Genome-wide association mapping combined with reverse genetics identifies new effectors of low water potential-induced proline accumulation in Arabidopsis

Deciphering the genetic landscape of seedling drought stress tolerance in wheat (Triticum aestivum L.) through genome-wide association studies

Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic basis of stress tolerance is important to develop drought resilient, high-yielding wheat cultivars. In this study, we investigated the effects of drought stress on seedling characteristics in an association panel consisting of 198 germplasm lines. Our findings revealed that drought stress had a detrimental effect on all the seedling characteristics under investigation with a maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain a deeper understanding, we conducted a genome-wide association analysis using 12,511 single nucleotide polymorphisms (SNPs), which led to the identification of 39 marker-trait associations (MTAs). Of these 39 MTAs, 13 were particularly noteworthy as they accounted for >10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were further utilized to extract 216 candidate gene (CGs) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with functional relevance to drought stress. These genes encoded the WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, Protein kinase domain, Cytochrome P450, Leucine-rich repeat domain superfamily, BURP domain, Calmodulin-binding protein60, Ubiquitin-like domain, etc. Findings from this study hold significant promise for wheat breeders as they provide direct assistance in selecting lines harboring favorable alleles for improved drought stress tolerance. Additionally, the identified SNPs and CGs will enable marker-assisted selection of potential genomic regions associated with enhanced drought stress tolerance in wheat.

Plant biochemical genetics in the multiomics era

Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.

Comprehensive Analysis of Universal Stress Protein Family Genes and Their Expression in Fusarium oxysporum Response of Populus davidiana × P. alba var. pyramidalis Louche Based on the Transcriptome

Universal stress proteins (USPs) are typical stress-inducible proteins that function directly in a variety of biotic or abiotic stresses and effectively protect plants from complex, adverse environments. However, the expression patterns of USP genes under pathogen stress and their molecular mechanisms in stress resistance have not been reported in detail. In this study, 46 USP genes were identified from Populus trichocarpa (PtrUSPs), and their biological characteristics were comprehensively analyzed based on phylogeny, physicochemical properties of proteins, and gene structures. The promoter regions of PtrUSPs contain a variety of cis-acting elements related to hormone and stress response. The results of a collinearity analysis showed that PtsrUSPs were highly conserved with homologous genes from four other representative species (Arabidopsis thaliana, Eucalyptus grandis, Glycine max, and Solanum lycopersicum). Furthermore, RNA-Seq analysis showed that the expression of 46 USPs from P. davidiana × P. alba var. pyramidalis Louche (PdpapUSPs) was significantly induced by Fusarium oxysporum. The co-expression network and gene ontology analysis of PtrUSPs showed that they participated in the response to stress and response to stimulus through precise coordination. The results of this paper systematically revealed the biological characteristics of PtrUSPs and the characteristics of their response to F. oxysporum stress, which will lay a theoretical foundation for improving genetic traits and the breeding of poplar disease-resistant varieties in subsequent studies.

Universal Stress Proteins: From Gene to Function

Universal stress proteins (USPs) exist across a wide range of species and are vital for survival under stressful conditions. Due to the increasingly harsh global environmental conditions, it is increasingly important to study the role of USPs in achieving stress tolerance. This review discusses the role of USPs in organisms from three aspects: (1) organisms generally have multiple USP genes that play specific roles at different developmental periods of the organism, and, due to their ubiquity, USPs can be used as an important indicator to study species evolution; (2) a comparison of the structures of USPs reveals that they generally bind ATP or its analogs at similar sequence positions, which may underlie the regulatory role of USPs; and (3) the functions of USPs in species are diverse, and are generally directly related to the stress tolerance. In microorganisms, USPs are associated with cell membrane formation, whereas in plants they may act as protein chaperones or RNA chaperones to help plants withstand stress at the molecular level and may also interact with other proteins to regulate normal plant activities. This review will provide directions for future research, focusing on USPs to provide clues for the development of stress-tolerant crop varieties and for the generation of novel green pesticide formulations in agriculture, and to better understand the evolution of drug resistance in pathogenic microorganisms in medicine.

Genome-Wide Association Study of Agronomic and Physiological Traits Related to Drought Tolerance in Potato

Potato (Solanum tuberosum L.) is often considered a water-sensitive crop and its production can be threatened by drought events, making water stress tolerance a trait of increasing interest. In this study, a panel of 144 tetraploid potato genotypes was evaluated for two consecutive years (2019 and 2020) to observe the variation of several physiological traits such as chlorophyll content and fluorescence, stomatal conductance, NDVI, and leaf area and circumference. In addition, agronomic parameters such as yield, tuber fresh weight, tuber number, starch content, dry matter and reducing sugars were determined. GGP V3 Potato array was used to genotype the population, obtaining a total of 18,259 high-quality SNP markers. Marker-trait association was performed using GWASpoly package in R software and Q + K linear mixed models were considered. This approach allowed us to identify eighteen SNP markers significantly associated with the studied traits in both treatments and years, which were related to genes with known functions. Markers related to chlorophyll content and number of tubers under control and stress conditions, and related to stomatal conductance, NDVI, yield and reducing sugar content under water stress, were identified. Although these markers were distributed throughout the genome, the SNPs associated with the traits under control conditions were found mainly on chromosome 11, while under stress conditions they were detected on chromosome 4. These results contribute to the knowledge of the mechanisms of potato tolerance to water stress and are useful for future marker-assisted selection programs.

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.

Pinpointing genomic loci for drought-induced proline and hydrogen peroxide accumulation in bread wheat under field conditions

BACKGROUND

Proline (Pro) and hydrogen peroxide (H₂O₂) play a critical role in plants during drought adaptation. Genetic mapping for drought-induced Pro and H₂O₂ production under field conditions is very limited in crop plants since their phenotyping with large populations is labor-intensive. A genome-wide association study (GWAS) of a diversity panel comprised of 184 bread wheat cultivars grown in natural field (control) and rain-out shelter (drought) environments was performed to identify candidate loci and genes regulating Pro and H₂O₂ accumulation induced by drought.

RESULTS

The GWAS identified top significant marker-trait associations (MTAs) on 1A and 2A chromosomes, respectively for Pro and H₂O₂ in response to drought. Similarly, MTAs for stress tolerance index (STI) of Pro and H₂O₂ were identified on 5B and 1B chromosomes, respectively. Total 143 significant MTAs were identified including 36 and 71 were linked to drought and 2 and 34 were linked to STI for Pro and H₂O_2, respectively. Next, linkage disequilibrium analysis revealed minor alleles of significant single-markers and haplotypes were associated with higher Pro and H₂O₂ accumulation under drought. Several putative candidate genes for Pro and H₂O₂ content encode proteins with kinase, transporter or protein-binding activities.

CONCLUSIONS

The identified genetic factors associated with Pro and H₂O₂ biosynthesis underlying drought adaptation lay a fundamental basis for functional studies and future marker-assisted breeding programs.

Natural diversity uncovers P5CS1 regulation and its role in drought stress tolerance and yield sustainability in barley

Proline accumulation is one of the major responses of plants to many abiotic stresses. However, the significance of proline accumulation for drought stress tolerance remains enigmatic in crop plants. First, we examined the natural variation of the pyrolline-5-carboxylate synthase (P5CS1) among 49 barley genotypes. Allele mining identified a previously unknown allelic series that showed polymorphisms at 42 cis-elements across the P5CS1 promoter. Selected haplotypes had quantitative variation in P5CS1 gene expression and proline accumulation, putatively influenced by both  abscisic acid-dependent and independent pathways under drought stress. Next, we introgressed the P5CS1 allele from a high proline accumulating wild barley accession ISR42-8 into cultivar Scarlett developing a near-isogenic line (NIL-143). NIL-143 accumulated higher proline concentrations than Scarlett under drought stress at seedling and reproductive stages. Under drought stress, NIL-143 showed less pigment damage, sustained photosynthetic health, and higher drought stress recovery compared to Scarlett. Further, the drought-induced damage to yield-related traits, mainly thousand-grain weight, was lower in NIL-143 compared with Scarlett in field conditions. Our data uncovered new variants of the P5CS1 promoter and the significance of the increased proline accumulation regulated by the P5CS1 allele of ISR42-8 in drought stress tolerance and yield stability in barley.

Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool

In this study, we performed a genotyping-by-sequencing analysis and a genome-wide association study of a soybean mutant diversity pool previously constructed by gamma irradiation. A GWAS was conducted to detect significant associations between 37,249 SNPs, 11 agronomic traits, and 6 phytochemical traits. In the merged data set, 66 SNPs on 13 chromosomes were highly associated (FDR p < 0.05) with the following 4 agronomic traits: days of flowering (33 SNPs), flower color (16 SNPs), node number (6 SNPs), and seed coat color (11 SNPs). These results are consistent with the findings of earlier studies on other genetic features (e.g., natural accessions and recombinant inbred lines). Therefore, our observations suggest that the genomic changes in the mutants generated by gamma irradiation occurred at the same loci as the mutations in the natural soybean population. These findings are indicative of the existence of mutation hotspots, or the acceleration of genome evolution in response to high doses of radiation. Moreover, this study demonstrated that the integration of GBS and GWAS to investigate a mutant population derived from gamma irradiation is suitable for dissecting the molecular basis of complex traits in soybeans.

Phosphate transporter PHT1;1 is a key determinant of phosphorus acquisition in Arabidopsis natural accessions

Phosphorus (P) is a mineral nutrient essential for plant growth and development, but most P in the soil is unavailable for plants. To understand the genetic basis of P acquisition regulation, we performed genome-wide association studies (GWASs) on a diversity panel of Arabidopsis (Arabidopsis thaliana). Two primary determinants of P acquisition were considered, namely, phosphate (Pi)-uptake activity and PHOSPHATE TRANSPORTER 1 (PHT1) protein abundance. Association mapping revealed a shared significant peak on chromosome 5 (Chr5) where the PHT1;1/2/3 genes reside, suggesting a connection between the regulation of Pi-uptake activity and PHT1 protein abundance. Genes encoding transcription factors, kinases, and a metalloprotease associated with both traits were also identified. Conditional GWAS followed by statistical analysis of genotype-dependent PHT1;1 expression and transcriptional activity assays revealed an epistatic interaction between PHT1;1 and MYB DOMAIN PROTEIN 52 (MYB52) on Chr1. Further, analyses of F1 hybrids generated by crossing two subgroups of natural accessions carrying specific PHT1;1- and MYB52-associated single nucleotide polymorphisms (SNPs) revealed strong effects of these variants on PHT1;1 expression and Pi uptake activity. Notably, the soil P contents in Arabidopsis habitats coincided with PHT1;1 haplotype, emphasizing how fine-tuned P acquisition activity through natural variants allows environmental adaptation. This study sheds light on the complex regulation of P acquisition and offers a framework to systematically assess the effectiveness of GWAS approaches in the study of quantitative traits.

Natural variation identifies new effectors of water-use efficiency in Arabidopsis

Water-use efficiency (WUE) is the ratio of biomass produced per unit of water consumed; thus, it can be altered by genetic factors that affect either side of the ratio. In the present study, we exploited natural variation for WUE to discover loci affecting either biomass accumulation or water use as factors affecting WUE. Genome-wide association studies (GWAS) using integrated WUE measured through carbon isotope discrimination (δ¹³C) of Arabidopsis thaliana accessions identified genomic regions associated with WUE. Reverse genetic analysis of 70 candidate genes selected based on the GWAS results and transcriptome data identified 25 genes affecting WUE as measured by gravimetric and δ¹³C analyses. Mutants of four genes had higher WUE than wild type, while mutants of the other 21 genes had lower WUE. The differences in WUE were caused by either altered biomass or water consumption (or both). Stomatal density (SD) was not a primary cause of altered WUE in these mutants. Leaf surface temperatures indicated that transpiration differed for mutants of 16 genes, but generally biomass accumulation had a greater effect on WUE. The genes we identified are involved in diverse cellular processes, including hormone and calcium signaling, meristematic activity, photosynthesis, flowering time, leaf/vasculature development, and cell wall composition; however, none of them had been previously linked to WUE. Thus, our study successfully identified effectors of WUE that can be used to understand the genetic basis of WUE and improve crop productivity.

Contrasting Water Withholding Responses of Young Maize Plants Reveal Link Between Lipid Peroxidation and Osmotic Regulation Corroborated by Genetic Analysis

Linking biochemistry and genetics of tolerance to osmotic stress is of interest for understanding plant adaptations to unfavorable conditions. The aims of this study were to investigate the variability in responses of panel of elite maize inbred lines to water withholding for stress-related traits through association study and to identify pathways linked to detected associations for better understanding of maize stress responses. Densely genotyped public and expired Plant Variety Protection Certificate (ex-PVP) inbred lines were planted in controlled conditions (16-h/8-h day/night, 25°C, 50% RH) in control (CO) and exposed to 10-day water withholding (WW). Traits analyzed were guaiacol peroxidase activity (GPOD), total protein content (PROT), lipid peroxidation (TBARS), hydrogen peroxide accumulation (H₂O₂), proline accumulation (proline), and current water content (CWC). Proline accumulation was found to be influenced by H₂O₂ and TBARS signaling pathways acting as an accumulation-switching mechanism. Most of the associations detected were for proline (29.4%) and TBARS (44.1%). Gene ontology (GO) enrichment analysis showed significant enrichment in regulation of integral membrane parts and peroxisomes along with regulation of transcription and polysaccharide catabolism. Dynamic studies involving inbreds with extreme phenotypes are needed to elucidate the role of this signaling mechanism in regulation of response to water deficit.

Selecting putative drought-tolerance markers in two contrasting soybeans

Identifying high-yield genotypes under low water availability is essential for soybean climate-smart breeding. However, a major bottleneck lies in phenotyping, particularly in selecting cost-efficient markers associated with stress tolerance and yield stabilization. Here, we conducted in-depth phenotyping experiments in two soybean genotypes with contrasting drought tolerance, MUNASQA (tolerant) and TJ2049 (susceptible), to better understand soybean stress physiology and identify/statistically validate drought-tolerance and yield-stabilization traits as potential breeding markers. Firstly, at the critical reproductive stage (R5), the molecular differences between the genotype's responses to mild water deficit were explored through massive analysis of cDNA ends (MACE)-transcriptomic and gene ontology. MUNASQA transcriptional profile, compared to TJ2049, revealed significant differences when responding to drought. Next, both genotypes were phenotyped under mild water deficit, imposed in vegetative (V3) and R5 stages, by evaluating 22 stress-response, growth, and water-use markers, which were subsequently correlated between phenological stages and with yield. Several markers showed high consistency, independent of the phenological stage, demonstrating the effectiveness of the phenotyping methodology and its possible use for early selection. Finally, these markers were classified and selected according to their cost-feasibility, statistical weight, and correlation with yield. Here, pubescence, stomatal density, and canopy temperature depression emerged as promising breeding markers for the early selection of drought-tolerant soybeans.

Intriguing Role of Proline in Redox Potential Conferring High Temperature Stress Tolerance

Proline is a proteinogenic amino acid synthesized from glutamate and ornithine. Pyrroline-5-carboxylate synthetase and pyrroline-5-carboxylate reductase are the two key enzymes involved in proline synthesis from glutamate. On the other hand, ornithine-δ-aminotransferase converts ornithine to pyrroline 5-carboxylate (P5C), an intermediate in the synthesis of proline as well as glutamate. Both proline dehydrogenase and P5C dehydrogenase convert proline back to glutamate. Proline accumulation is widespread in response to environmental challenges such as high temperatures, and it is known to defend plants against unpropitious situations promoting plant growth and flowering. While proline accumulation is positively correlated with heat stress tolerance in some crops, it has detrimental consequences in others. Although it has been established that proline is a key osmolyte, its exact physiological function during heat stress and plant ontogeny remains unknown. Emerging evidence pointed out its role as an overriding molecule in alleviating high temperature stress (HTS) by quenching singlet oxygen and superoxide radicals. Proline cycle acts as a shuttle and the redox couple (NAD+/NADH, NADP+/NADPH) appears to be highly crucial for energy transfer among different cellular compartments during plant development, exposure to HTS conditions and also during the recovery of stress. In this review, the progress made in recent years regarding its involvement in heat stress tolerance is highlighted.

Genetic dissection of seed characteristics in field pennycress via genome-wide association mapping studies

Field pennycress (Thlaspi arvense L.) is a new winter annual cash cover crop with high oil content and seed yield, excellent winter hardiness, early maturation, and resistance to most pests and diseases. It provides living cover on fallow croplands between summer seasons, and in doing so reduces nutrient leaching into water sources, mitigates soil erosion, and suppresses weed growth. The first ever genome-wide association study (GWAS) was conducted on a pennycress diversity panel to identify marker trait associations with important seed size and composition related traits. The entire population was phenotyped in three total environments over 2 yr, and seed area, length, width, thousand grain weight, total oil, and total protein were measured post-harvest with specialized high-throughput imaging and near-infrared spectroscopy. Basic unbiased linear prediction values were calculated for each trait. Seed size traits tended to have higher entry mean reliabilities (0.76-0.79) compared with oil content (0.51) and protein content (0.37). Genotyping-by-sequencing identified 33,606 high quality genome-wide single nucleotide polymorphism (SNPs) that were coupled with phenotypic data to perform GWAS for seed area, length, width, thousand grain weight, total oil, and total protein content. Fifty-nine total marker-trait associations were identified revealing genomic regions controlling each trait. The significant SNPs explained 0.06-0.18% of the total variance for that trait in our population. A list of candidate genes was identified based on their functional annotations and characterization in other species. Our results confirm that GWAS is an efficient strategy to identify significant marker-trait associations that can be incorporated into marker-assisted selection pipelines to accelerate pennycress breeding progress.

GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress

Flooding causes severe crop losses in many parts of the world. Genetic variation in flooding tolerance exists in many species; however, there are few examples for the identification of tolerance genes and their underlying function. We conducted a genome-wide association study (GWAS) in 387 Arabidopsis (Arabidopsis thaliana) accessions. Plants were subjected to prolonged submergence followed by desubmergence, and seven traits (score, water content, Fv/Fm, and concentrations of nitrate, chlorophyll, protein, and starch) were quantified to characterize their acclimation responses. These traits showed substantial variation across the range of accessions. A total of 35 highly significant single-nucleotide polymorphisms (SNPs) were identified across the 20 GWA datasets, pointing to 22 candidate genes, with functions in TCA cycle, DNA modification, and cell division. Detailed functional characterization of one candidate gene, ACONITASE3 (ACO3), was performed. Chromatin immunoprecipitation followed by sequencing showed that a single nucleotide polymorphism in the ACO3 promoter co-located with the binding site of the master regulator of retrograde signaling ANAC017, while subcellular localization of an ACO3-YFP fusion protein confirmed a mitochondrial localization during submergence. Analysis of mutant and overexpression lines determined changes in trait parameters that correlated with altered submergence tolerance and were consistent with the GWAS results. Subsequent RNA-seq experiments suggested that impairing ACO3 function increases the sensitivity to submergence by altering ethylene signaling, whereas ACO3 overexpression leads to tolerance by metabolic priming. These results indicate that ACO3 impacts submergence tolerance through integration of carbon and nitrogen metabolism via the mitochondrial TCA cycle and impacts stress signaling during acclimation to stress.

Proline metabolism as regulatory hub

Proline is a multifunctional amino acid that is accumulated in high concentrations in plants under various stress conditions. Proline accumulation is intimately connected to many cellular processes, such as osmotic pressure, energy status, nutrient availability, changes in redox balance, and defenses against pathogens. Proline biosynthesis and catabolism is linked to photosynthesis and mitochondrial respiration, respectively. Proline can function as a signal, modulating gene expression and certain metabolic processes. We review important findings on proline metabolism and function of the last decade, giving a more informative picture about the function of this unusual amino acid in maintaining cellular homeostasis, modulating plant development, and promoting stress acclimation.

The proline cycle as an eukaryotic redox valve

The amino acid proline has been known for many years to be a component of proteins as well as an osmolyte. Many recent studies have demonstrated that proline has other roles such as regulating redox balance and energy status. In animals and plants, the well-described proline cycle is concomitantly responsible for the preferential accumulation of proline and shuttling of redox equivalents from the cytosol to mitochondria. The impact of the proline cycle goes beyond regulating proline levels. In this review, we focus on recent evidence of how the proline cycle regulates redox status in relation to other redox shuttles. We discuss how the interconversion of proline and glutamate shuttles reducing power between cellular compartments. Spatial aspects of the proline cycle in the entire plant are considered in terms of proline transport between organs with different metabolic regimes (photosynthesis versus respiration). Furthermore, we highlight the importance of this shuttle in the regulation of energy and redox power in plants, through a particularly intricate coordination, notably between mitochondria and cytosol.

Genome-wide analysis of the Universal stress protein A gene family in Vitis and expression in response to abiotic stress

Universal Stress Protein A (USPA) plays critical roles in the regulation of growth, development and response to abiotic stress in plants. To date, most research related to the role of USPA in plants has been carried out in herbaceous models such as Arabidopsis, rice and soybean. Here, we used bioinformatics approaches to identify 21 USPA genes in the genome of Vitis vinifera L. Phylogenetic analysis revealed that VvUSPAs could be divided into eight clades. Based on predicted chromosomal locations, we identified 16 pairs of syntenic, orthologous genes between A. thaliana and V. vinifera. Further promoter cis-elements analysis, together with identification of potential microRNA (miRNA) binding sites, suggested that at least some of the VvUSPAs participate in response to phytohormones and abiotic stress. To add support for this, we analyzed the developmental and stress-responsive expression patterns of the homologous USPA genes in the drought-resistant wild Vitis yeshanensis accession 'Yanshan-1' and the drought-sensitive Vitis riparia accession 'He'an'. Most of the USPA genes were upregulated in different degrees in the two genotypes after drought stress and exposure to ethephon (ETH), abscisic acid (ABA) and methyl jasmonate (MeJA). Individual USPA genes showed various tissue-specific expression patterns. Heterologous expression of five selected genes (VvUSPA2, VvUSPA3, VvUSPA11, VvUSPA13 and VvUSPA16) in Escherichia coli (E. coli) enhanced resistance to drought stress. Our study provides a model for mapping gene function in response to abiotic stress and identified three candidate genes, VvUSPA3, VvUSPA11 and VvUSPA16, as regulators of drought response in V. vinifera.

Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis

Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways. It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner. However, the identities of the protein kinases/phosphatases involved in this mechanism and their roles in the regulation of the tricarboxylic acid (TCA) cycle remain unclear. In this study, we isolated and characterized plants lacking two mitochondrially targeted phosphatases (Sal2 and PP2c63) along with pyruvate dehydrogenase kinase (PDK). Protein-protein interaction analysis, quantitative phosphoproteomics, and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex (PDC), while PP2c63 nonspecifically regulates PDC. When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants, protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC, while Sal2 only indirectly affects TCA cycle enzymes. Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle, and that altered metabolism in the sal2 pp2c63 double mutant compromises plant growth. These results are discussed in the context of current models of the control of respiration in plants.

Genome-wide association study of cyanogenic glycosides, proline, sugars, and pigments in Eucalyptus cladocalyx after 18 consecutive dry summers

Natural variation of cyanogenic glycosides, soluble sugars, proline, and nondestructive optical sensing of pigments (chlorophyll, flavonols, and anthocyanins) was examined in ex situ natural populations of Eucalyptus cladocalyx F. Muell. grown under dry environmental conditions in the southern Atacama Desert, Chile. After 18 consecutive dry seasons, considerable plant-to-plant phenotypic variation for all the traits was observed in the field. For example, leaf hydrogen cyanide (HCN) concentrations varied from 0 (two acyanogenic individuals) to 1.54 mg cyanide g^-1 DW. Subsequent genome-wide association study revealed associations with several genes with a known function in plants. HCN content was associated robustly with genes encoding Cytochrome P450 proteins, and with genes involved in the detoxification mechanism of HCN in cells (β-cyanoalanine synthase and cyanoalanine nitrilase). Another important finding was that sugars, proline, and pigment content were linked to genes involved in transport, biosynthesis, and/or catabolism. Estimates of genomic heritability (based on haplotypes) ranged between 0.46 and 0.84 (HCN and proline content, respectively). Proline and soluble sugars had the highest predictive ability of genomic prediction models (PA = 0.65 and PA = 0.71, respectively). PA values for HCN content and flavonols were relatively moderate, with estimates ranging from 0.44 to 0.50. These findings provide new understanding on the genetic architecture of cyanogenic capacity, and other key complex traits in cyanogenic E. cladocalyx.

Arsenic Stress-Related F-Box (ASRF) gene regulates arsenic stress tolerance in Arabidopsis thaliana

Arsenic (As), a non-biodegradable contaminant, is extremely toxic to plants and animals in its inorganic form. As negatively affects plant growth and development, primarily by inducing oxidative stress through redox imbalance. Here we characterized the Arabidopsis F-box protein gene AT2G16220 (Arsenic Stress-Related F-box (ASRF)) that we identified in the genome-wide association study. The asrf mutant seedlings showed high sensitivity to arsenate (As^V) stress. As^V significantly affected asrf seedling growth when germinated on or exposed to As^V-supplemented growth regimes. As^V stress significantly induced production of reactive oxygen species and proline accumulation in asrf, so the asrf maintained high proline content, possibly for cellular protection and redox homeostasis. Heterozygous seedlings (Col-0 x asrf, F1 progeny) were relatively less affected by As^V stress than asrf mutant but showed slightly reduced growth compared with the Col-0 wild type, which suggests that the homozygous ASRF locus is important for As^V stress resistance. Transcriptome analysis involving the mutant and wild type revealed altered phosphate homeostasis in asrf seedlings, which implies that ASRF is required for maintaining phosphate and cellular- homeostasis under excess As^V. Our findings confirm the roles of ASRF in As stress tolerance in plants, for a novel way to mitigate arsenic stress.

Morphological and metabolic profiling of a tropical-adapted potato association panel subjected to water recovery treatment reveals new insights into plant vigor

Potato (Solanum tuberosum L.) is one of the world's most important crops, but it is facing major challenges due to climatic changes. To investigate the effects of intermittent drought on the natural variability of plant morphology and tuber metabolism in a novel potato association panel comprising 258 varieties we performed an augmented block design field study under normal irrigation and under water-deficit and recovery conditions in Ica, Peru. All potato genotypes were profiled for 45 morphological traits and 42 central metabolites via nuclear magnetic resonance. Statistical tests and norm of reaction analysis revealed that the observed variations were trait specific, that is, genotypic versus environmental. Principal component analysis showed a separation of samples as a result of conditional changes. To explore the relational ties between morphological traits and metabolites, correlation-based network analysis was employed, constructing one network for normal irrigation and one network for water-recovery samples. Community detection and difference network analysis highlighted the differences between the two networks, revealing a significant correlational link between fumarate and plant vigor. A genome-wide association study was performed for each metabolic trait. Eleven single nucleotide polymorphism (SNP) markers were associated with fumarate. Gene Ontology analysis of quantitative trait loci regions associated with fumarate revealed an enrichment of genes regulating metabolic processes. Three of the 11 SNPs were located within genes, coding for a protein of unknown function, a RING domain protein and a zinc finger protein ZAT2. Our findings have important implications for future potato breeding regimes, especially in countries suffering from climate change.

Genome-wide association study identifies candidate genes related to oleic acid content in soybean seeds

BACKGROUND

Soybean oil is a complex mixture of five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic). Soybean oil with a high oleic acid content is desirable because this monounsaturated fatty acid improves the oxidative stability of the oil. To investigate the genetic architecture of oleic acid in soybean seeds, 260 soybean germplasms from Northeast China were collected as natural populations. A genome-wide association study (GWAS) was conducted on a panel of 260 germplasm resources.

RESULTS

Phenotypic identification results showed that the oleic acid content varied from 8.2 to 35.0%. A total of 2,311,337 single-nucleotide polymorphism (SNP) markers were obtained. GWAS analysis showed that there were many genes related to oleic acid content with a contribution rate of 7%. The candidate genes Glyma.11G229600.1 on chromosome 11 and Glyma.04G102900.1 on chromosome 4 were detected in a 2-year-long GWAS. The candidate gene Glyma.11G229600.1 showed a positive correlation with the oleic acid content, and the correlation coefficient was 0.980, while Glyma.04G102900.1 showed a negative correlation, with a coefficient of - 0.964.

CONCLUSIONS

Glyma.04G102900.1 on chromosome 4 and Glyma.11G229600.1 on chromosome 11 were detected in both analyses (2018 and 2019). Glyma.04G102900.1 and Glyma.11G229600.1 are new key candidate genes related to oleic acid in soybean seeds. These results will be useful for high-oleic soybean breeding.

Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis

Organogenesis in plants occurs across all stages of the life cycle. Although previous studies have identified many genes as important for either vegetative or reproductive development at the RNA level, global information on translational and post-translational levels remains limited. In this study, six Arabidopsis stages/organs were analyzed using quantitative proteomics and phosphoproteomics, identifying 2187 non-redundant proteins and evidence for 1194 phosphoproteins. Compared to the expression observed in cauline leaves, the expression of 1445, 1644, and 1377 proteins showed greater than 1.5-fold alterations in stage 1–9 flowers, stage 10–12 flowers, and open flowers, respectively. Among these, 294 phosphoproteins with 472 phosphorylation sites were newly uncovered, including 275 phosphoproteins showing differential expression patterns, providing molecular markers and possible candidates for functional studies. Proteins encoded by genes preferentially expressed in anther (15), meiocyte (4), or pollen (15) were enriched in reproductive organs, and mutants of two anther-preferentially expressed proteins, acos5 and mee48, showed obviously reduced male fertility with abnormally organized pollen exine. In addition, more phosphorylated proteins were identified in reproductive stages (1149) than in the vegetative organs (995). The floral organ-preferential phosphorylation of GRP17, CDC2/CDKA.1, and ATSK11 was confirmed with western blot analysis. Moreover, phosphorylation levels of CDPK6 and MAPK6 and their interacting proteins were elevated in reproductive tissues. Overall, our study yielded extensive data on protein expression and phosphorylation at six stages/organs and provides an important resource for future studies investigating the regulatory mechanisms governing plant development.

A Genome-Wide Association Study of Coleoptile Length in Different Chinese Wheat Landraces

From the perspective of wheat yield improvement, the coleoptile is vital for successful crop establishment, and long coleoptile lengths (CLs) are preferred in wheat-growing regions where deep planting is practiced. To determine the genetic basis of CL, we performed a genome-wide association study on a set of 707 Chinese wheat landraces using 18,594 single-nucleotide polymorphisms and 38,678 diversity array technology sequencing markers. We accordingly detected a total of 29 significant markers [-log₁₀ ^(P) > 4.76] distributed on chromosomes 2B, 2D, 3A, 4A, 5A, 6A, 6B, 6D, and 7B. Based on linkage disequilibrium decay distance, we identified a total of 17 quantitative trait loci associated with CL, among which QCl.sicau-6B.2, located at 508.17-509.26 Mb on chromosome 6B, was recognized as a novel major locus. We subsequently developed a high-resolution melt marker for QCl.sicau-6B.2, which was validated in an F _{2 : 3} population. Our findings provide important insights into the genetic mechanisms underlying coleoptile growth and could be applied to marker-assisted wheat selection.

mGWAS Uncovers Gln-Glucosinolate Seed-Specific Interaction and its Role in Metabolic Homeostasis

Gln is a key player in plant metabolism. It is one of the major free amino acids that is transported into the developing seed and is central for nitrogen metabolism. However, Gln natural variation and its regulation and interaction with other metabolic processes in seeds remain poorly understood. To investigate the latter, we performed a metabolic genome-wide association study (mGWAS) of Gln-related traits measured from the dry seeds of the Arabidopsis (Arabidopsis thaliana) diversity panel using all potential ratios between Gln and the other members of the Glu family as traits. This semicombinatorial approach yielded multiple candidate genes that, upon further analysis, revealed an unexpected association between the aliphatic glucosinolates (GLS) and the Gln-related traits. This finding was confirmed by an independent quantitative trait loci mapping and statistical analysis of the relationships between the Gln-related traits and the presence of specific GLS in seeds. Moreover, an analysis of Arabidopsis mutants lacking GLS showed an extensive seed-specific impact on Gln levels and composition that manifested early in seed development. The elimination of GLS in seeds was associated with a large effect on seed nitrogen and sulfur homeostasis, which conceivably led to the Gln response. This finding indicates that both Gln and GLS play key roles in shaping the seed metabolic homeostasis. It also implies that select secondary metabolites might have key functions in primary seed metabolism. Finally, our study shows that an mGWAS performed on dry seeds can uncover key metabolic interactions that occur early in seed development.

Dissection of Phenotypic and Genetic Variation of Drought-Related Traits in Diverse Chinese Wheat Landraces

Variations in 16 seedling traits under normal and drought conditions were investigated. Extremely resistant and sensitive accessions were identified for future analyses. Under normal and drought conditions, 57 and 29 QTL were identified, respectively. A total of 77 candidate genes were identified, and four were validated by qRT-PCR. Drought is one of the most important abiotic stressors affecting wheat (Triticum aestivum L.) production. To improve wheat yield, a better understanding of the genetic control of traits governing drought resistance is paramount. Here, using 645 wheat landraces, we evaluated 16 seedling traits related to root and shoot growth and water content under normal and drought (induced by polyethylene glycol) conditions. Extremely resistant and sensitive accessions were identified for future drought-resistance breeding and further genetic analyses. A genome-wide association study was performed for the 16 traits using 52,118 diversity arrays technology sequencing (DArT-seq) markers. A total of 57 quantitative trait loci (QTL) were detected for seven traits under normal conditions, whereas 29 QTL were detected for eight traits under drought conditions. On the basis of these markers, we identified 56 candidate genes for six seedling traits under normal conditions, and 21 candidate genes for seven seedling traits under drought conditions. Four candidate genes were validated under normal and drought conditions using quantitative reverse transcription polymerase chain reaction (qRT-PCR) data. The co-localization of the flowering date and drought-related traits indicates that the regulatory networks of flowering may also respond to drought stress or are associated with the correlated responses of these traits. The phenotypic and genetic elucidation of drought-related traits will assist future gene discovery efforts and provide a basis for breeding drought-resistant wheat cultivars.

Differential characterization of physiological and biochemical responses during drought stress in finger millet varieties

Drought is the most perilous abiotic stress that affects finger millet growth and productivity worldwide. For the successful production of finger millet, selection of drought tolerant varieties is necessary and critical stages under drought stress, germination and early seedling growth, ought to be fully understood. This study investigated the physiological and biochemical responses of six finger millet varieties (GBK043137, GBK043128, GBK043124, GBK043122, GBK043094 and GBK043050) under mannitol-induced drought stress. Seeds were germinated in sterile soil and irrigated with various concentrations of mannitol (200, 400 and 600 mM) for 2 weeks. In a comparative analysis relative water content (RWC), chlorophyll, proline and malondialdehyde (MDA) contents were measured to obtain the physiological and biochemical characteristics of drought stress. The results showed that increased levels of drought stress seriously decreased germination and early seedling growth of finger millet varieties. However, root growth was increased. In addition, exposition to drought stress triggered a significant decrease in relative water content and chlorophyll content reduction, and the biochemical parameters assay showed less reduction in RWC. Furthermore, oxidative damage indicating parameters, such as proline concentration and MDA content, increased. Varieties GBK043137 and GBK043094 were less affected by drought than the other varieties as shown by significant changes in their physiological parameters. Our findings reveal the differences between the physiological and biochemical responses of finger millet to drought and are vital for breeding and selecting drought tolerant varieties of finger millet. Further, genomic and molecular investigations need to be undertaken to gain a deeper insight into the detailed mechanisms of drought tolerance in finger millet.

Genome-wide association study (GWAS) of leaf cuticular wax components in Camelina sativa identifies genetic loci related to intracellular wax transport

BACKGROUND

It is important to explore renewable alternatives (e.g. biofuels) that can produce energy sources to help reduce reliance on fossil oils, and reduce greenhouse gases and waste solids resulted from fossil oils consumption. Camelina sativa is an oilseed crop which has received increasing attention due to its short life cycle, broader adaptation regions, high oil content, high level of omega-3 unsaturated fatty acids, and low-input requirements in agriculture practices. To expand its Camelina production areas into arid regions, there is a need to breed for new drought-tolerant cultivars. Leaf cuticular wax is known to facilitate plant development and growth under water-limited conditions. Dissecting the genetic loci underlying leaf cuticular waxes is important to breed for cultivars with improved drought tolerance.

RESULTS

Here we combined phenotypic data and single nucleotide polymorphism (SNP) data from a spring C. sativa diversity panel using genotyping-by-sequencing (GBS) technology, to perform a large-scale genome-wide association study (GWAS) on leaf wax compositions. A total of 42 SNP markers were significantly associated with 15 leaf wax traits including major wax components such as total primary alcohols, total alkanes, and total wax esters as well as their constituents. The vast majority of significant SNPs were associated with long-chain carbon monomers (carbon chain length longer than C28), indicating the important effects of long-chain carbon monomers on leaf total wax biosynthesis. These SNP markers are located on genes directly or indirectly related to wax biosynthesis such as maintaining endoplasmic reticulum (ER) morphology and enabling normal wax secretion from ER to plasma membrane or Golgi network-mediated transport.

CONCLUSIONS

These loci could potentially serve as candidates for the genetic control involved in intracellular wax transport that might directly or indirectly facilitate leaf wax accumulation in C. sativa and can be used in future marker-assisted selection (MAS) to breed for the cultivars with high wax content to improve drought tolerance.

Genome-wide association analysis of salinity responsive traits in Medicago truncatula

Salinity stress is an important cause of crop yield loss in many parts of the world. Here, we performed genome-wide association studies of salinity-stress responsive traits in 132 HapMap genotypes of the model legume Medicago truncatula. Plants grown in soil were subjected to a step-wise increase in NaCl concentration, from 0 through 0.5% and 1.0% to 1.5%, and the following traits were measured: vigor, shoot biomass, shoot water content, leaf chlorophyll content, leaf size, and leaf and root concentrations of proline and major ions (Na+ , Cl- , K+ , Ca2+ , etc.). Genome-wide association studies were carried out using 2.5 million single nucleotide polymorphisms, and 12 genomic regions associated with at least four traits each were identified. Transcript-level analysis of the top eight candidate genes in five extreme genotypes revealed association between salinity tolerance and transcript-level changes for seven of the genes, encoding a vacuolar H+ -ATPase, two transcription factors, two proteins involved in vesicle trafficking, one peroxidase, and a protein of unknown function. Earlier functional studies on putative orthologues of two of the top eight genes (a vacuolar H+ -ATPase and a peroxidase) demonstrated their involvement in plant salinity tolerance.

Stress Adaptive Plasticity: Aegilops tauschii and Triticum dicoccoides as Potential Donors of Drought Associated Morpho-Physiological Traits in Wheat

The inconsistent prevalence of abiotic stress in most of the agroecosystems can be addressed through deployment of plant material with stress adaptive plasticity. The present study explores water stress induced plasticity for early root-shoot development, proline induction and cell membrane injury in 57 accessions of Aegilops tauschii (DD-genome) and 26 accessions of Triticum dicoccoides (AABB-genome) along with durum and bread wheat cultivars. Thirty three Ae. tauschii accessions and 18 T. dicoccoides accessions showed an increase in root dry weight (ranging from 1.8 to 294.75%) under water stress. Shoot parameters- length and biomass, by and large were suppressed by water stress, but genotypes with stress adaptive plasticity leading to improvement of shoot traits (e.g., Ae tauschii accession 14191 and T. dicoccoides accession 7130) could be identified. Water stress induced active responses, rather than passive repartitioning of biomass was indicated by better shoot growth in seedlings of genotypes with enhanced root growth under stress. Membrane injury seemed to work as a trigger to activate water stress adaptive cellular machinery and was found positively correlated with several root-shoot based adaptive responses in seedlings. Stress induced proline accumulation in leaf tissue showed marked inter- and intra-specific genetic variation but hardly any association with stress adaptive plasticity. Genotypic variation for early stage plasticity traits viz., change in root dry weight, shoot length, shoot fresh weight, shoot dry weight and membrane injury positively correlated with grain weight based stress tolerance index (r = 0.267, r = 0.404, r = 0.299, r = 0.526, and r = 0.359, respectively). In another such trend, adaptive seedling plasticity correlated positively with resistance to early flowering under stress (r = 0.372 with membrane injury, r = 0.286 with change in root length, r = 0.352 with change in shoot length, r = 0.268 with change in shoot dry weight). Overall, Ae. tauschii accessions 9816, 14109, 14128, and T. dicoccoides accessions 5259 and 7130 were identified as potential donors of stress adaptive plasticity. The prospect of the study for molecular marker tagging, cloning of plasticity genes and creation of elite synthetic hexaploid donors is discussed.

Natural variation in cytokinin maintenance improves salt tolerance in apple rootstocks

Plants experiencing salt-induced stress often reduce cytokinin levels during the early phases of stress-response. Interestingly, we found that the cytokinin content in the apple rootstock "robusta" was maintained at a high level under salt stress. Through screening genes involved in cytokinin biosynthesis and catabolism, we found that the high expression levels of IPT5b in robusta roots were involved in maintaining the high cytokinin content. We identified a 42 bp deletion in the promoter region of IPT5b, which elevated IPT5b expression levels, and this deletion was linked to salt tolerance in robusta×M.9 segregating population. The 42 bp deletion resulted in the deletion of a Proline Response Element (ProRE), and our results suggest that ProRE negatively regulates IPT5b expression in response to proline. Under salt stress, the robusta cultivar maintains high cytokinin levels as IPT5b expression cannot be inhibited by proline due to the deletion of ProRE, leading to improve salt tolerance.

Impact of Climate Change on Crops Adaptation and Strategies to Tackle Its Outcome: A Review

Agriculture and climate change are internally correlated with each other in various aspects, as climate change is the main cause of biotic and abiotic stresses, which have adverse effects on the agriculture of a region. The land and its agriculture are being affected by climate changes in different ways, e.g., variations in annual rainfall, average temperature, heat waves, modifications in weeds, pests or microbes, global change of atmospheric CO₂ or ozone level, and fluctuations in sea level. The threat of varying global climate has greatly driven the attention of scientists, as these variations are imparting negative impact on global crop production and compromising food security worldwide. According to some predicted reports, agriculture is considered the most endangered activity adversely affected by climate changes. To date, food security and ecosystem resilience are the most concerning subjects worldwide. Climate-smart agriculture is the only way to lower the negative impact of climate variations on crop adaptation, before it might affect global crop production drastically. In this review paper, we summarize the causes of climate change, stresses produced due to climate change, impacts on crops, modern breeding technologies, and biotechnological strategies to cope with climate change, in order to develop climate resilient crops. Revolutions in genetic engineering techniques can also aid in overcoming food security issues against extreme environmental conditions, by producing transgenic plants.

De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway

Oroxylum indicum (L.) Kurz is a medicinally important and rare tree species of the family Bignoniaceae. It is rich in flavonoid content and its mature roots are extensively used in Ayurvedic formulations. O. indicum specific flavonoids like oroxylin B, prunetin and oroxindin possess antibacterial, antiproliferative, antioxidant and anticancerous properties, signifying its importance in modern medicine. In the present study, de novo transcriptome analysis of O. indicum root was performed to elucidate the genes involved in flavonoid metabolism. A total of 24,625,398 high quality reads were assembled into 121,286 transcripts with N50 value 1783. The BLASTx search of 81,002 clustered transcripts against Viridiplantae Uniprot database led to annotation of 46,517 transcripts. Furthermore, Gene ontology (GO) revealed that 34,231 transcripts mapped to 3049 GO terms and KEGG analysis demonstrated that 4570 transcripts plausibly involved in 132 biosynthetic pathways. The transcriptome data indicated that cinnamyl-alcohol dehydrogenase (OinCAD) was abundant in phenylpropanoid pathway genes while; naringenin chalcone synthase (OinCHS), flavone synthase (OinFNS) and flavonoid 3', 5'-methyltransferase (OinF35 MT) were abundant in flavonoid, isoflavonoid, flavone and flavonol biosynthesis pathways, respectively. Transcription factor analysis demonstrated the abundance of MYB, bHLH and WD40 transcription factor families, which regulate the flavonoid biosynthesis. Flavonoid pathway genes displayed differential expression in young and old roots of O. indicum. The transcriptome led to the identification of 31 diverse full length Cytochrome P450 (CYP450) genes which may be involved in biosynthesis of specialized metabolites and flavonoids like baicalein and baicalin. Thus, the information obtained in this study will be a valuable tool for identifying genes and developing system biology approaches for in vitro synthesis of specialized O. indicum metabolites.

Natural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis

Soil water uptake by roots is a key component of plant performance and adaptation to adverse environments. Here, we use a genome-wide association analysis to identify the XYLEM NAC DOMAIN 1 (XND1) transcription factor as a negative regulator of Arabidopsis root hydraulic conductivity (Lp_r). The distinct functionalities of a series of natural XND1 variants and a single nucleotide polymorphism that determines XND1 translation efficiency demonstrate the significance of XND1 natural variation at species-wide level. Phenotyping of xnd1 mutants and natural XND1 variants show that XND1 modulates Lp_r through action on xylem formation and potential indirect effects on aquaporin function and that it diminishes drought stress tolerance. XND1 also mediates the inhibition of xylem formation by the bacterial elicitor flagellin and counteracts plant infection by the root pathogen Ralstonia solanacearum. Thus, genetic variation at XND1, and xylem differentiation contribute to resolving the major trade-off between abiotic and biotic stress resistance in Arabidopsis.

Soil water uptake is a major determinant of plant performance and stress tolerance. Here the authors show that, by affecting xylem formation in the root, natural variation at the Arabidopsis XND1 locus has contrasting effects on root hydraulics and drought tolerance versus pathogen resistance.

Genome-wide association mapping in Arabidopsis identifies novel genes underlying quantitative disease resistance to Alternaria brassicae

Quantitative disease resistance (QDR) is the predominant form of resistance against necrotrophic pathogens. The genes and mechanisms underlying QDR are not well known. In the current study, the Arabidopsis-Alternaria brassicae pathosystem was used to uncover the genetic architecture underlying resistance to A. brassicae in a set of geographically diverse Arabidopsis accessions. Arabidopsis accessions revealed a rich variation in the host responses to the pathogen, varying from complete resistance to high susceptibility. Genome-wide association (GWA) mapping revealed multiple regions to be associated with disease resistance. A subset of genes prioritized on the basis of gene annotations and evidence of transcriptional regulation in other biotic stresses was analysed using a reverse genetics approach employing T-DNA insertion mutants. The mutants of three genes, namely At1g06990 (GDSL-motif lipase), At3g25180 (CYP82G1) and At5g37500 (GORK), displayed an enhanced susceptibility relative to the wild-type. These genes are involved in the development of morphological phenotypes (stomatal aperture) and secondary metabolite synthesis, thus defining some of the diverse facets of quantitative resistance against A. brassicae.

Genome-Wide Association Studies of Image Traits Reveal Genetic Architecture of Drought Resistance in Rice

Understanding how plants respond to drought can benefit drought resistance (DR) breeding. Using a non-destructive phenotyping facility, 51 image-based traits (i-traits) for 507 rice accessions were extracted. These i-traits can be used to monitor drought responses and evaluate DR. High heritability and large variation of these traits was observed under drought stress in the natural population. A genome-wide association study (GWAS) of i-traits and traditional DR traits identified 470 association loci, some containing known DR-related genes. Of these 470 loci, 443 loci (94%) were identified using i-traits, 437 loci (93%) co-localized with previously reported DR-related quantitative trait loci, and 313 loci (66.6%) were reproducibly identified by GWAS in different years. Association networks, established based on GWAS results, revealed hub i-traits and hub loci. This demonstrates the feasibility and necessity of dissecting the complex DR trait into heritable and simple i-traits. As proof of principle, we illustrated the power of this integrated approach to identify previously unreported DR-related genes. OsPP15 was associated with a hub i-trait, and its role in DR was confirmed by genetic transformation experiments. Furthermore, i-traits can be used for DR linkage analyses, and 69 i-trait locus associations were identified by both GWAS and linkage analysis of a recombinant inbred line population. Finally, we confirmed the relevance of i-traits to DR in the field. Our study provides a promising novel approach for the genetic dissection and discovery of causal genes for DR.

Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]

Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.

SELENOPROTEIN O is a chloroplast protein involved in ROS scavenging and its absence increases dehydration tolerance in Arabidopsis thaliana

The evolutionary conserved family of Selenoproteins performs redox-regulatory functions in bacteria, archaea and eukaryotes. Among them, members of the SELENOPROTEIN O (SELO) subfamily are located in mammalian and yeast mitochondria, but their functions are thus far enigmatic. Screening of T-DNA knockout mutants for resistance to the proline analogue thioproline (T4C), identified mutant alleles of the plant SELO homologue in Arabidopsis thaliana. Absence of SELO resulted in a stress-induced transcriptional activation instead of silencing of mitochondrial proline dehydrogenase, and also high elevation of Δ(1)-pyrroline-5-carboxylate dehydrogenase involved in degradation of proline, thereby alleviating T4C inhibition and lessening drought-induced proline accumulation. Unlike its animal homologues, SELO was localized to chloroplasts of plants ectopically expressing SELO-GFP. The protein was co-fractionated with thylakoid membrane complexes, and co-immunoprecipitated with FNR, PGRL1 and STN7, all involved in regulating PSI and downstream electron flow. The selo mutants displayed extended survival under dehydration, accompanied by longer photosynthetic activity, compared with wild-type plants. Enhanced expression of genes encoding ROS scavenging enzymes in the unstressed selo mutant correlated with higher oxidant scavenging capacity and reduced methyl viologen damage. The study elucidates SELO as a PSI-related component involved in regulating ROS levels and stress responses.

Genetic Components of Root Architecture Remodeling in Response to Salt Stress

Salinity of the soil is highly detrimental to plant growth. Plants respond by a redistribution of root mass between main and lateral roots, yet the genetic machinery underlying this process is still largely unknown. Here, we describe the natural variation among 347 Arabidopsis thaliana accessions in root system architecture (RSA) and identify the traits with highest natural variation in their response to salt. Salt-induced changes in RSA were associated with 100 genetic loci using genome-wide association studies. Two candidate loci associated with lateral root development were validated and further investigated. Changes in CYP79B2 expression in salt stress positively correlated with lateral root development in accessions, and cyp79b2 cyp79b3 double mutants developed fewer and shorter lateral roots under salt stress, but not in control conditions. By contrast, high HKT1 expression in the root repressed lateral root development, which could be partially rescued by addition of potassium. The collected data and multivariate analysis of multiple RSA traits, available through the Salt_NV_Root App, capture root responses to salinity. Together, our results provide a better understanding of effective RSA remodeling responses, and the genetic components involved, for plant performance in stress conditions.

Twenty-Five Years of Investigating the Universal Stress Protein: Function, Structure, and Applications

Since the initial discovery of universal stress protein A (UspA) 25 years ago, remarkable advances in molecular and biochemical technologies have revolutionized our understanding of biology. Many studies using these technologies have focused on characterization of the uspA gene and Usp-type proteins. These studies have identified the conservation of Usp-like proteins across bacteria, archaea, plants, and even some invertebrate animals. Regulation of these proteins under diverse stresses has been associated with different stress-response genes including spoT and relA in the stringent response and the dosR two-component signaling pathways. These and other foundational studies suggest Usps serve regulatory and protective roles to enable adaptation and survival under external stresses. Despite these foundational studies, many bacterial species have multiple paralogs of genes encoding these proteins and ablation of the genes does not provide a distinct phenotype. This outcome has limited our understanding of the biochemical functions of these proteins. Here, we summarize the current knowledge of Usps in general and UspA in particular across different genera as well as conclusions about their functions from seminal studies in diverse organisms. Our objective has been to organize the foundational studies in this field to identify the significant impediments to further understanding of Usp functions at the molecular level. We propose ideas and experimental approaches that may overcome these impediments and drive future development of molecular approaches to understand and target Usps as central regulators of stress adaptation and survival. Despite the fact that the full functions of Usps are still not known, creative many applications have already been proposed, tested, and used. The complementary approaches of basic research and applications, along with new technology and analytic tools, may yield the elusive yet critical functions of universal stress proteins in diverse systems.

Natural variation identifies genes affecting drought-induced abscisic acid accumulation in Arabidopsis thaliana

Accumulation of the stress hormone abscisic acid (ABA) in response to drought and low water-potential controls many downstream acclimation mechanisms. However, mechanisms controlling ABA accumulation itself are less known. There was a 10-fold range of variation in ABA levels among nearly 300 Arabidopsis thaliana accessions exposed to the same low water-potential severity. Genome-wide association analysis (GWAS) identified genomic regions containing clusters of ABA-associated SNPs. Candidate genes within these regions included few genes with known stress or ABA-related function. The GWAS data were used to guide reverse genetic analysis, which found effectors of ABA accumulation. These included plasma-membrane-localized signaling proteins such as receptor-like kinases, aspartic protease, a putative lipid-binding START domain protein, and other membrane proteins of unknown function as well as a RING U-box protein and possible effect of tonoplast transport on ABA accumulation. Putative loss-of-function polymorphisms within the START domain protein were associated with climate factors at accession sites of origin, indicating its potential involvement in drought adaptation. Overall, using ABA accumulation as a basis for a combined GWAS-reverse genetic strategy revealed the broad natural variation in low-water-potential-induced ABA accumulation and was successful in identifying genes that affect ABA levels and may act in upstream drought-related sensing and signaling mechanisms. ABA effector loci were identified even when each one was of incremental effect, consistent with control of ABA accumulation being distributed among the many branches of ABA metabolism or mediated by genes with partially redundant function.

Genome-Wide Association Mapping Reveals That Specific and Pleiotropic Regulatory Mechanisms Fine-Tune Central Metabolism and Growth in Arabidopsis

Central metabolism is a coordinated network that is regulated at multiple levels by resource availability and by environmental and developmental cues. Its genetic architecture has been investigated by mapping metabolite quantitative trait loci (QTL). A more direct approach is to identify enzyme activity QTL, which distinguishes between cis-QTL in structural genes encoding enzymes and regulatory trans-QTL. Using genome-wide association studies, we mapped QTL for 24 enzyme activities, nine metabolites, three structural components, and biomass in Arabidopsis thaliana We detected strong cis-QTL for five enzyme activities. A cis-QTL for UDP-glucose pyrophosphorylase activity in the UGP1 promoter is maintained through balancing selection. Variation in acid invertase activity reflects multiple evolutionary events in the promoter and coding region of VAC-INVcis-QTL were also detected for ADP-glucose pyrophosphorylase, fumarase, and phosphoglucose isomerase activity. We detected many trans-QTL, including transcription factors, E3 ligases, protein targeting components, and protein kinases, and validated some by knockout analysis. trans-QTL are more frequent but tend to have smaller individual effects than cis-QTL. We detected many colocalized QTL, including a multitrait QTL on chromosome 4 that affects six enzyme activities, three metabolites, protein, and biomass. These traits are coordinately modified by different ACCELERATED CELL DEATH6 alleles, revealing a trade-off between metabolism and defense against biotic stress.

Multilevel Regulation of Abiotic Stress Responses in Plants

The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.