus) is an economically important cucurbitaceous crop worldwide. The productivity of watermelon is affected by both biotic and abiotic stresses. Flooding has significant impacts on the growth of watermelons by causing oxygen deficiency and a loss of agricultural productivity. Currently, we used the triploid and diploid watermelon Zhengzhou No.3 to study the dynamics of metabolites in response to flooding stress. Quantification of metabolites was performed by UPLC-ESI-MS/MS at different time intervals i.e., 0, 3, 5 and 7 days under flooding stress. We observed that the activities of oxidants were higher in the diploid watermelon, whereas the higher antioxidant activities in the triploid watermelon makes them more resistant to the flooding stress. We also observed that the root activity and the chlorophyll in the triploid watermelon plants were higher as compared to the diploid watermelon plants. Co-expression network analysis leads to the identification of twenty-four hub metabolites that might be the key metabolites linked to flooding tolerance. Resolving the underlying mechanisms for flooding tolerance and identification of key molecules serving as indicators for breeding criteria are necessary for developing flooding-resistant varieties.

Modeling-based age-dependent analysis reveals the net patterns of ethylene-dependent and -independent aerenchyma formation in rice and maize roots

Plants require oxygen for the functioning of roots, and thus the establishment of a long-distance diffusion path from above-water tissues to the submerged roots is essential to survive flooding. Rice (Oryza sativa) constitutively forms aerenchyma (gas spaces) under aerobic conditions, and induces its formation in response to low-oxygen conditions. Constitutive aerenchyma formation in rice roots is regulated by the phytohormone auxin, whereas ethylene stimulates inducible aerenchyma formation. However, the net patterns of the ethylene-dependent and -independent (auxin-dependent) aerenchyma formation remain unclear. In the present study, we used a modeling approach to determine age-dependent aerenchyma formation in the wild-type rice and reduced culm number 1 mutant, in which ethylene production is reduced, to reveal the net patterns of ethylene-dependent and -independent aerenchyma formation. Subsequent comparison of age-dependent aerenchyma formation between rice and maize roots suggested that more rapid induction of ethylene-dependent aerenchyma formation and more aerenchyma in rice roots are essential to achieve efficient oxygen diffusion under low-oxygen conditions. Moreover, rice roots showed rapid increase in the expression levels of ethylene biosynthesis and responsive genes, suggesting that the local ethylene production at an early time point after root-cell emergence contributes to the rapid induction of the ethylene-dependent aerenchyma formation in rice. DATA AVAILABILITY: All data included in this study are available upon request by contact with the corresponding author.

A new major QTL for flag leaf thickness in barley (Hordeum vulgare L.)

BACKGROUND

Carbohydrate accumulation of photosynthetic organs, mainly leaves, are the primary sources of grain yield in cereals. The flag leaf plays a vital role in seed development, which is probably the most neglected morphological characteristic during traditional selection processes.

RESULTS

In this experiment, four flag leaf morphological traits and seven yield-related traits were investigated in a DH population derived from a cross between a wild barley and an Australian malting barley cultivar. Flag leaf thickness (FLT) showed significantly positive correlations with grain size. Four QTL, located on chromosomes 1H, 2H, 3H, and 5H, respectively, were identified for FLT. Among them, a major QTL was located on chromosome 3H with a LOD value of 18.4 and determined 32% of the phenotypic variation. This QTL showed close links but not pleiotropism to the previously reported semi-dwarf gene sdw1 from the cultivated barley. This QTL was not reported before and the thick leaf allele from the wild barley could provide a useful source for improving grain yield through breeding.

CONCLUSIONS

Our results also provided valuable evidence that source traits and sink traits in barley are tightly connected and suggest further improvement of barley yield potential with enhanced and balanced source and sink relationships by exploiting potentialities of the wild barley resources. Moreover, this study will provide a novel sight on understanding the evolution and development of leaf morphology in barley and improving barley production by rewilding for lost superior traits during plant evolution.

Overview of Identified Genomic Regions Associated with Various Agronomic and Physiological Traits in Barley under Abiotic Stresses

Climate change has caused breeders to focus on varieties that are able to grow under unfavorable conditions, such as drought, high and low temperatures, salinity, and other stressors. In recent decades, progress in biotechnology and its related tools has provided opportunities to dissect and decipher the genetic basis of tolerance to various stress conditions. One such approach is the identification of genomic regions that are linked with specific or multiple characteristics. Cereal crops have a key role in supplying the energy required for human and animal populations. However, crop products are dramatically affected by various environmental stresses. Barley (Hordeum vulgare L.) is one of the oldest domesticated crops that is cultivated globally. Research has shown that, compared with other cereals, barley is well adapted to various harsh environmental conditions. There is ample literature regarding these responses to abiotic stressors, as well as the genomic regions associated with the various morpho-physiological and biochemical traits of stress tolerance. This review focuses on (i) identifying the tolerance mechanisms that are important for stable growth and development, and (ii) the applicability of QTL mapping and association analysis in identifying genomic regions linked with stress-tolerance traits, in order to help breeders in marker-assisted selection (MAS) to quickly screen tolerant germplasms in their breeding cycles. Overall, the information presented here will inform and assist future barley breeding programs.

Genome-Wide Association Study Reveals Marker Trait Associations (MTA) for Waterlogging-Triggered Adventitious Roots and Aerenchyma Formation in Barley

Waterlogging is an environmental stress, which severely affects barley growth and development. Limited availability of oxygen in the root zone negatively affects the metabolism of the whole plant. Adventitious roots (AR) and root cortical aerenchyma (RCA) formation are the most important adaptive traits that contribute to a plant's ability to survive in waterlogged soil conditions. This study used a genome-wide association (GWAS) approach using 18,132 single nucleotide polymorphisms (SNPs) in a panel of 697 barley genotypes to reveal marker trait associations (MTA) conferring the above adaptive traits. Experiments were conducted over two consecutive years in tanks filled with soil and then validated in field experiments. GWAS analysis was conducted using general linear models (GLM), mixed linear models (MLM), and fixed and random model circulating probability unification models (FarmCPU model), with the FarmCPU showing to be the best suited model. Six and five significant (approximately -log₁₀ (p) ≥ 5.5) MTA were identified for AR and RCA formation under waterlogged conditions, respectively. The highest -log₁₀ (p) MTA for adventitious root and aerenchyma formation were approximately 9 and 8 on chromosome 2H and 4H, respectively. The combination of different MTA showed to be more effective in forming RCA and producing more AR under waterlogging stress. Genes from major facilitator superfamily (MFS) transporter and leucine-rich repeat (LRR) families for AR formation, and ethylene responsive factor (ERF) family genes and potassium transporter family genes for RCA formation were the potential candidate genes involved under waterlogging conditions. Several genotypes, which performed consistently well under different conditions, can be used in breeding programs to develop waterlogging-tolerant varieties.

Crop traits enabling yield gains under more frequent extreme climatic events

Climate change (CC) in central China will change seasonal patterns of agricultural production through increasingly frequent extreme climatic events (ECEs). Breeding climate-resilient wheat (Triticum aestivum L.) genotypes may mitigate adverse effects of ECEs on crop productivity. To reveal crop traits conducive to long-term yield improvement in the target population of environments, we created 8,192 virtual genotypes with contrasting but realistic ranges of phenology, productivity and waterlogging tolerance. Using these virtual genotypes, we conducted a genotype (G) by environment (E) by management (M) factorial analysis (G×E×M) using locations distributed across the entire cereal cropping zone in mid-China. The G×E×M invoked locally-specific sowing dates under future climates that were premised on shared socioeconomic pathways SSP5-8.5, with a time horizon centred on 2080. Across the simulated adaptation landscape, productivity was primarily driven by yield components and phenology (average grain yield increase of 6-69% across sites with optimal combinations of these traits). When incident solar radiation was not limiting carbon assimilation, ideotypes with higher grain yields were characterised by earlier flowering, higher radiation-use efficiency and larger maximum kernel size. At sites with limited solar radiation, crops required longer growing periods to realise genetic yield potential, although higher radiation-use efficiency and larger maximum kernel size were again prospective traits enabling higher rates of yield gains. By 2080, extreme waterlogging stress in some regions of mid-China will impact substantially on productivity, with yield penalties of up to 1,010 kg ha^-1. Ideotypes with optimal G×M could mitigate yield penalty caused by waterlogging by up to 15% under future climates. These results help distil promising crop trait by best management practice combinations that enable higher yields and robust adaptation to future climates and more frequent extreme climatic events, including flash flooding and soil waterlogging.

Genetic Dissection of Mature Root Characteristics by Genome-Wide Association Studies in Rapeseed (Brassica napus L.)

Roots are complicated quantitative characteristics that play an essential role in absorbing water and nutrients. To uncover the genetic variations for root-related traits in rapeseed, twelve mature root traits of a Brassica napus association panel were investigated in the field within three environments. All traits showed significant phenotypic variation among genotypes, with heritabilities ranging from 55.18% to 79.68%. Genome-wide association studies (GWAS) using 20,131 SNPs discovered 172 marker-trait associations, including 103 significant SNPs (-log10 (p) > 4.30) that explained 5.24-20.31% of the phenotypic variance. With the linkage disequilibrium r² > 0.2, these significant associations were binned into 40 quantitative trait loci (QTL) clusters. Among them, 14 important QTL clusters were discovered in two environments and/or with phenotypic contributions greater than 10%. By analyzing the genomic regions within 100 kb upstream and downstream of the peak SNPs within the 14 loci, 334 annotated genes were found. Among these, 32 genes were potentially associated with root development according to their expression analysis. Furthermore, the protein interaction network using the 334 annotated genes gave nine genes involved in a substantial number of interactions, including a key gene associated with root development, BnaC09g36350D. This research provides the groundwork for deciphering B. napus' genetic variations and improving its root system architecture.

Rewilding crops for climate resilience: economic analysis and de novo domestication strategies

To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by current agronomical and breeding practices, due to the impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze the impact of global climate trends on crop productivity and show that the overall loss in crop production from climate-driven abiotic stresses may exceed US$170 billion year-1 and represents a major threat to global food security. We also show that abiotic stress tolerance had been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness the potential of climate-resilient genes present in wild relatives, the complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development of efficient cell-based high-throughput phenotyping platforms allowing assessment of the in planta operation of key genes.

Genome-Wide Association Study of Waterlogging Tolerance in Barley (Hordeum vulgare L.) Under Controlled Field Conditions

Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8-11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.

Opportunities for Improving Waterlogging Tolerance in Cereal Crops-Physiological Traits and Genetic Mechanisms

Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley.

Experimental comparison of two methods to study barley responses to partial submergence

BACKGROUND

Crop yield is dependent on climate conditions, which are becoming both more variable and extreme in some areas of the world as a consequence of global climate change. Increased precipitation and flooding events are the cause of important yield losses due to waterlogging or (partial) submergence of crops in the field. Our ability to screen efficiently and quickly for varieties that have increased tolerance to waterlogging or (partial) submergence is important. Barley, a staple crop worldwide, is particularly sensitive to waterlogging. Screening for waterlogging tolerant barley varieties has been ongoing for many years, but methods used to screen vary greatly, from the type of soil used to the time at which the treatment is applied. This variation makes it difficult to cross-compare results.

RESULTS

Here, we have devised a scoring system to assess barley tolerance to waterlogging and compare two different methods when partial submergence is applied with either water or a starch solution at an early developmental stage, which is particularly sensitive to waterlogging or partial submergence. The use of a starch solution has been previously shown to result in more reducing soil conditions and has been used to screen for waterlogging tolerance.

CONCLUSIONS

Our results show that the two methods provide similar results to qualitatively rank varieties as tolerant or sensitive, while also affecting plants differently, in that application of a starch solution results in stronger and earlier symptoms than applying partial submergence with water.

QTLs for constitutive aerenchyma from Zea nicaraguensis improve tolerance of maize to root-zone oxygen deficiency

Zea nicaraguensis is a wild relative of Zea mays subsp. mays (maize) that has high waterlogging tolerance. One of its traits is constitutive aerenchyma formation (CAF) in roots and this may be one of the reasons for the tolerance, but it has not yet been proven by comparing plants that differ only in CAF in the same genetic background. We therefore produced an introgression line AE24-50-44-91 (IL-AE91) possessing four quantitative trait loci for CAF from Z. nicaraguensis in the background of maize (inbred line Mi29). The degree of root CAF in IL-AE91 was intermediate between that of Mi29 and Z. nicaraguensis. Seedlings of IL-AE91 grown aerobically were more tolerant to transfer to oxygen-deficient conditions than were Mi29 seedlings. On day 2 of oxygen deficiency, the root extension rate and viability of root-tip cells in IL-AE91 were ~2.7 and ~1.3 times greater, respectively, than they were in Mi29. On day 4, the area of aerenchyma at 80 mm from the root tips was ~1.5 times greater in IL-AE91 and radial oxygen loss from the apical parts of roots was ~3.4 times higher than in Mi29. These results demonstrate that CAF reduces the stress from low external oxygen levels caused by soil waterlogging.

Genomic regions on chromosome 5H containing a novel QTL conferring barley yellow dwarf virus-PAV (BYDV-PAV) tolerance in barley

Barley yellow dwarf virus is a widespread disease affecting plant growth and yield in cereal crops including barley. Complete resistance to BYDV encoded by a single gene is lacking in barley. To identify novel resistance genes that can be further utilised in breeding for plant disease resistance, a doubled haploid population originated from a cultivated barley with a known resistance gene and a wild barley was constructed and assessed for barley yellow dwarf tolerance in three trials with two in Tasmania (TAS) and one in Western Australia (WA). We identified two Quantitative trait loci (QTL) in both Tasmanian trials, and four QTL in Western Australian trial. Two QTL from TAS trials were also detected from WA. The QTL on chromosome 3H corresponds to the known major resistance gene Ryd2. The other QTL, Qbyd-5H, represents a potential new resistance locus and contributed 7.0~10.4% of total phenotypic variation in the three trials. It was mapped within the interval of 125.76~139.24 cM of chromosome 5H. Two additional minor effect QTL were identified on chromosome 7H from WA trial, contributing slightly less effect on BYD tolerance. The consistently detected new gene on chromosome 5H will potentially serve as a novel source of tolerance to achieve more sustainable resistance to BYDV in barley.

AdRAP2.3, a Novel Ethylene Response Factor VII from Actinidia deliciosa, Enhances Waterlogging Resistance in Transgenic Tobacco through Improving Expression Levels of PDC and ADH Genes

APETALA2/ethylene-responsive factor superfamily (AP2/ERF) is a transcription factor involved in abiotic stresses, for instance, cold, drought, and low oxygen. In this study, a novel ethylene-responsive transcription factor named AdRAP2.3 was isolated from Actinidia deliciosa 'Jinkui'. AdRAP2.3 transcription levels in other reproductive organs except for the pistil were higher than those in the vegetative organs (root, stem, and leaf) in kiwi fruit. Plant hormones (Salicylic acid (SA), Methyl-jasmonate acid (MeJA), 1-Aminocyclopropanecarboxylic Acid (ACC), Abscisic acid (ABA)), abiotic stresses (waterlogging, heat, 4 °C and NaCl) and biotic stress (Pseudomonas Syringae pv. Actinidiae, Psa) could induce the expression of AdRAP2.3 gene in kiwi fruit. Overexpression of the AdRAP2.3 gene conferred waterlogging stress tolerance in transgenic tobacco plants. When completely submerged, the survival rate, fresh weight, and dry weight of transgenic tobacco lines were significantly higher than those of wile type (WT). Upon the roots being submerged, transgenic tobacco lines grew aerial roots earlier. Overexpression of AdRAP2.3 in transgenic tobacco improved the pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) enzyme activities, and improved the expression levels of waterlogging mark genes NtPDC, NtADH, NtHB1, NtHB2, NtPCO1, and NtPCO2 in roots under waterlogging treatment. Overall, these results demonstrated that AdRAP2.3 might play an important role in resistance to waterlogging through regulation of PDC and ADH genes in kiwi fruit.

Soil and Crop Management Practices to Minimize the Impact of Waterlogging on Crop Productivity

Waterlogging remains a significant constraint to cereal production across the globe in areas with high rainfall and/or poor drainage. Improving tolerance of plants to waterlogging is the most economical way of tackling the problem. However, under severe waterlogging combined agronomic, engineering and genetic solutions will be more effective. A wide range of agronomic and engineering solutions are currently being used by grain growers to reduce losses from waterlogging. In this scoping study, we reviewed the effects of waterlogging on plant growth, and advantages and disadvantages of various agronomic and engineering solutions which are used to mitigate waterlogging damage. Further research should be focused on: cost/benefit analyses of different drainage strategies; understanding the mechanisms of nutrient loss during waterlogging and quantifying the benefits of nutrient application; increasing soil profile de-watering through soil improvement and agronomic strategies; revealing specificity of the interaction between different management practices and environment as well as among management practices; and more importantly, combined genetic, agronomic and engineering strategies for varying environments.

Identification of QTL Related to ROS Formation under Hypoxia and Their Association with Waterlogging and Salt Tolerance in Barley

Waterlogging is a serious environmental problem that limits agricultural production in low-lying rainfed areas around the world. The major constraint that plants face in a waterlogging situation is the reduced oxygen availability. Accordingly, all previous efforts of plant breeders focused on traits providing adequate supply of oxygen to roots under waterlogging conditions, such as enhanced aerenchyma formation or reduced radial oxygen loss. However, reduced oxygen concentration in waterlogged soils also leads to oxygen deficiency in plant tissues, resulting in an excessive accumulation of reactive oxygen species (ROS) in plants. To the best of our knowledge, this trait has never been targeted in breeding programs and thus represents an untapped resource for improving plant performance in waterlogged soils. To identify the quantitative trait loci (QTL) for ROS tolerance in barley, 187 double haploid (DH) lines from a cross between TX9425 and Naso Nijo were screened for superoxide anion (O₂•-) and hydrogen peroxide (H₂O₂)-two major ROS species accumulated under hypoxia stress. We show that quantifying ROS content after 48 h hypoxia could be a fast and reliable approach for the selection of waterlogging tolerant barley genotypes. The same QTL on chromosome 2H was identified for both O₂•- (QSO.TxNn.2H) and H₂O₂ (QHP.TxNn.2H) contents. This QTL was located at the same position as the QTL for the overall waterlogging and salt tolerance reported in previous studies, explaining 23% and 24% of the phenotypic variation for O₂•- and H₂O2 contents, respectively. The analysis showed a causal association between ROS production and both waterlogging and salt stress tolerance. Waterlogging and salinity are two major abiotic factors affecting crop production around the globe and frequently occur together. The markers associated with this QTL could potentially be used in future breeding programs to improve waterlogging and salinity tolerance.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r ² = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r ² = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.

Improving Flooding Tolerance of Crop Plants

A major problem of climate change is the increasing duration and frequency of heavy rainfall events. This leads to soil flooding that negatively affects plant growth, eventually leading to death of plants if the flooding persists for several days. Most crop plants are very sensitive to flooding, and dramatic yield losses occur due to flooding each year. This review summarizes recent progress and approaches to enhance crop resistance to flooding. Most experiments have been done on maize, barley, and soybean. Work on other crops such as wheat and rape has only started. The most promising traits that might enhance crop flooding tolerance are anatomical adaptations such as aerenchyma formation, the formation of a barrier against radial oxygen loss, and the growth of adventitious roots. Metabolic adaptations might be able to improve waterlogging tolerance as well, but more studies are needed in this direction. Reasonable approaches for future studies are quantitative trait locus (QTL) analyses or genome-wide association (GWA) studies in combination with specific tolerance traits that can be easily assessed. The usage of flooding-tolerant relatives or ancestral cultivars of the crop of interest in these experiments might enhance the chances of finding useful tolerance traits to be used in breeding.

Waterlogging affects plant morphology and the expression of key genes in tef (Eragrostis tef)

Tef [Eragrostis tef (Zucc.) Trotter], an allotetraploid cereal that is a staple food to over 60 million people in the Horn of Africa, has a high nutritional content and is resistant to many biotic and abiotic stresses such as waterlogging and drought. Three tef genotypes, Alba, Tsedey, and Quncho, were subjected to waterlogging conditions and their growth, physiology, and change in transcript expression were measured with the goal of identifying targets for breeding cultivars with improved waterlogging tolerance. Root and shoot growth and dry weight were observed over 22 days. Stomatal conductance and chlorophyll and carotenoid contents were quantified. Microscopy was used to monitor changes in the stem cross sections. Illumina RNA sequencing was used to obtain the expression profiles of tef under flooding and control conditions and was verified using qPCR. Results indicated differences in growth between the three genotypes. Waterlogged Tsedey plants grew higher and had more root biomass than normally watered Tsedey plants. Quncho and Alba genotypes were more susceptible to the excess moisture stress. The effects of these changes were observed on the plant physiology. Among the three tested tef genotypes, Tsedey formed more aerenchyma than Alba and had accelerated growth under waterlogging. Tsedey and Quncho had constitutive aerenchyma. Genes affecting carbohydrate metabolism, cell growth, response to reactive oxygen species, transport, signaling, and stress responses were found to change under excess moisture stress. In general, these results show the presence of substantial anatomical and physiological differences among tef genotypes when waterlogged during the early growth stage.

Dynamic and epistatic QTL mapping reveals the complex genetic architecture of waterlogging tolerance in chrysanthemum

37 unconditional QTLs, 51 conditional QTLs and considerable epistatic QTLs were detected for waterlogging tolerance, and six favourable combinations were selected accelerating the possible application of MAS in chrysanthemum breeding. Chrysanthemum is seriously impacted by soil waterlogging. To determine the genetic characteristics of waterlogging tolerance (WAT) in chrysanthemum, a population of 162 F₁ lines was used to construct a genetic map to identify the dynamic and epistatic quantitative trait loci (QTLs) for four WAT traits: wilting index (WI), dead leaf ratio (DLR), chlorosis score (Score) and membership function value of waterlogging (MFVW). The h _B² for the WAT traits ranged from 0.49 to 0.64, and transgressive segregation was observed in both directions. A total of 37 unconditional consensus QTLs with 5.81-18.21% phenotypic variation explanation (PVE) and 51 conditional consensus QTLs with 5.90-24.56% PVE were detected. Interestingly, three unconditional consensus QTLs were consistently identified across different stages, whereas no conditional consensus QTLs were consistently expressed. In addition, considerable epistatic QTLs, all with PVE values ranging from 0.01 to 8.87%, were detected by a joint analysis of WAT phenotypes. These results illustrated that the QTLs (genes) controlling WAT were environmentally dependent and selectively expressed at different times and indicated that both additive and epistatic effects underlie the inheritance of WAT in chrysanthemum. The findings of the current study provide insights into the complex genetic architecture of WAT, and the identification of favourable alleles represents an important step towards the application of molecular marker-assisted selection (MAS) and QTL pyramiding in chrysanthemum WAT breeding programmes.