Identification of functional genetic variations underlying drought tolerance in maize using SNP markers

Single nucleotide polymorphism (SNP) is a common form of genetic variation and popularly exists in maize genome. An Illumina GoldenGate assay with 1 536 SNP markers was used to genotype maize inbred lines and identified the functional genetic variations underlying drought tolerance by association analysis. Across 80 lines, 1 006 polymorphic SNPs (65.5% of the total) in the assay with good call quality were used to estimate the pattern of genetic diversity, population structure, and familial relatedness. The analysis showed the best number of fixed subgroups was six, which was consistent with their original sources and results using only simple sequence repeat markers. Pairwise linkage disequilibrium (LD) and association mapping with phenotypic traits investigated under water-stressed and well-watered regimes showed rapid LD decline within 100-500 kb along the physical distance of each chromosome, and that 29 SNPs were associated with at least two phenotypic traits in one or more environments, which were related to drought-tolerant or drought-responsive genes. These drought-tolerant SNPs could be converted into functional markers and then used for maize improvement by marker-assisted selection.     

Genetic variation in ZmTIP1 contributes to root hair elongation and drought tolerance in maize

Drought is a major abiotic stress that threatens maize production globally. A previous genome‐wide association study identified a significant association between the natural variation of ZmTIP1 and the drought tolerance of maize seedlings. Here, we report on comprehensive genetic and functional analysis, indicating that ZmTIP1, which encodes a functional S‐acyltransferase, plays a positive role in regulating the length of root hairs and the level of drought tolerance in maize. We show that enhancing ZmTIP1 expression in transgenic Arabidopsis and maize increased root hair length, as well as plant tolerance to water deficit. In contrast, ZmTIP1 transposon‐insertional mutants displayed the opposite phenotype. A calcium‐dependent protein kinase, ZmCPK9, was identified as a substrate protein of ZmTIP1, and ZmTIP1‐mediated palmitoylation of two cysteine residues facilitated the ZmCPK9 PM association. The results of this research enrich our knowledge about ZmTIP1‐mediated protein S‐acylation modifications in relation to the regulation of root hair elongation and drought tolerance. Additionally, the identification of a favourable allele of ZmTIP1 also provides a valuable genetic resource or selection target for the genetic improvement of maize.     

Two consensus quantitative trait loci clusters controlling anthesis–silking interval, ear setting and grain yield might be related with drought tolerance in maize

Unravelling the molecular basis of drought tolerance will provide novel opportunities for improving crop yield under water-limited conditions. The present study was conducted to identify quantitative trait loci (QTLs) controlling anthesis–silking interval (ASI), ear setting percentage (ESP) and grain yield (GY). The mapping population included 234 F₂ plants derived from the cross X178 (drought tolerant) × B73 (drought susceptible). The corresponding F_2:3 progenies, along with their parents, were evaluated for the above-mentioned traits under both well-watered and water-stressed field conditions in three different trials carried out in central and southern China. Interval mapping and composite interval mapping identified 45 and 65 QTLs for the investigated traits, respectively. Two QTL clusters influencing ASI and ESP on chromosomes 1 (bin 1.03) and 9 (bins 9.03–9.05) were identified in more than two environments, showing sizeable additive effects and contribution to phenotypic variance; these two QTL clusters influenced GY only in one environment. No significant interaction was detected between the two genomic regions. A comparative analysis of these two QTL clusters with the QTLs controlling maize drought tolerance previously described in three mapping populations confirmed and extended their relevance for marker-assisted breeding to improve maize production under water-limited conditions.     

Identification of genetic variants associated with maize flowering time using an extremely large multi‐genetic background population

Flowering time is one of the major adaptive traits in domestication of maize and an important selection criterion in breeding. To detect more maize flowering time variants we evaluated flowering time traits using an extremely large multi‐ genetic background population that contained more than 8000 lines under multiple Sino‐United States environments. The population included two nested association mapping (NAM) panels and a natural association panel. Nearly 1 million single‐nucleotide polymorphisms (SNPs) were used in the analyses. Through the parallel linkage analysis of the two NAM panels, both common and unique flowering time regions were detected. Genome wide, a total of 90 flowering time regions were identified. One‐third of these regions were connected to traits associated with the environmental sensitivity of maize flowering time. The genome‐wide association study of the three panels identified nearly 1000 flowering time‐associated SNPs, mainly distributed around 220 candidate genes (within a distance of 1 Mb). Interestingly, two types of regions were significantly enriched for these associated SNPs – one was the candidate gene regions and the other was the approximately 5 kb regions away from the candidate genes. Moreover, the associated SNPs exhibited high accuracy for predicting flowering time.     

Reflectance and biochemical responses of maize plants to drought and re‐watering cycles

The ability to recover from drought stress after re‐watering is an important feature that will enable plants to cope with the predicted increase in episodic drought. The effects of pre‐drought and re‐watering conditions on leaf spectral properties and their relationships with the biochemical processes that underlie the recovery from pre‐drought conditions should be better understood. The reflectance spectra, 10 spectral reflectance indices (SRIs) and biochemical characteristics of maize (Zea mays) leaves were monitored 7, 14, 21 and 28 days after the initiation of soil drought stress during two successive cycles of drought and re‐watering periods. The leaf reflectance of the two inbred maize lines increased under the drought stress, especially in the visible spectral range. In addition, an obvious recovery of the leaf reflectance was only observed in the first re‐watering period, and its value remained higher than that of the control plants during the second recovery period. A recovery lag in the pigment contents was also observed during the second cycle. The recovery variations in the pattern and magnitude of the SRIs and the total contents of C, N and P that were measured in response to the re‐watering during both cycles were diverse and complex; both full and partial recoveries were observed. The SRIs representing different physiological attributes of plant growth, including the water index, red edge position, photochemical reflectance index and near‐infrared reflectance at 800 nm, showed strong linear relationships (P < 0.01 or 0.05) with the growth and biochemical traits across the successive drought and re‐watering cycles. The results suggest that maize plants can adjust their leaf reflectance properties and employ growth and biochemical strategies to adapt to cyclic drought stress and recover from drought stress after re‐watering.     

Microarray analysis reveals the changes of circular RNA expression and molecular mechanism in acute lung injury mouse model

Acute lung injury (ALI) is a severe disease with sudden onset, rapid progression, poor treatment response, and high mortality. An increasing number of studies had found that circular RNAs (circRNAs) has significant functions in various diseases, while the role of circRNAs in ALI is not yet clear. The purpose of this study was to find circRNAs related to ALI and their mechanism of action. Expression profiles of lung circRNAs and messenger RNAs (mRNAs) were analyzed by microarray in the ALI mice models and healthy controlled mice. Differentially expressed RNAs were identified, function and pathways were analyzed by bioinformatics analysis. Moreover, the results of the microarray were verified by real-time PCR. We identified 2262 differentially expressed mRNAs and 581 circRNAs between ALI mice and control. Validation of candidate circRNAs by real-time PCR indicates that the majority of circRNAs identified by microarray are reliable and worthy of further study. ALI induced circRNAs primarily function in the metabolic regulatory process. Moreover, differentially expressed circRNAs were mainly involved in signaling pathways of mitogen-activated protein kinases, focal adhesion, FoxO, neurotrophin, and Wnt. In addition, a competitive endogenous RNA network was constructed to further interpret the molecular mechanism of ALI. This study observed significantly changed circRNAs profiles in LPS-induced mouse model and revealed a potential role of circRNAs in ALI.     

Two calcium-dependent protein kinases enhance maize drought tolerance by activating anion channel ZmSLAC1 in guard cells

Stomatal closure is an important process to prevent water loss in plants response to drought stress, which is finely modulated by ion channels together with their regulators in guard cells, especially the S-type anion channel AtSLAC1 in Arabidopsis. However, the functional characterization and regulation analyses of anion channels in gramineous crops, such as in maize guard cells are still limited. In this study, we identified an S-type anion channel ZmSLAC1 that was preferentially expressed in maize guard cells and involved in stomatal closure under drought stress. We found that two Ca²⁺-dependent protein kinases ZmCPK35 and ZmCPK37 were expressed in maize guard cells and localized on the plasma membrane. Lesion of ZmCPK37 resulted in drought-sensitive phenotypes. Mutation of ZmSLAC1 and ZmCPK37 impaired ABA-activated S-type anion currents in maize guard cells, while the S-type anion currents were increased in the guard cells of ZmCPK35- and ZmCPK37-overexpression lines. Electrophysiological characterization in maize guard cells and Xenopus oocytes indicated that ZmCPK35 and ZmCPK37 could activate ZmSLAC1-mediated Cl^- and NO₃^- currents. The maize inbred and hybrid lines overexpressing ZmCPK35 and ZmCPK37 exhibited enhanced tolerance and increased yield under drought conditions. In conclusion, our results demonstrate that ZmSLAC1 plays crucial roles in stomatal closure in maize, whose activity is regulated by ZmCPK35 and ZmCPK37. Elevation of ZmCPK35 and ZmCPK37 expression levels is a feasible way to improve maize drought tolerance as well as reduce yield loss under drought stress.     

Ride to cell wall: Arabidopsis XTH11, XTH29 and XTH33 exhibit different secretion pathways and responses to heat and drought stress

The xyloglucan endotransglucosylase/hydrolases (XTHs) are enzymes involved in cell wall assembly and growth regulation, cleaving and re-joining hemicellulose chains in the xyloglucan–cellulose network. Here, in a homologous system, we compare the secretion patterns of XTH11, XTH33 and XTH29, three members of the Arabidopsis thaliana XTH family, selected for the presence (XTH11 and XTH33) or absence (XTH29) of a signal peptide, and the presence of a transmembrane domain (XTH33). We show that XTH11 and XTH33 reached, respectively, the cell wall and plasma membrane through a conventional protein secretion (CPS) pathway, whereas XTH29 moves towards the apoplast following an unconventional protein secretion (UPS) mediated by exocyst-positive organelles (EXPOs). All XTHs share a common C-terminal functional domain (XET-C) that, for XTH29 and a restricted number of other XTHs (27, 28 and 30), continues with an extraterminal region (ETR) of 45 amino acids. We suggest that this region is necessary for the correct cell wall targeting of XTH29, as the ETR-truncated protein never reaches its final destination and is not recruited by EXPOs. Furthermore, quantitative real-time polymerase chain reaction analyses performed on 4-week-old Arabidopsis seedlings exposed to drought and heat stress suggest a different involvement of the three XTHs in cell wall remodeling under abiotic stress, evidencing stress-, organ- and time-dependent variations in the expression levels. Significantly, XTH29, codifying the only XTH that follows a UPS pathway, is highly upregulated with respect to XTH11 and XTH33, which code for CPS-secreted proteins.     

Effects of moderate drought on ascorbate peroxidase and glutathione reductase activities in mesophyll and bundle sheath cells of maize

Mesophyll and bundle sheath cells of maize leaves ( Zea mays L.) both contain the enzymes ascorbate peroxidase (AP; EC 1.11.1.11) and glutathione reductase (GR; EC 1.6.4.2) which are involved in hydrogen peroxide detoxification. Since bundle sheath cells of maize are deficient in photosystem II and have high CO₂ levels, oxidative stress may be less severe in these cells than in mesophyll cells. The present study was conducted to determine if AP and GR activity levels preferentially increase in mesophyll cells relative to bundle sheath cells when plants are subjected to moderate drought. Although drought inhibited the growth of greenhouse-grown plants, it did not affect the levels of protein, chlorophyll or AP. GR was unaffected by drought in whole leaf tissue and mesophyll cells, but did increase slightly in bundle sheath cells. This slight increase is of questionable biological importance. AP and GR activity levels were similar in mesophyll cells, bundle sheath cells and in whole leaf tissue. The data suggest that moderate drought has little effect on enzymes of the hydrogen peroxide scavenging system and that mesophyll and bundle sheath cells may be exposed to similar levels of hydrogen peroxide.     

UPLC‐HRMS‐based untargeted metabolic profiling reveals changes in chickpea (Cicer arietinum) metabolome following long‐term drought stress

Genetic improvement for drought tolerance in chickpea requires a solid understanding of biochemical processes involved with different physiological mechanisms. The objective of this study is to demonstrate genetic variations in altered metabolic levels in chickpea varieties (tolerant and sensitive) grown under contrasting water regimes through ultrahigh‐performance liquid chromatography/high‐resolution mass spectrometry‐based untargeted metabolomic profiling. Chickpea plants were exposed to drought stress at the 3‐leaf stage for 25 days, and the leaves were harvested at 14 and 25 days after the imposition of drought stress. Stress produced significant reduction in chlorophyll content, F_v/F_m, relative water content, and shoot and root dry weight. Twenty known metabolites were identified as most important by 2 different methods including significant analysis of metabolites and partial least squares discriminant analysis. The most pronounced increase in accumulation due to drought stress was demonstrated for allantoin, l ‐proline, l ‐arginine, l ‐histidine, l ‐isoleucine, and tryptophan. Metabolites that showed a decreased level of accumulation under drought conditions were choline, phenylalanine, gamma‐aminobutyric acid, alanine, phenylalanine, tyrosine, glucosamine, guanine, and aspartic acid. Aminoacyl‐tRNA and plant secondary metabolite biosynthesis and amino acid metabolism or synthesis pathways were involved in producing genetic variation under drought conditions. Metabolic changes in light of drought conditions highlighted pools of metabolites that affect the metabolic and physiological adjustment in chickpea that reduced drought impacts.     

Genetic and molecular approaches to the study of the anaerobic response and tissue specific gene expression in maize

Abstract. Plant gene expression is regulated during development and in response to environmental stimuli. For example, the pattern of gene expression in roots changes dramatically when seedlings are placed under low oxygen conditions. Roots respond to anaerobiosis by increasing cytosolic-glycolytic enzyme activity. Through the use of genetic and molecular techniques we have begun to characterize the differential expression of isozymes which show increased synthesis under anaerobic conditions and tissue specific expression during plant development.     

Oxygen isotope enrichment (Δ18O) reflects yield potential and drought resistance in maize

Measurement of stable isotopes in plant dry matter is a useful phenotypic tool for speeding up breeding advance in C₃ crops exposed to different water regimes. However, the situation in C₄ crops is far from resolved, since their photosynthetic metabolism precludes (at least in maize) the use of carbon isotope discrimination. This paper investigates the use of oxygen isotope enrichment (Δ¹⁸O) as a new secondary trait for yield potential and drought resistance in maize ( Zea mays L). A set of tropical maize hybrids developed by the International Maize and Wheat Improvement Center was grown under three contrasting water regimes in field conditions. Water regimes clearly affected plant growth and yield. In accordance with the current theory, a decrease in water input was translated into large decreases in stomatal conductance and increases in leaf temperature together with concomitant ¹⁸O enrichment of plant matter (leaves and kernels). In addition, kernel Δ¹⁸O correlated negatively with grain yield under well-watered and intermediate water stress conditions, while it correlated positively under severe water stress conditions. Therefore, genotypes showing lower kernel Δ¹⁸O under well-watered and intermediate water stress had higher yields in these environments, while the opposite trend was found under severe water stress conditions. This illustrates the usefulness of Δ¹⁸O for selecting the genotypes best suited to differing water conditions.     

European and African maize cultivars differ in their physiological and molecular responses to mycorrhizal infection

Physiological and molecular responses to phosphorus (P) supply and mycorrhizal infection by Glomus intraradices were compared in European (River) and African (H511) maize (Zea mays) cultivars to examine the extent to which these responses differed between plants developed for use in high- and low-nutrient-input agricultural systems. Biomass, photosynthetic rates, nutrient and carbohydrate contents, mycorrhizal colonization and nutrient-responsive phosphate transporter gene expression were measured in nonmycorrhizal and mycorrhizal plants grown at different inorganic phosphorus (P(i)) supply rates. Nonmycorrhizal River plants grew poorly at low P(i) but were highly responsive to mycorrhizal infection; there were large increases in biomass, tissue P content and the rate of photosynthesis and a decline in the expression of phosphate transporter genes. Nonmycorrhizal H511 plants grew better than River plants at low P(i), and had a higher root : shoot ratio. However, the responses of H511 plants to higher P(i) supplies and mycorrhizal infection were much more limited than those of River plants. The adaptations that allowed nonmycorrhizal H511 plants to perform well in low-P soils limited their ability to respond to higher nutrient supply rates and mycorrhizal infection. The European variety had not lost the ability to respond to mycorrhizas and may have traits useful for low-nutrient agriculture where mycorrhizal symbioses are established.