Relationship of leaf oxygen and carbon isotopic composition with transpiration efficiency in the C4 grasses Setaria viridis and Setaria italica

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C₄ photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.

The genetic architecture of leaf stable carbon isotope composition in Zea mays and the effect of transpiration efficiency on leaf elemental accumulation

With increased demand on freshwater resources for agriculture, it is imperative that more water-use efficient crops are developed. Leaf stable carbon isotope composition, δ13C, is a proxy for transpiration efficiency and a possible tool for breeders, but the underlying mechanisms effecting δ13C in C4 plants are not known. It has been suggested that differences in specific leaf area (SLA), which potentially reflects variation in internal CO2 diffusion, can impact leaf δ13C. Furthermore, although it is known that water movement is important for elemental uptake, it is not clear how manipulation of transpiration for increased water-use efficiency may impact nutrient accumulation. Here, we characterize the genetic architecture of leaf δ13C and test its relationship to SLA and the ionome in five populations of maize. Five significant QTL for leaf δ13C were identified, including novel QTL as well as some that were identified previously in maize kernels. One of the QTL regions contains an Erecta-like gene, the ortholog of which has been shown to regulate transpiration efficiency and leaf δ13C in Arabidopsis. QTL for δ13C were located in the same general chromosome region, but slightly shifted, when comparing data from two different years. Our data does not support a relationship between δ13C and SLA, and of the 19 elements analyzed, only a weak correlation between molybdenum and δ13C was detected. Together these data add to the genetic understanding of leaf δ13C in maize and suggest that improvements to plant water use may be possible without significantly influencing elemental homeostasis.

The carbon isotopic signature of C4 crops and its applicability in breeding for climate resilience

KEY MESSAGE

Carbon isotope discrimination is a promising trait for indirect screening for improved water use efficiency of C4 crops. In the context of a changing climate, drought is one of the major factors limiting plant growth and yield. Hence, breeding efforts are directed toward improving water use efficiency (WUE) as a key factor in climate resilience and sustainability of crop production. As WUE is a complex trait and its evaluation is rather resource consuming, proxy traits, which are easier to screen and reliably reflect variation in WUE, are needed. In C3 crops, a trait established to be indicative for WUE is the carbon isotopic composition (δ13C) of plant material, which reflects the preferential assimilation of the lighter carbon isotope 12C over 13C during photosynthesis. In C4 crops, carbon fixation is more complex and δ13C thus depends on many more factors than in C3 crops. Recent physiological and genetic studies indicate a correlation between δ13C and WUE also in C4 crops, as well as a colocalization of quantitative trait loci for the two traits. Moreover, significant intraspecific variation as well as a medium to high heritability of δ13C has been shown in some of the main C4 crops, such as maize, sorghum and sugarcane, indicating its potential for indirect selection and breeding. Further research on physiological, genetic and environmental components influencing δ13C is needed to support its application in improving WUE and making C4 crops resilient to climate change.

Combination of Stable Isotope Analysis and Chemometrics to Discriminate Geoclimatically and Temporally the Virgin Olive Oils from Three Mediterranean Countries

The knowledge of the isotopic composition of virgin olive oil (VOO) allows the evaluation of authenticity and geographical origin, being an important tool against fraud. This study aimed to assess if VOOs produced in three Mediterranean regions could be discriminated on the basis of multivariate statistical analysis of geoclimatic and isotopic data. A total of 138 geo-referenced VOO samples from Portugal, France and Turkey from two different cultivation years were collected. The isotopic composition (δ13C, δ2H and δ18O) of VOOs was obtained using an elemental analyzer coupled to an isotope ratio mass spectrometer (EA-IRMS). One-way analysis of variance for δ13C, δ2H and δ18O showed some significant differences either between crop years or geoclimatic conditions. Based on multiple regression analyses using meteorological and geographical parameters, a meteoric water line for olive oil from Portugal, France and Turkey, in two harvest years, were created to assess the impact of climate change on their δ2H and δ18O values. Principal component analysis and Linear Discriminant Analysis, used to sort samples according to geoclimatic origin, performed best for French and Portuguese olive oils. In light of the results, multivariate isotopic analysis of VOO samples may discriminate not only between geoclimatic regions but also among cultivation years.

Mesophyll CO2 conductance and leakiness are not responsive to short- and long-term soil water limitations in the C4 plant Sorghum bicolor

Breeding economically important C₄ crops for enhanced whole-plant water-use efficiency (WUE_plant ) is needed for sustainable agriculture. WUE_plant is a complex trait and an efficient phenotyping method that reports on components of WUE_plant , such as intrinsic water-use efficiency (WUE_i , the rate of leaf CO₂ assimilation relative to water loss via stomatal conductance), is needed. In C₄ plants, theoretical models suggest that leaf carbon isotope composition (δ¹³ C), when the efficiency of the CO₂ -concentrating mechanism (leakiness, ϕ) remains constant, can be used to screen for WUE_i . The limited information about how ϕ responds to water limitations confines the application of δ¹³ C for WUE_i screening of C₄ crops. The current research aimed to test the response of ϕ to short- or long-term moderate water limitations, and the relationship of δ¹³ C with WUE_i and WUE_plant , by addressing potential mesophyll CO₂ conductance (g_m ) and biochemical limitations in the C₄ plant Sorghum bicolor. We demonstrate that g_m and ϕ are not responsive to short- or long-term water limitations. Additionally, δ¹³ C was not correlated with gas-exchange estimates of WUE_i under short- and long-term water limitations, but showed a significant negative relationship with WUE_plant . The observed association between the δ¹³ C and WUE_plant suggests an intrinsic link of δ¹³ C with WUE_i in this C₄ plant, and can potentially be used as a screening tool for WUE_plant in sorghum.

A genetic link between leaf carbon isotope composition and whole-plant water use efficiency in the C4 grass Setaria

Genetic selection for whole-plant water use efficiency (yield per transpiration; WUE_plant ) in any crop-breeding programme requires high-throughput phenotyping of component traits of WUE_plant such as intrinsic water use efficiency (WUE_i ; CO₂ assimilation rate per stomatal conductance). Measuring WUE_i by gas exchange measurements is laborious and time consuming and may not reflect an integrated WUE_i over the life of the leaf. Alternatively, leaf carbon stable isotope composition (δ¹³ C_leaf ) has been suggested as a potential time-integrated proxy for WUE_i that may provide a tool to screen for WUE_plant . However, a genetic link between δ¹³ C_leaf and WUE_plant in a C₄ species has not been well established. Therefore, to determine if there is a genetic relationship in a C₄ plant between δ¹³ C_leaf and WUE_plant under well watered and water-limited growth conditions, a high-throughput phenotyping facility was used to measure WUE_plant in a recombinant inbred line (RIL) population created between the C₄ grasses Setaria viridis and S. italica. Three quantitative trait loci (QTL) for δ¹³ C_leaf were found and co-localized with transpiration, biomass accumulation, and WUE_plant . Additionally, WUE_plant for each of the δ¹³ C_leaf QTL allele classes was negatively correlated with δ¹³ C_leaf , as would be predicted when WUE_i influences WUE_plant . These results demonstrate that δ¹³ C_leaf is genetically linked to WUE_plant , likely to be through their relationship with WUE_i , and can be used as a high-throughput proxy to screen for WUE_plant in these C₄ species.

Similar potential of foliar δ13C and silicon levels for inferring local climate information in the Tibetan Plateau region

Stable carbon isotope ratios (δ¹³C) are widely used as climate proxies for assessing and predicting climatic information at an annual resolution. However, the detailed information in the isotopes that results from intra-annual climate scenarios and is associated with mineral accumulation remains unclear. Combined with investigations of elements and ash contents, variations in foliar δ¹³C in relation to annual, winter and summer climate scenarios were investigated in a dendroclimatologically important tree species Sabina przewalskii Kom. Foliar δ¹³C exhibited a significant negative correlation with mean annual temperature, mean annual precipitation and mean annual relative humidity as well as significant positive correlations with elevation. Climatic factors in winter and summer have opposite effects on the variation of δ¹³C. The beneficial mineral element Si had a significant positive correlation with foliar δ¹³C, whereas the essential mineral elements K, Ca, and Mg did not. Specifically, Si and δ¹³C have similar correlations with climate factors and elevation. These results suggest that measurement of Si content has a similar potential to δ¹³C for use as an alternative climate indicator when detailed climatic information may otherwise be limited and provide a basis for understanding the integration of δ¹³C in plant responses to climate.

Leaf Gas Exchange, Plant Water Relations and Water Use Efficiency of Vigna Unguiculata L. Walp. Inoculated with Rhizobia under Different Soil Water Regimes

Impact of soil water regimes on physiological responses and water use efficiency (WUE) for Vigna unguiculata L. Walp. (cowpea) inoculated with rhizobia still remains implicit. Therefore, the goal of the current study was to examine the leaf gas exchange, abscisic acid (ABA) and hydraulic signaling, WUE and carbon and oxygen isotopic compositions (δ13C and δ18O) of cowpea under different soil water levels. The treatments included soil water regimes at three levels (90%, 70%, and 50% of soil water holding capacity (SWHC)) and two inoculation forms (inoculated and non-inoculated with rhizobia). The results showed that across the inoculation treatments, reduced soil water regimes depressed both stomatal conductance (gs) and photosynthesis (An) of the leaves, nonetheless, the decrease of gs was more pronounced compared with the reduction in An. Consequently, the intrinsic water use efficiency (WUEi) was improved in the treatments under decreased soil water conditions. Plant WUE was also improved when soil water contents decreased as exemplified by the increased leaf δ13C and δ18O, indicating the enhanced plant WUE was mainly attributed to the decrease of gs. Significant interactions between soil water regimes and rhizobia treatments for root water potential (RWP), leaf water potential (LWP), and gs were found due to the different responses of rhizobia to varied soil water regimes. Inoculation could improve plant water status and gs under 70% and 90% SWHC compared to 50% SWHC with negative effect from rhizobia. A moderate soil water regime is suggested for cowpea production in terms of high WUE with a minor biomass reduction.

Leaf stable carbon isotope composition reflects transpiration efficiency in Zea mays

The increasing demand for food production and predicted climate change scenarios highlight the need for improvements in crop sustainability. The efficient use of water will become increasingly important for rain-fed agricultural crops even in fertile regions that have historically received ample precipitation. Improvements in water-use efficiency in Zea mays have been limited, and warrant a renewed effort aided by molecular breeding approaches. Progress has been constrained by the difficulty of measuring water-use in a field environment. The stable carbon isotope composition (δ¹³ C) of the leaf has been proposed as an integrated signature of carbon fixation with a link to stomatal conductance. However, additional factors affecting leaf δ¹³ C exist, and a limited number of studies have explored this trait in Z. mays. Here we present an extensive characterization of leaf δ¹³ C in Z. mays. Significant variation in leaf δ¹³ C exists across diverse lines of Z. mays, which we show to be heritable across several environments. Furthermore, we examine temporal and spatial variation in leaf δ¹³ C to determine the optimum sampling time to maximize the use of leaf δ¹³ C as a trait. Finally, our results demonstrate the relationship between transpiration and leaf δ¹³ C in the field and the greenhouse. Decreasing transpiration and soil moisture are associated with decreasing leaf δ¹³ C. Taken together these results outline a strategy for using leaf δ¹³ C and reveal its usefulness as a measure of transpiration efficiency under well-watered conditions rather than a predictor of performance under drought.

Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C4 Grass Setaria

Plant growth and water use are interrelated processes influenced by genetically controlled morphological and biochemical characteristics. Improving plant water use efficiency (WUE) to sustain growth in different environments is an important breeding objective that can improve crop yields and enhance agricultural sustainability. However, genetic improvement of WUE using traditional methods has proven difficult due to the low throughput and environmental heterogeneity of field settings. To overcome these limitations, this study utilizes a high-throughput phenotyping platform to quantify plant size and water use of an interspecific Setaria italica × Setaria viridis recombinant inbred line population at daily intervals in both well-watered and water-limited conditions. Our findings indicate that measurements of plant size and water use are correlated strongly in this system; therefore, a linear modeling approach was used to partition this relationship into predicted values of plant size given water use and deviations from this relationship at the genotype level. The resulting traits describing plant size, water use, and WUE all were heritable and responsive to soil water availability, allowing for a genetic dissection of the components of plant WUE under different watering treatments. Linkage mapping identified major loci underlying two different pleiotropic components of WUE. This study indicates that alleles controlling WUE derived from both wild and domesticated accessions can be utilized to predictably modulate trait values given a specified precipitation regime in the model C4 genus Setaria.