Variation in key leaf photosynthetic traits across wheat wild relatives is accession dependent not species dependent

Physiological adaptation to irradiance in duckweeds is species and accession specific and depends on light habitat niche

Duckweeds span 36 species of free-floating aquatic organisms with body sizes ranging from 2 mm to 10 mm, where each plant body plan is reduced to a largely leaf-like structure. As an emerging crop, their fast growth rates offer potential for cultivation in closed systems. We describe a novel UK collection derived from low light (dLL) or high light (dHL) habitats, profiled for growth, photosynthesis, and photoprotection (non-photochemical quenching, NPQ) responses. Twenty-three accessions of three Lemna species and one Spirodela polyrhiza were grown under relatively low light (LL: 100 μmol m-2 s-1) and high light (HL: 350 μmol m-2 s-1) intensities. We observed broad within- and between-species level variation in photosynthesis acclimation. Duckweeds grown under HL exhibited a lower growth rate, biomass, chlorophyll, and quantum yield of photosynthesis. In HL compared with LL, carotenoid de-epoxidation state and NPQ were higher, whilst PSII efficiency (φPSII) and Chl a:b ratios were unchanged. The dLL plants showed relatively stronger acclimation to HL compared with dHL plants, especially Lemna japonica accessions. These achieved faster growth in HL with concurrent higher carotenoid levels and NPQ, and less degradation of chlorophyll. We conclude that these data support local adaptation to the light environment in duckweed affecting acclimation in controlled conditions.

The impact of growth at elevated [CO2] on stomatal anatomy and behavior differs between wheat species and cultivars

The ability of plants to respond to changes in the environment is crucial to their survival and reproductive success. The impact of increasing the atmospheric CO2 concentration (a[CO2]), mediated by behavioral and developmental responses of stomata, on crop performance remains a concern under all climate change scenarios, with potential impacts on future food security. To identify possible beneficial traits that could be exploited for future breeding, phenotypic variation in morphological traits including stomatal size and density, as well as physiological responses and, critically, the effect of growth [CO2] on these traits, was assessed in six wheat relative accessions (including Aegilops tauschii, Triticum turgidum ssp. Dicoccoides, and T. turgidum ssp. dicoccon) and five elite bread wheat T. aestivum cultivars. Exploiting a range of different species and ploidy, we identified key differences in photosynthetic capacity between elite hexaploid wheat and wheat relatives. We also report differences in the speed of stomatal responses which were found to be faster in wheat relatives than in elite cultivars, a trait that could be useful for enhanced photosynthetic carbon gain and water use efficiency. Furthermore, these traits do not all appear to be influenced by elevated [CO2], and determining the underlying genetics will be critical for future breeding programmes.

Mass screening of rice mutant populations at low CO2 for identification of lowered photorespiration and respiration rates

INTRODUCTION

Identifying rice (Oryza sativa) germplasm with improved efficiency of primary metabolism is of utmost importance in order to increase yields. One such approach can be attained through screening genetically diverse populations under altered environmental conditions. Growth or treatment under low carbon dioxide (CO₂) concentrations can be used as a means of revealing altered leaf photorespiration, respiration and other metabolic variants.

METHODS

We developed a pipeline for very high throughput treatment of gamma- and ethyl methanesulfonate- (EMS) induced mutant populations of IR64 rice seedlings at very low CO₂ for 7 days. 1050 seedlings per batch at 5^th leaf stage were exposed to 60 ppm CO₂ for the first day and 30 ppm for the remaining three days. Following this, putative candidates were identified by measuring chlorophyll depletion using SPAD. Screening results showed a distinct difference between the mutants and the WTs.

RESULTS AND DISCUSSION

The mean chlorophyll loss in WTs ranged from 65% to 11% respectively, whereas in the mutant lines chlorophyll loss ranged from 0 to 100%, suggesting considerable phenotypic variation. Rice mutants with a reduced chlorophyll reduction (<10%) were identified as 'Chlorophyll retention mutants' (CRMs) under low CO₂ stress. In total, 1909 mutant lines (14,000 seedlings) were screened for chlorophyll content under 30 ppm CO_2, with 26 lines selected for detailed screening. These 26 putative candidates were self-seeded to produce an M₅ generation, used to determine the genetic control of the altered response to low CO_2. Gas exchange of light and CO₂ response revealed that there were significant variations among photosynthetic properties in two selected rice mutants. The CO₂ compensation points in the absence of photorespiration and leaf respiration rates were lower than the WTs and anatomical analyses showed that CRM 29 had improved mesophyll cell area. We propose that this approach is useful for generating new material for breeding rice with improved primary metabolism.

Longer epidermal cells underlie a quantitative source of variation in wheat flag leaf size

The wheat flag leaf is the main contributor of photosynthetic assimilates to developing grains. Understanding how canopy architecture strategies affect source strength and yield will aid improved crop design. We used an eight-founder population to investigate the genetic architecture of flag leaf area, length, width and angle in European wheat. For the strongest genetic locus identified, we subsequently created a near-isogenic line (NIL) pair for more detailed investigation across seven test environments. Genetic control of traits investigated was highly polygenic, with colocalisation of replicated quantitative trait loci (QTL) for one or more traits identifying 24 loci. For QTL QFll.niab-5A.1 (FLL5A), development of a NIL pair found the FLL5A+ allele commonly conferred a c. 7% increase in flag and second leaf length and a more erect leaf angle, resulting in higher flag and/or second leaf area. Increased FLL5A-mediated flag leaf length was associated with: (1) longer pavement cells and (2) larger stomata at lower density, with a trend for decreased maximum stomatal conductance (G_smax ) per unit leaf area. For FLL5A, cell size rather than number predominantly determined leaf length. The observed trade-offs between leaf size and stomatal morphology highlight the need for future studies to consider these traits at the whole-leaf level.

A 'wiring diagram' for source strength traits impacting wheat yield potential

Source traits are currently of great interest for the enhancement of yield potential; for example, much effort is being expended to find ways of modifying photosynthesis. However, photosynthesis is but one component of crop regulation, so sink activities and the coordination of diverse processes throughout the crop must be considered in an integrated, systems approach. A set of 'wiring diagrams' has been devised as a visual tool to integrate the interactions of component processes at different stages of wheat development. They enable the roles of chloroplast, leaf, and whole-canopy processes to be seen in the context of sink development and crop growth as a whole. In this review, we dissect source traits both anatomically (foliar and non-foliar) and temporally (pre- and post-anthesis), and consider the evidence for their regulation at local and whole-plant/crop levels. We consider how the formation of a canopy creates challenges (self-occlusion) and opportunities (dynamic photosynthesis) for components of photosynthesis. Lastly, we discuss the regulation of source activity by feedback regulation. The review is written in the framework of the wiring diagrams which, as integrated descriptors of traits underpinning grain yield, are designed to provide a potential workspace for breeders and other crop scientists that, along with high-throughput and precision phenotyping data, genetics, and bioinformatics, will help build future dynamic models of trait and gene interactions to achieve yield gains in wheat and other field crops.

Genetics as a key to improving crop photosynthesis

Since the basic biochemical mechanisms of photosynthesis are remarkably conserved among plant species, genetic modification approaches have so far been the main route to improve the photosynthetic performance of crops. Yet, phenotypic variation observed in wild species and between varieties of crop species implies there is standing natural genetic variation for photosynthesis, offering a largely unexplored resource to use for breeding crops with improved photosynthesis and higher yields. The reason this has not yet been explored is that the variation probably involves thousands of genes, each contributing only a little to photosynthesis, making them hard to identify without proper phenotyping and genetic tools. This is changing, though, and increasingly studies report on quantitative trait loci for photosynthetic phenotypes. So far, hardly any of these quantitative trait loci have been used in marker assisted breeding or genomic selection approaches to improve crop photosynthesis and yield, and hardly ever have the underlying causal genes been identified. We propose to take the genetics of photosynthesis to a higher level, and identify the genes and alleles nature has used for millions of years to tune photosynthesis to be in line with local environmental conditions. We will need to determine the physiological function of the genes and alleles, and design novel strategies to use this knowledge to improve crop photosynthesis through conventional plant breeding, based on readily available crop plant germplasm. In this work, we present and discuss the genetic methods needed to reveal natural genetic variation, and elaborate on how to apply this to improve crop photosynthesis.

A model-guided holistic review of exploiting natural variation of photosynthesis traits in crop improvement

Breeding for improved leaf photosynthesis is considered as a viable approach to increase crop yield. Whether it should be improved in combination with other traits has not been assessed critically. Based on the quantitative crop model GECROS that interconnects various traits to crop productivity, we review natural variation in relevant traits, from biochemical aspects of leaf photosynthesis to morpho-physiological crop characteristics. While large phenotypic variations (sometimes >2-fold) for leaf photosynthesis and its underlying biochemical parameters were reported, few quantitative trait loci (QTL) were identified, accounting for a small percentage of phenotypic variation. More QTL were reported for sink size (that feeds back on photosynthesis) or morpho-physiological traits (that affect canopy productivity and duration), together explaining a much greater percentage of their phenotypic variation. Traits for both photosynthetic rate and sustaining it during grain filling were strongly related to nitrogen-related traits. Much of the molecular basis of known photosynthesis QTL thus resides in genes controlling photosynthesis indirectly. Simulation using GECROS demonstrated the overwhelming importance of electron transport parameters, compared with the maximum Rubisco activity that largely determines the commonly studied light-saturated photosynthetic rate. Exploiting photosynthetic natural variation might significantly improve crop yield if nitrogen uptake, sink capacity, and other morpho-physiological traits are co-selected synergistically.

Variation of Photosynthetic Induction in Major Horticultural Crops Is Mostly Driven by Differences in Stomatal Traits

Under natural conditions, irradiance frequently fluctuates, causing net photosynthesis rate (A) to respond slowly and reducing the yields. We quantified the genotypic variation of photosynthetic induction in 19 genotypes among the following six horticultural crops: basil, chrysanthemum, cucumber, lettuce, tomato, and rose. Kinetics of photosynthetic induction and the stomatal opening were measured by exposing shade-adapted leaves (50 μmol m-2 s-1) to a high irradiance (1000 μmol m-2 s-1) until A reached a steady state. Rubisco activation rate was estimated by the kinetics of carboxylation capacity, which was quantified using dynamic A vs. [CO2] curves. Generally, variations in photosynthetic induction kinetics were larger between crops and smaller between cultivars of the same crop. Time until reaching 20-90% of full A induction varied by 40-60% across genotypes, and this was driven by a variation in the stomatal opening rather than Rubisco activation kinetics. Stomatal conductance kinetics were partly determined by differences in the stomatal size and density; species with densely packed, smaller stomata (e.g., cucumber) tended to open their stomata faster, adapting stomatal conductance more rapidly and efficiently than species with larger but fewer stomata (e.g., chrysanthemum). We conclude that manipulating stomatal traits may speed up photosynthetic induction and growth of horticultural crops under natural irradiance fluctuations.

Progenitor species hold untapped diversity for potential climate-responsive traits for use in wheat breeding and crop improvement

Climate change will have numerous impacts on crop production worldwide necessitating a broadening of the germplasm base required to source and incorporate novel traits. Major variation exists in crop progenitor species for seasonal adaptation, photosynthetic characteristics, and root system architecture. Wheat is crucial for securing future food and nutrition security and its evolutionary history and progenitor diversity offer opportunities to mine favourable functional variation in the primary gene pool. Here we provide a review of the status of characterisation of wheat progenitor variation and the potential to use this knowledge to inform the use of variation in other cereal crops. Although significant knowledge of progenitor variation has been generated, we make recommendations for further work required to systematically characterise underlying genetics and physiological mechanisms and propose steps for effective use in breeding. This will enable targeted exploitation of useful variation, supported by the growing portfolio of genomics and accelerated breeding approaches. The knowledge and approaches generated are also likely to be useful across wider crop improvement.

Changes in root microbiome during wheat evolution

Background

Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.

Results

In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.

Conclusions

This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.

Advances in optical phenotyping of cereal crops

Optical sensors and sensing-based phenotyping techniques have become mainstream approaches in high-throughput phenotyping for improving trait selection and genetic gains in crops. We review recent progress and contemporary applications of optical sensing-based phenotyping (OSP) techniques in cereal crops and highlight optical sensing principles for spectral response and sensor specifications. Further, we group phenotypic traits determined by OSP into four categories - morphological, biochemical, physiological, and performance traits - and illustrate appropriate sensors for each extraction. In addition to the current status, we discuss the challenges of OSP and provide possible solutions. We propose that optical sensing-based traits need to be explored further, and that standardization of the language of phenotyping and worldwide collaboration between phenotyping researchers and other fields need to be established.

Photosynthesis research under climate change

Increasing global population and climate change uncertainties have compelled increased photosynthetic efficiency and yields to ensure food security over the coming decades. Potentially, genetic manipulation and minimization of carbon or energy losses can be ideal to boost photosynthetic efficiency or crop productivity. Despite significant efforts, limited success has been achieved. There is a need for thorough improvement in key photosynthetic limiting factors, such as stomatal conductance, mesophyll conductance, biochemical capacity combined with Rubisco, the Calvin-Benson cycle, thylakoid membrane electron transport, nonphotochemical quenching, and carbon metabolism or fixation pathways. In addition, the mechanistic basis for the enhancement in photosynthetic adaptation to environmental variables such as light intensity, temperature and elevated CO₂ requires further investigation. This review sheds light on strategies to improve plant photosynthesis by targeting these intrinsic photosynthetic limitations and external environmental factors.

The effect of canopy architecture on the patterning of "windflecks" within a wheat canopy

Under field conditions, plants are subject to wind-induced movement which creates fluctuations of light intensity and spectral quality reaching the leaves, defined here as windflecks. Within this study, irradiance within two contrasting wheat (Triticum aestivum) canopies during full sun conditions was measured using a spectroradiometer to determine the frequency, duration and magnitude of low- to high-light events plus the spectral composition during wind-induced movement. Similarly, a static canopy was modelled using three-dimensional reconstruction and ray tracing to determine fleck characteristics without the presence of wind. Corresponding architectural traits were measured manually and in silico including plant height, leaf area and angle plus biomechanical properties. Light intensity can differ up to 40% during a windfleck, with changes occurring on a sub-second scale compared to ~5 min in canopies not subject to wind. Features such as a shorter height, more erect leaf stature and having an open structure led to an increased frequency and reduced time interval of light flecks in the CMH79A canopy compared to Paragon. This finding illustrates the potential for architectural traits to be selected to improve the canopy light environment and provides the foundation to further explore the links between plant form and function in crop canopies.

Nocturnal stomatal conductance in wheat is growth-stage specific and shows genotypic variation

Nocturnal stomatal conductance (g_sn ) represents a significant source of water loss, with implications for metabolism, thermal regulation and water-use efficiency. With increasing nocturnal temperatures due to climate change, it is vital to identify and understand variation in the magnitude and responses of g_sn in major crops. We assessed interspecific variation in g_sn and daytime stomatal conductance (g_s ) in a wild relative and modern spring wheat genotype. To investigate intraspecific variation, we grew six modern wheat genotypes and two landraces under well watered, simulated field conditions. For the diurnal data, higher g_sn in the wild relative was associated with significantly lower nocturnal respiration and higher daytime CO₂ assimilation while both species exhibited declines in g_sn post-dusk and pre-dawn. Lifetime g_sn achieved rates of 5.7-18.9% of g_s . Magnitude of g_sn was genotype specific 'and positively correlated with g_s . g_sn and g_s were significantly higher on the adaxial surface. No relationship was determined between harvest characteristics, stomatal morphology and g_sn , while cuticular conductance was genotype specific. Finally, for the majority of genotypes, g_sn declined with age. Here we present the discovery that variation in g_sn occurs across developmental, morphological and temporal scales in nonstressed wheat, presenting opportunities for exploiting intrinsic variation under heat or water stressed conditions.

Targeted metabolite profiling as a top-down approach to uncover interspecies diversity and identify key conserved operational features in the Calvin-Benson cycle

Improving photosynthesis is a promising avenue to increase crop yield. This will be aided by better understanding of natural variance in photosynthesis. Profiling of Calvin-Benson cycle (CBC) metabolites provides a top-down strategy to uncover interspecies diversity in CBC operation. In a study of four C4 and five C3 species, principal components analysis separated C4 species from C3 species and also separated different C4 species. These separations were driven by metabolites that reflect known species differences in their biochemistry and pathways. Unexpectedly, there was also considerable diversity between the C3 species. Falling atmospheric CO2 and changing temperature, nitrogen, and water availability have driven evolution of C4 photosynthesis in multiple lineages. We propose that analogous selective pressures drove lineage-dependent evolution of the CBC in C3 species. Examples of species-dependent variation include differences in the balance between the CBC and the light reactions, and in the balance between regulated steps in the CBC. Metabolite profiles also reveal conserved features including inactivation of enzymes in low irradiance, and maintenance of CBC metabolites at relatively high levels in the absence of net CO2 fixation. These features may be important for photosynthetic efficiency in low light, fluctuating irradiance, and when stomata close due to low water availability.

Dynamics of photosynthetic induction and relaxation within the canopy of rice and two wild relatives

Wild rice species are a source of genetic material for improving cultivated rice (Oryza sativa) and a means to understand its evolutionary history. Renewed interest in non-steady-state photosynthesis in crops has taken place due its potential in improving sustainable productivity. Variation was characterized for photosynthetic induction and relaxation at two leaf canopy levels in three rice species. The wild rice accessions had 16%-40% higher rates of leaf CO2 uptake (A) during photosynthetic induction relative to the O. sativa accession. However, O. sativa had an overall higher photosynthetic capacity when compared to accessions of its wild progenitors. Additionally, O. sativa had a faster stomatal closing response, resulting in higher intrinsic water-use efficiency during high-to-low light transitions. Leaf position in the canopy had a significant effect on non-steady-state photosynthesis, but not steady-state photosynthesis. The results show potential to utilize wild material to refine plant models and improve non-steady-state photosynthesis in cultivated rice for increased productivity.