High-throughput phenotyping of seminal root traits in wheat

Comparative stress physiological analysis of aluminium stress tolerance of indigenous maize (Zea mays L.) cultivars of eastern Himalaya

Yield potential of maize having distinct genetic diversity in Eastern Himalayan Region (EHR) hill ecologies is often limited by Al toxicity caused due to soil acidity. Stress physiological analysis of local check exposed to 0-300 μM Al under sand culture revealed that 150 μM Al as critical and 200 μM Al as tolerable limit. Increase in Al from 0 to 300 μM reduced total chlorophyll, carotenoids by 74.8 % and 44.7 % respectively and enhanced anthocyanin by 35.3 % whereas LA, SLW and SL have reduced by 81.3%, 21.3 % and 47.8 % respectively. R/S ratio was 51.0 and 13.7 % higher at lower Al levels (50 μM and 100 μM) and photosynthetic, transpiration rate and TDM were 62.5 %, 42.9 % and 78.6 % lower at higher Al (300 μM) as compared to control. TRL, RSA, RDW and RV at higher Al (300 μM) were 92.6 %, 98.7 %, 78.7 and 97.5 % lower over control respectively. Root and shoot Al and PUpE at higher Al (300 μM) was 194.0, 69.2 and 830 % higher whereas PUE decreased to 88.5 % over control. Evaluation of 31 indigenous maize cultivars at 0, 150, and 250 μM Al in sand culture, alongside tolerance scoring and assessment, revealed that Megha-9, Megha-10, and MZM-19 exhibits high Al tolerance, Megha-1, MZM-22, and MZM-42 demonstrated moderate tolerance, whereas Uruapara, Sublgarh, and BRL Para were identified as Al-sensitive. Stress physiological parameters like SDW, TDM, TRL, SL and LA contributed 46.02 % of variability to PC1, whereas A, RV, RSA, anthocyanin and Chlorophyll_b, contributed 13.56 % of variability to PC2. Highest values of CMS, SL, LP, LA, TRL and anthocyanin were recorded in cluster I having sensitive cultivars while highest CMS, SL, LA, LP, TRL and RSA were found in cluster II having moderately tolerant cultivars and highest mean values for TRL, RSA, LP, LA, CMS and SL were recorded in cluster III having highly Al stress tolerant cultivars. The traits viz., A, RV, RSA, anthocyanin and Chlorophyll_b, total chlorophyll and TDM were emanated as physio-morphological for assessing Al toxicity stress tolerance in Maize with high divergence values. Tolerant cultivars showing 63.4 % and 22.4 % higher anthocyanin at 150 μM Al and 250 μM Al than moderately tolerant one in acid soil experiment with increased root Al, shoot Al, root P and shoot P by 42.6 %, 11 %, 95.1 % and 34 % respectively were emerged as promising for novel maize improvement under acid soils of EHR.

Does late water deficit induce root growth or senescence in wheat?

In crops like wheat, terminal drought is one of the principal stress factors limiting productivity in rain-fed systems. However, little is known about root development after heading, when water uptake can be critical to wheat crops. The impact of water-stress on root growth was investigated in two wheat cultivars, Scout and Mace, under well-watered and post-anthesis water stress in three experiments. Plants were grown outside in 1.5-m long pots at a density similar to local recommended farming practice. Differences in root development were observed between genotypes, especially for water stress conditions under which Scout developed and maintained a larger root system than Mace. While under well-watered conditions both genotypes had shallow roots that appeared to senesce after heading, a moderate water stress stimulated shallow-root growth in Scout but accelerated senescence in Mace. For deep roots, post-heading biomass growth was observed for both genotypes in well-watered conditions, while under moderate water stress, only Scout maintained net growth as Mace deep roots senesced. Water stress of severe intensity affected both genotypes similarly, with root senescence at all depths. Senescence was also observed above ground. Under well-watered conditions, Scout retained leaf greenness (i.e. stay-green phenotype) for slightly longer than Mace. The difference between genotypes accentuated under moderate water stress, with rapid post-anthesis leaf senescence in Mace while Scout leaf greenness was affected little if at all by the stress. As an overall result, grain biomass per plant ('yield') was similar in the two genotypes under well-watered conditions, but more affected by a moderate stress in Mace than Scout. The findings from this study will assist improvement in modelling root systems of crop models, development of relevant phenotyping methods and selection of cultivars with better adaptation to drought.

Positional cloning and characterization reveal the role of TaSRN-3D and TaBSR1 in the regulation of seminal root number in wheat

Seminal roots play a critical role in water and nutrient absorption, particularly in the early developmental stages of wheat. However, the genes responsible for controlling SRN in wheat remain largely unknown. Genetic mapping and functional analyses identified a candidate gene (TraesCS3D01G137200, TaSRN-3D) encoding a Ser/Thr kinase glycogen synthase kinase 3 (STKc_GSK3) that regulated SRN in wheat. Additionally, experiments involving hormone treatment, nitrate absorption and protein interaction were conducted to explore the regulatory mechanism of TaSRN-3D. Results showed that the TaSRN-3D4332 allele inhibited seminal roots initiation and development, while loss-of-function mutants showed significantly higher seminal root number (SRN). Exogenous application of epi-brassinolide could increase the SRN in a HS2-allelic background. Furthermore, chlorate sensitivity and 15N uptake assays revealed that a higher number of seminal roots promoted nitrate accumulation. TaBSR1 (BIN2-related SRN Regulator 1, orthologous to OsGRF4/GL2 in rice) acts as an interactor of TaSRN-3D and promotes TaBSR1 degradation to reduce SRN. This study provides valuable insights into understanding the genetic basis and regulatory network of SRN in wheat, highlighting their roles as potential targets for root-based improvement in wheat breeding.

Durum wheat (Triticum turgidum L. var. durum) root system response to drought and salt stresses and genetic characterization for root-related traits

Abiotic stresses such as drought and salt are significant threats to crop productivity. The root system adaptation and tolerance to abiotic stresses are regulated by many biochemical reactions, which create a complex and multigenic response. The present study aims to evaluate the diversity of root responses to cyclic abiotic stress in three modern durum wheat varieties and one hydric stress-tolerant landrace in a pot experiment from seedling to more advanced plant development stages. The genotypes responded to abiotic stress during the whole experiment very differently, and at the end of the experiment, nine out of the 13 traits for the landrace J. Khetifa were significantly higher than other genotypes. Moreover, single sequence repeat (SSR) genetic analysis revealed high polymorphism among the genotypes screened and interesting private alleles associated with root system architecture traits. We propose that the markers used in this study could be a resource as material for durum wheat breeding programs based on marker-assisted selection to increase the vegetal material with high drought and salt stress tolerance and to identify candidates with strong early vigor and efficient root systems. This study provides appropriate genetic materials for marker-assisted breeding programs as well as a basic study for the genetic diversity of root traits of durum wheat crops.

Root system architecture change in response to waterlogging stress in a 448 global collection of rapeseeds (Brassica napus L.)

MAIN CONCLUSIONS

A novel image-based screening method for precisely identifying genotypic variations in rapeseed RSA under waterlogging stress was developed. Five key root traits were confirmed as good indicators of waterlogging and might be employed in breeding, particularly when using the MFVW approach. Waterlogging is a vital environmental factor that has detrimental effects on the growth and development of rapeseed (Brassica napus L.). Plant roots suffer from hypoxia under waterlogging, which ultimately confers yield penalty. Therefore, it is crucially important to understand the genetic variation of root system architecture (RSA) in response to waterlogging stress to guide the selection of new tolerant cultivars with favorable roots. This research was conducted to investigate RSA traits using image-based screening techniques to better understand how RSA changes over time during waterlogging at the seedling stage. First, we performed a t-test by comparing the relative root trait value between four tolerant and four sensitive accessions. The most important root characteristics associated with waterlogging tolerance at 12 h are total root length (TRL), total root surface area (TRSA), total root volume (TRV), total number of tips (TNT), and total number of forks (TNF). The root structures of 448 rapeseed accessions with or without waterlogging showed notable genetic diversity, and all traits were generally restrained under waterlogging conditions, except for the total root average diameter. Additionally, according to the evaluation and integration analysis of 448 accessions, we identified that five traits, TRL, TRSA, TRV, TNT, and TNF, were the most reliable traits for screening waterlogging-tolerant accessions. Using analysis of the membership function value (MFVW) and D-value of the five selected traits, 25 extremely waterlogging-tolerant materials were screened out. Waterlogging significantly reduced RSA, inhibiting root growth compared to the control. Additionally, waterlogging increased lipid peroxidation, accompanied by a decrease in the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). This study effectively improves our understanding of the response of RSA to waterlogging. The image-based screening method developed in this study provides a new scientific guidance for quickly examining the basic RSA changes and precisely predicting waterlogging-tolerant rapeseed germplasms, thus expanding the genetic diversity of waterlogging-tolerant rapeseed germplasm available for breeding.

Genetic dissection of root architecture in Ethiopian sorghum landraces

KEY MESSAGE

This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.

A bench-top Dark-Root device built with LEGO® bricks enables a non-invasive plant root development analysis in soil conditions mirroring nature

Roots are the hidden parts of plants, anchoring their above-ground counterparts in the soil. They are responsible for water and nutrient uptake and for interacting with biotic and abiotic factors in the soil. The root system architecture (RSA) and its plasticity are crucial for resource acquisition and consequently correlate with plant performance while being highly dependent on the surrounding environment, such as soil properties and therefore environmental conditions. Thus, especially for crop plants and regarding agricultural challenges, it is essential to perform molecular and phenotypic analyses of the root system under conditions as near as possible to nature (#asnearaspossibletonature). To prevent root illumination during experimental procedures, which would heavily affect root development, Dark-Root (D-Root) devices (DRDs) have been developed. In this article, we describe the construction and different applications of a sustainable, affordable, flexible, and easy to assemble open-hardware bench-top LEGO® DRD, the DRD-BIBLOX (Brick Black Box). The DRD-BIBLOX consists of one or more 3D-printed rhizoboxes, which can be filled with soil while still providing root visibility. The rhizoboxes sit in a scaffold of secondhand LEGO® bricks, which allows root development in the dark and non-invasive root tracking with an infrared (IR) camera and an IR light-emitting diode (LED) cluster. Proteomic analyses confirmed significant effects of root illumination on barley root and shoot proteomes. Additionally, we confirmed the significant effect of root illumination on barley root and shoot phenotypes. Our data therefore reinforces the importance of the application of field conditions in the lab and the value of our novel device, the DRD-BIBLOX. We further provide a DRD-BIBLOX application spectrum, spanning from investigating a variety of plant species and soil conditions and simulating different environmental conditions and stresses, to proteomic and phenotypic analyses, including early root tracking in the dark.

An improved U-Net-based in situ root system phenotype segmentation method for plants

The condition of plant root systems plays an important role in plant growth and development. The Minirhizotron method is an important tool to detect the dynamic growth and development of plant root systems. Currently, most researchers use manual methods or software to segment the root system for analysis and study. This method is time-consuming and requires a high level of operation. The complex background and variable environment in soils make traditional automated root system segmentation methods difficult to implement. Inspired by deep learning in medical imaging, which is used to segment pathological regions to help determine diseases, we propose a deep learning method for the root segmentation task. U-Net is chosen as the basis, and the encoder layer is replaced by the ResNet Block, which can reduce the training volume of the model and improve the feature utilization capability; the PSA module is added to the up-sampling part of U-Net to improve the segmentation accuracy of the object through multi-scale features and attention fusion; a new loss function is used to avoid the extreme imbalance and data imbalance problems of backgrounds such as root system and soil. After experimental comparison and analysis, the improved network demonstrates better performance. In the test set of the peanut root segmentation task, a pixel accuracy of 0.9917 and Intersection Over Union of 0.9548 were achieved, with an F1-score of 95.10. Finally, we used the Transfer Learning approach to conduct segmentation experiments on the corn in situ root system dataset. The experiments show that the improved network has a good learning effect and transferability.

Crop root system plasticity for improved yields in saline soils

Crop yields must increase to meet the demands of a growing world population. Soil salinization is increasing due to the impacts of climate change, reducing the area of arable land for crop production. Plant root systems are plastic, and their architecture can be modulated to (1) acquire nutrients and water for growth, and (2) respond to hostile soil environments. Saline soils inhibit primary root growth and alter root system architecture (RSA) of crop plants. In this review, we explore how crop root systems respond and adapt to salinity, focusing predominately on the staple cereal crops wheat, maize, rice, and barley, that all play a major role in global food security. Cereal crops are classified as glycophytes (salt-sensitive) however salt-tolerance can differ both between species and within a species. In the past, due to the inherent difficulties associated with visualising and measuring root traits, crop breeding strategies have tended to focus on optimising shoot traits. High-resolution phenotyping techniques now make it possible to visualise and measure root traits in soil systems. A steep, deep and cheap root ideotype has been proposed for water and nitrogen capture. Changes in RSA can be an adaptive strategy to avoid saline soils whilst optimising nutrient and water acquisition. In this review we propose a new model for designing crops with a salt-tolerant root ideotype. The proposed root ideotype would exhibit root plasticity to adapt to saline soils, root anatomical changes to conserve energy and restrict sodium (Na⁺) uptake, and transport mechanisms to reduce the amount of Na⁺ transported to leaves. In the future, combining high-resolution root phenotyping with advances in crop genetics will allow us to uncover root traits in complex crop species such as wheat, that can be incorporated into crop breeding programs for yield stability in saline soils.

Differences in Root Morphologies of Contrasting Wheat (Triticum aestivum) Genotypes Are Robust of a Drought Treatment

We aimed to assess the effect of water deprivation on root traits and to establish if the wheat cultivars Spica and Maringa would be useful as parental germplasm for a genetic analysis of root traits. Plants were grown in two markedly different soils under well-watered and water-limited treatments in controlled environment growth cabinets. The drought treatment was imposed as a gradual depletion of water over 28 days as seedlings grew from a defined starting moisture content. The root traits analyzed included length, nodal root number, thickness and nodal root angle. The relative differences in traits between genotypes generally proved to be robust in terms of water treatment and soil type. Maringa had a shallower nodal root angle than Spica, which was driven by the nodal roots. By contrast, the seminal roots of Maringa were found to be similar to or even steeper than those of Spica. We conclude that the differences in root traits between Spica and Maringa were robust to the drought treatment and soil types. Phenotyping on well-watered soil is relevant for identifying traits potentially involved in conferring water use efficiency. Furthermore, Spica and Maringa are suitable parental germplasm for developing populations to determine the genetics of key root traits.

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.

Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway

Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.

Phenotypic Diversity of Seminal Root Traits in Bread Wheat Germplasm from Different Origins

Bread wheat (Triticum aestivum L.) is a major staple crop, and more adapted varieties are needed to ensure productivity under unpredictable stress scenarios resulting from climate changes. In the development of new genotypes, root system traits are essential since roots have a key function in water and nutrient uptake, and root architecture determines the plant's ability to spatially explore the soil resources. Genetic variation in wheat root system may be assessed at the early stages of development. This study evaluates in vitro and at the seedling stage, the genetic diversity of root growth angle (RGA), seminal root number (SRN), and radicle length (RadL) in 30 bread wheat genotypes from different origins and belonging to distinct evolutive or breeding groups. SRN and RadL were analyzed at 1, 2, 3 and 6 days after sowing (DAS) and RGA was measured through the angle between the first pair of seminal roots. A large variability was found in RGA values that ranged from 63° to 122°. Although differences were found between genotypes within the same groups, the narrower angles tended to occur among landraces, while the higher RGA values were observed in advanced lines and Australian varieties. Differences were also observed as regards the SRN (1.0-3.0, 2.7-4.7, 3.2-5.0 and 4.4-6.3 at 1, 2, 3 and 6 DAS, respectively) and RadL (0.1-1.5, 2.1-5.0, 4.0-7.5 and 5.1-13.7 cm at 1, 2, 3 and 6 DAS, respectively). Genetic variability in root traits at seedling stage allows more rapid selection of genotypes better adapted to environmental and soil constraints, necessary to Portuguese Wheat Breeding Program. It will also contribute to the definition of wheat ideotypes with improved performance under Mediterranean climate conditions.

Seedling and field assessment of wheat (Triticum aestivum L.) dwarfing genes and their influence on root traits in multiple genetic backgrounds

Deployment of the Rht-B1b and Rht-D1b dwarfing genes helped facilitate the Green Revolution to increase wheat yields globally. Much is known of the influence of these genes on plant height and agronomic performance, but not of their effects on root architecture. We assessed 29 near-isogenic lines (NILs) representing 11 Green Revolution and alternative dwarfing genes across multiple genetic backgrounds for root architecture characteristics in controlled and field environments. Genetic background did not influence plant height, but had a small and significant (P<0.05) effect on root architecture. All dwarfing gene NILs were significantly (P<0.01) shorter compared with tall controls. The Green Revolution Rht-B1b and Rht-D1b sometimes had longer seedling roots but were not different from their respective tall controls for root depth in the field. The Rht8, Rht12, and Rht18 dwarfing gene NILs produced long seminal roots in seedling pouches, and a greater maximum rooting depth (MRD) and root penetration rate (RPR) in the field. Genotypic increases in MRD and RPR were strongly correlated with increased harvest index and grain yield, particularly in dry environments. Careful root phenotyping highlights the potential of novel dwarfing genes for wheat genetic improvement under water-limited conditions.

Genotypic variation and covariation in wheat seedling seminal root architecture and grain yield under field conditions

Greater embryo size in a large and carefully phenotyped mapping population was genetically associated with a greater number of longer seminal roots to increase grain yield in droughted field environments. Breeding modification of root architecture is challenging in field environments owing to genetic and phenotypic complexity, and poor repeatability with root sampling. Seeds from a large mapping population varying in embryo size were harvested from a common glasshouse and standardised to a common size before assessing in rolled germination paper at 12 and 20 °C for seedling growth. Differences in genotype means were large and heritabilities high (h² = 0.55-0.93) indicating strong and repeatable genotypic differences for most root traits. Seminal roots 1 to 3 were produced on all seedlings, whereas growth of seminal roots 4, 5 and 6 was associated with differences in embryo size. Increases in seminal root number from 4 to 6 per plant were strongly, genetically correlated with increases in total seminal length (r_g = 0.84, < 0.01). Multivariate analysis confirmed initiation and growth of seminal roots 1, 2 and 3, and of roots 4, 5 and 6 behaved as genetically independent (r_Pg = 0.15 ns) cohorts. Tails representing extremes in seedling root length and number were associated with significant differences in grain yield of up to 35% in droughted field environments but were not different in irrigated environments. Increases in grain yield were linked to greater lengths of seminal roots 4, 5 and 6 and were largely independent of plant height or development. This is the first report on the genetic relationship of seedling root architecture and embryo size, and potential in selection of seminal root size for accessing deep-soil moisture in droughted environments.

Recent trends in root phenomics of plant systems with available methods- discrepancies and consonances

The phenotyping of plant roots is a challenging task and poses a major lacuna in plant root research. Roots rhizospheric zone is affected by several environmental cues among which salinity, drought, heavy metal and soil pH are key players. Among biological factors, fungal, nematode and bacterial interactions with roots are vital for improving nutrient uptake efficiency in plants. The subterranean nature of a plant root and the limited number of approaches for root phenotyping offers a great challenge to the plant breeders to select a desirable root trait under different stress conditions. Identification of key root traits can provide a basic understanding for generating crop plants with enhanced ability to withstand various biotic or abiotic stresses. For instance, crops with improved soil exploration potential, phosphate uptake efficiency, water use efficiency and others. Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide precise and desired root quantification attributes. Though 3D imaging by X-ray computed tomography (X-ray-CT) and magnetic resonance imaging techniques are complex, however, it provides the most applicable and practically relevant data for quantifying root system architecture traits. This review outlines the current developments in root studies including recent approaches viz. X-ray-CT, MRI, thermal infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it offers multiple advantages by removing discrepancies and providing the actual practical significance of plant roots for breeding programs.

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.

The root system architecture of wheat establishing in soil is associated with varying elongation rates of seminal roots: quantification using 4D magnetic resonance imaging

Seedling establishment is the first stage of crop productivity, and root phenotypes at seed emergence are critical to a successful start of shoot growth as well as for water and nutrient uptake. In this study, we investigate seedling establishment in winter wheat utilizing a newly developed workflow based on magnetic resonance imaging (MRI). Using the eight parents of the MAGIC (multi-parent advanced generation inter-cross) population we analysed the 4D root architecture of 288 individual seedlings grown in natural soils with plant neighbors over 3 d of development. Time of root and shoot emergence, total length, angle, and depth of the axile roots varied significantly among these genotypes. The temporal data resolved rates of elongation of primary roots and first and second seminal root pairs. Genotypes with slowly elongating primary roots had rapidly elongating first and second seminal root pairs and vice versa, resulting in variation in root system architecture mediated not only by root angle but also by initiation and relative elongation of axile roots. We demonstrated that our novel MRI workflow with a unique planting design and automated measurements allowed medium throughput phenotyping of wheat roots in 4D and could give new insights into regulation of root system architecture.

Genetic Analysis of Platform-Phenotyped Root System Architecture of Bread and Durum Wheat in Relation to Agronomic Traits

Roots are essential for water and nutrient uptake but are rarely the direct target of breeding efforts. To characterize the genetic variability of wheat root architecture, the root and shoot traits of 200 durum and 715 bread wheat varieties were measured at a young stage on a high-throughput phenotyping platform. Heritability of platform traits ranged from 0.40 for root biomass in durum wheat to 0.82 for the number of tillers. Field phenotyping data for yield components and SNP genotyping were already available for all the genotypes. Taking differences in earliness into account, several significant correlations between root traits and field agronomic performances were found, suggesting that plants investing more resources in roots in some stressed environments favored water and nutrient uptake, with improved wheat yield. We identified 100 quantitative trait locus (QTLs) of root traits in the bread wheat panels and 34 in the durum wheat panel. Most colocalized with QTLs of traits measured in field conditions, including yield components and earliness for bread wheat, but only in a few environments. Stress and climatic indicators explained the differential effect of some platform QTLs on yield, which was positive, null, or negative depending on the environmental conditions. Modern breeding has led to deeper rooting but fewer seminal roots in bread wheat. The number of tillers has been increased in bread wheat, but decreased in durum wheat, and while the root-shoot ratio for bread wheat has remained stable, for durum wheat it has been increased. Breeding for root traits or designing ideotypes might help to maintain current yield while adapting to specific drought scenarios.

High accuracy of genome-enabled prediction of belowground and physiological traits in barley seedlings

In plants, the study of belowground traits is gaining momentum due to their importance on yield formation and the uptake of water and nutrients. In several cereal crops, seminal root number and seminal root angle are proxy traits of the root system architecture at the mature stages, which in turn contributes to modulating the uptake of water and nutrients. Along with seminal root number and seminal root angle, experimental evidence indicates that the transpiration rate response to evaporative demand or vapor pressure deficit is a key physiological trait that might be targeted to cope with drought tolerance as the reduction of the water flux to leaves for limiting transpiration rate at high levels of vapor pressure deficit allows to better manage soil moisture. In the present study, we examined the phenotypic diversity of seminal root number, seminal root angle, and transpiration rate at the seedling stage in a panel of 8-way Multiparent Advanced Generation Inter-Crosses lines of winter barley and correlated these traits with grain yield measured in different site-by-season combinations. Second, phenotypic and genotypic data of the Multiparent Advanced Generation Inter-Crosses population were combined to fit and cross-validate different genomic prediction models for these belowground and physiological traits. Genomic prediction models for seminal root number were fitted using threshold and log-normal models, considering these data as ordinal discrete variable and as count data, respectively, while for seminal root angle and transpiration rate, genomic prediction was implemented using models based on extended genomic best linear unbiased predictors. The results presented in this study show that genome-enabled prediction models of seminal root number, seminal root angle, and transpiration rate data have high predictive ability and that the best models investigated in the present study include first-order additive × additive epistatic interaction effects. Our analyses indicate that beyond grain yield, genomic prediction models might be used to predict belowground and physiological traits and pave the way to practical applications for barley improvement.

The impact of PEG-induced drought stress on seed germination and seedling growth of different bread wheat (Triticum aestivum L.) genotypes

Wheat is an important crop, used as staple food in numerous countries around the world. However, wheat productivity is low in the developing world due to several biotic and abiotic stresses, particularly drought stress. Non-availability of drought-tolerant wheat genotypes at different growth stages is the major constraint in improving wheat productivity in the developing world. Therefore, screening/developing drought-tolerant genotypes at different growth stages could improve the productivity of wheat. This study assessed seed germination and seedling growth of eight wheat genotypes under polyethylene glycol (PEG)-induced stress. Two PEG-induced osmotic potentials (i.e., -0.6 and -1.2 MPa) were included in the study along with control (0 MPa). Wheat genotypes included in the study were 'KLR-16', 'B6', 'J10', '716', 'A12', 'Seher', 'KTDH-16', and 'J4'. Data relating to seed germination percentage, root and shoot length, fresh and dry weight of roots and shoot, root/shoot length ratio and chlorophyll content were recorded. The studied parameters were significantly altered by individual and interactive effects of genotypes and PEG-induced osmotic potentials. Seed germination and growth parameters were reduced by osmotic potentials; however, huge differences were noted among genotypes. A reduction of 32.83 to 53.50% was recorded in seed germination, 24.611 to 47.75% in root length, 37.83 to 53.72% in shoot length, and 53.35 to 65.16% in root fresh weight. The genotypes, 'J4', 'KLR-16' and 'KTDH-16', particularly 'J4' better tolerated increasing osmotic potentials compared to the rest of the genotypes included in the study. Principal component analysis segregated these genotypes from the rest of the genotypes included in the study indicated that these can be used in the future studies to improve the drought tolerance of wheat crop. The genotype 'J4' can be used as a breeding material to develop drought resistant wheat genotypes.

A toolkit to rapidly modify root systems through single plant selection

BACKGROUND

The incorporation of root traits into elite germplasm is typically a slow process. Thus, innovative approaches are required to accelerate research and pre-breeding programs targeting root traits to improve yield stability in different environments and soil types. Marker-assisted selection (MAS) can help to speed up the process by selecting key genes or quantitative trait loci (QTL) associated with root traits. However, this approach is limited due to the complex genetic control of root traits and the limited number of well-characterised large effect QTL. Coupling MAS with phenotyping could increase the reliability of selection. Here we present a useful framework to rapidly modify root traits in elite germplasm. In this wheat exemplar, a single plant selection (SPS) approach combined three main elements: phenotypic selection (in this case for seminal root angle); MAS using KASP markers (targeting a root biomass QTL); and speed breeding to accelerate each cycle.

RESULTS

To develop a SPS approach that integrates non-destructive screening for seminal root angle and root biomass, two initial experiments were conducted. Firstly, we demonstrated that transplanting wheat seedlings from clear pots (for seminal root angle assessment) into sand pots (for root biomass assessment) did not impact the ability to differentiate genotypes with high and low root biomass. Secondly, we demonstrated that visual scores for root biomass were correlated with root dry weight (r = 0.72), indicating that single plants could be evaluated for root biomass in a non-destructive manner. To highlight the potential of the approach, we applied SPS in a backcrossing program which integrated MAS and speed breeding for the purpose of rapidly modifying the root system of elite bread wheat line Borlaug100. Bi-directional selection for root angle in segregating generations successfully shifted the mean root angle by 30° in the subsequent generation (P ≤ 0.05). Within 18 months, BC₂F₄:F₅ introgression lines were developed that displayed a full range of root configurations, while retaining similar above-ground traits to the recurrent parent. Notably, the seminal root angle displayed by introgression lines varied more than 30° compared to the recurrent parent, resulting in lines with both narrow and wide root angles, and high and low root biomass phenotypes.

CONCLUSION

The SPS approach enables researchers and plant breeders to rapidly manipulate root traits of future crop varieties, which could help improve productivity in the face of increasing environmental fluctuations. The newly developed elite wheat lines with modified root traits provide valuable materials to study the value of different root systems to support yield in different environments and soil types.

Dissecting the Genetics of Early Vigour to Design Drought-Adapted Wheat

Due to the climate change and an increased frequency of drought, it is of enormous importance to identify and to develop traits that result in adaptation and in improvement of crop yield stability in drought-prone regions with low rainfall. Early vigour, defined as the rapid development of leaf area in early developmental stages, is reported to contribute to stronger plant vitality, which, in turn, can enhance resilience to erratic drought periods. Furthermore, early vigour improves weed competitiveness and nutrient uptake. Here, two sets of a multi-reference nested association mapping (MR-NAM) population of bread wheat (Triticum aestivum ssp. aestivum L.) were used to investigate early vigour in a rain-fed field environment for 3 years, and additionally assessed under controlled conditions in a greenhouse experiment. The normalised difference vegetation index (NDVI) calculated from red/infrared light reflectance was used to quantify early vigour in the field, revealing a correlation (p < 0.05; r = 0.39) between the spectral measurement and the length of the second leaf. Under controlled environmental conditions, the measured projected leaf area, using a green-pixel counter, was also correlated to the leaf area of the second leaf (p < 0.05; r = 0.38), as well as to the recorded biomass (p < 0.01; r = 0.71). Subsequently, genetic determination of early vigour was tested by conducting a genome-wide association study (GWAS) for the proxy traits, revealing 42 markers associated with vegetation index and two markers associated with projected leaf area. There are several quantitative trait loci that are collocated with loci for plant developmental traits including plant height on chromosome 2D (log₁₀ (P) = 3.19; PVE = 0.035), coleoptile length on chromosome 1B (-log₁₀ (P) = 3.24; PVE = 0.112), as well as stay-green and vernalisation on chromosome 5A (-log₁₀ (P) = 3.14; PVE = 0.115).

A Large Root Phenome Dataset Wide-Opened the Potential for Underground Breeding in Soybean

The root is the most critical plant organ for water and nutrient acquisition. Although the root is vital for water and nutrient uptake, the diverse root characters of soybean still need to be identified owing to the difficulty of root sampling. In this study, we used 150 wild and 50 cultivated soybean varieties to collect root image samples. We analyzed root morphological traits using acquired-image. Except for the main total length (MTL), the root morphological traits for most cultivated and wild plants were significantly different. According to correlation analysis, the wild and cultivated plants showed a significant correlation among total root length (TRL), projected area (PA), forks, total lateral length (TLL), link average diameter, and MTL. In particular, TRL was highly correlated with PA in both cultivated (0.92) and wild (0.82) plants compared with between MTL (0.43 for cultivated and 0.27 for wild) and TLL (0.82 for cultivated and 0.52 for wild). According to principal component analysis results, both plants could be separated; however, there was some overlap of the traits among the wild and cultivated individuals from some regions. Nevertheless, variation among the cultivated plants was higher than that found in the wild plants. Furthermore, three groups, including MTL, TLL, and the remaining traits, could explain all the variances.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

Wheat root systems as a breeding target for climate resilience

In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.

Deciphering the genetic basis of wheat seminal root anatomy uncovers ancestral axial conductance alleles

Root axial conductance, which describes the ability of water to move through the xylem, contributes to the rate of water uptake from the soil throughout the whole plant lifecycle. Under the rainfed wheat agro-system, grain-filling is typically occurring during declining water availability (i.e., terminal drought). Therefore, preserving soil water moisture during grain filling could serve as a key adaptive trait. We hypothesized that lower wheat root axial conductance can promote higher yields under terminal drought. A segregating population derived from a cross between durum wheat and its direct progenitor wild emmer wheat was used to underpin the genetic basis of seminal root architectural and functional traits. We detected 75 QTL associated with seminal roots morphological, anatomical and physiological traits, with several hotspots harbouring co-localized QTL. We further validated the axial conductance and central metaxylem QTL using wild introgression lines. Field-based characterization of genotypes with contrasting axial conductance suggested the contribution of low axial conductance as a mechanism for water conservation during grain filling and consequent increase in grain size and yield. Our findings underscore the potential of harnessing wild alleles to reshape the wheat root system architecture and associated hydraulic properties for greater adaptability under changing climate.

Characterizing reduced height wheat mutants for traits affecting abiotic stress and photosynthesis during seedling growth

Most high-yielding, semidwarf wheat (Triticum aestivum L.) grown around the world contains either Rht1 or Rht2 genes. The success of these high-yielding cultivars is greatest in the most productive farming environments but provide marginal benefits in less favorable growing conditions such as shallow soils and low-precipitation dryland farming. Further, growing evidence suggests semidwarf genes not only affect early seedling growth but limit grain yield, especially under abiotic stress conditions. There are 23 other reduced-height mutants reported in wheat, most of which have not been functionally characterized. We evaluated these mutants along with their parents for several traits affecting seedling emergence, early seedling growth, and photosynthetic efficiency. Two- to seven-fold differences in coleoptile length, first leaf length, root length, and root angle were observed among the genotypes. Most of the mutations had a positive effect on root length, while the root angle narrowed. Coleoptile and first leaf lengths were strongly correlated with emergence. A specialized deep planting experiment identified Rht5, Rht6, Rht8, and Rht13 with significantly improved seedling emergence compared to the parent. Among the mutants, Rht4, Rht19, and Rht12 ranked highest for photosynthetic traits while Rht9, Rht16, and Rht15 performed best for early seedling growth parameters. Considering all traits collectively, Rht15 showed the most promise for utilization in marginal environments followed by Rht19 and Rht16. These wheat mutants may be useful for deciphering the underlying molecular mechanisms of understudied traits and breeding programs in arid and semiarid regions where deep planting is practiced.

Root and canopy traits and adaptability genes explain drought tolerance responses in winter wheat

Bread wheat (Triticum aestivum L) is one of the three main staple crops worldwide contributing 20% calories in the human diet. Drought stress is the main factor limiting yields and threatening food security, with climate change resulting in more frequent and intense drought. Developing drought-tolerant wheat cultivars is a promising way forward. The use of holistic approaches that include high-throughput phenotyping and genetic markers in selection could help in accelerating genetic gains. Fifty advanced breeding lines were selected from the CIMMYT Turkey winter wheat breeding program and studied under irrigated and semiarid conditions in two years. High-throughput phenotyping was done for wheat crown root traits and canopy senescence dynamics using vegetation indices (green area using RGB images and Normalized Difference Vegetation Index using spectral reflectance). In addition, genotyping by KASP markers for adaptability genes was done. Overall, under semiarid conditions yield reduced by 3.09 t ha^-1 (-46.8%) compared to irrigated conditions. Genotypes responded differently under drought stress and genotypes 39 (VORONA/HD24-12//GUN/7/VEE#8//…/8/ALTAY), 18 (BiII98) and 29 (NIKIFOR//KROSHKA) were the most drought tolerant. Root traits including shallow nodal root angle under irrigated conditions and root number per shoot under semiarid conditions were correlated with increased grain yield. RGB based vegetation index measuring canopy green area at anthesis was better correlated with GY than NDVI was with GY under drought. The markers for five established functional genes (PRR73.A1 –flowering time, TEF-7A –grain size and weight, TaCwi.4A - yield under drought, Dreb1- drought tolerance, and ISBW11.GY.QTL.CANDIDATE- grain yield) were associated with different drought-tolerance traits in this experiment. We conclude that–genotypes 39, 18 and 29 could be used for drought tolerance breeding. The trait combinations of canopy green area at anthesis, and root number per shoot along with key drought adaptability makers (TaCwi.4A and Dreb1) could be used in screening drought tolerance wheat breeding lines.

Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System

BACKGROUND

Aerobic rice production (AP) may be a solution to the looming water crisis by utilising less water compared to traditional flooded culture. As such, development of genotypes with narrow root cone angle (RCA) is considered a key AP adaptation trait as it could lead to deeper rooting and ensure water uptake at depth. Quantitative trait loci (QTL) and genes associated with rooting angle have been identified in rice, but usually in conventional transplanted systems or in upland and drought conditions. This study aimed to identify QTL associated with RCA in AP systems using a recombinant inbred line population derived from IRAT109.

RESULTS

Four experiments conducted in glasshouse and aerobic field conditions revealed significant genotypic variation existed for RCA in the population. Single and multiple QTL models identified the presence of eight QTL distributed in chromosomes 1, 2, 3, 4, and 11. Combined, these QTL explained 36.7-51.2% of the genotypic variance in RCA present in the population. Two QTL, qRCA1.1 and qRCA1.3, were novel and may be new targets for improvement of RCA. Genotypes with higher number of favourable QTL alleles tended to have narrower RCA. qRCA4 was shown to be a major and stable QTL explaining up to 24.3% of the genotypic variation, and the presence of the target allele resulted in as much as 8.6° narrower RCA. Several genes related to abiotic stress stimulus response were found in the qRCA4 region.

CONCLUSION

Stable and novel genomic regions associated with RCA have been identified. Genotypes which had combinations of these QTL, resulted in a narrower RCA phenotype. Allele mining, gene cloning, and physiological dissection should aid in understanding the molecular function and mechanisms underlying RCA and these QTL. Ultimately, our work provides an opportunity for breeding programs to develop genotypes with narrow RCA and deep roots for improved adaptation in an AP system for sustainable rice production.

Assessment of root phenotypes in mungbean mini-core collection (MMC) from the World Vegetable Center (AVRDC) Taiwan

Mungbean (Vigna radiata L.) is an important food grain legume, but its production capacity is threatened by global warming, which can intensify plant stress and limit future production. Identifying new variation of key root traits in mungbean will provide the basis for breeding lines with effective root characteristics for improved water uptake to mitigate heat and drought stress. The AVRDC mungbean mini core collection consisting of 296 genotypes was screened under modified semi-hydroponic screening conditions to determine the variation for fourteen root-related traits. The AVRDC mungbean mini core collection displayed wide variations for the primary root length, total surface area, and total root length, and based on agglomerative hierarchical clustering eight homogeneous groups displaying different root traits could be identified. Germplasm with potentially favorable root traits has been identified for further studies to identify the donor genotypes for breeding cultivars with enhanced adaptation to water-deficit stress and other stress conditions.

High-throughput phenotyping analysis of maize at the seedling stage using end-to-end segmentation network

Image processing technologies are available for high-throughput acquisition and analysis of phenotypes for crop populations, which is of great significance for crop growth monitoring, evaluation of seedling condition, and cultivation management. However, existing methods rely on empirical segmentation thresholds, thus can have insufficient accuracy of extracted phenotypes. Taking maize as an example crop, we propose a phenotype extraction approach from top-view images at the seedling stage. An end-to-end segmentation network, named PlantU-net, which uses a small amount of training data, was explored to realize automatic segmentation of top-view images of a maize population at the seedling stage. Morphological and color related phenotypes were automatic extracted, including maize shoot coverage, circumscribed radius, aspect ratio, and plant azimuth plane angle. The results show that the approach can segment the shoots at the seedling stage from top-view images, obtained either from the UAV or tractor-based high-throughput phenotyping platform. The average segmentation accuracy, recall rate, and F1 score are 0.96, 0.98, and 0.97, respectively. The extracted phenotypes, including maize shoot coverage, circumscribed radius, aspect ratio, and plant azimuth plane angle, are highly correlated with manual measurements (R2 = 0.96-0.99). This approach requires less training data and thus has better expansibility. It provides practical means for high-throughput phenotyping analysis of early growth stage crop populations.

Root architecture for improved resource capture: trade-offs in complex environments

Root architecture is a promising breeding target for developing resource-efficient crops. Breeders and plant physiologists have called for root ideotypes that have narrow, deep root systems for improved water and nitrate capture, or wide, shallower root systems for better uptake of less mobile topsoil nutrients such as phosphorus. Yet evidence of relationships between root architecture and crop yield is limited. Many studies focus on the response to a single constraint, despite the fact that crops are frequently exposed to multiple soil constraints. For example, in dryland soils under no-till management, topsoil nutrient stratification is an emergent profile characteristic, leading to spatial separation of water and nutrients as the soil profile dries. This results in spatio-temporal trade-offs between efficient resource capture and pre-defined root ideotypes developed to counter a single constraint. We believe there is need to identify and better understand trade-offs involved in the efficient capture of multiple, spatially disjunct soil resources. Additionally, how these trade-offs interact with genotype (root architecture), environment (soil constraints), and management (agronomy) are critical unknowns. We argue that identifying root traits that enable efficient capture of multiple soil resources under fluctuating environmental constraints is a key step towards meeting the challenges of global food security.

Root phenotypes of young wheat plants grown in controlled environments show inconsistent correlation with mature root traits in the field

Using a field to lab approach, mature deep-rooting traits in wheat were correlated to root phenotypes measured on young plants from controlled conditions. Mature deep-rooting root traits of 20 wheat genotypes at maturity were established via coring in three field trials across 2 years. Field traits were correlated to phenotypes expressed by the 20 genotypes after growth in four commonly used lab screens: (i) soil tubes for root emergence, elongation, length, and branching at four ages to 34 days after sowing (DAS); (ii) paper pouches 7 DAS and (iii) agar chambers for primary root (PR) number and angles at 8 DAS; and (iv) soil baskets for PR and nodal root (NR) number and angle at 42 DAS. Correlations between lab and field root traits (r2=0.45-0.73) were highly inconsistent, with many traits uncorrelated and no one lab phenotype correlating similarly across three field experiments. Phenotypes most positively associated with deep field roots were: longest PR and NR axiles from the soil tube screen at 20 DAS; and narrow PR angle and wide NR angle from soil baskets at 42 DAS. Paper and agar PR angles were positively and significantly correlated to each other, but only wide outer PRs in the paper screen correlated positively to shallower field root traits. NR phenotypes in soil baskets were not predicted by PR phenotypes in any screen, suggesting independent developmental controls and value in measuring both root types in lab screens. Strong temporal and edaphic effects on mature root traits, and a lack of understanding of root trait changes during plant development, are major challenges in creating controlled-environment root screens for mature root traits in the field.

Effects of breeding history and crop management on the root architecture of wheat

AIMS

Selection for optimal root system architecture (RSA) is important to ensure genetic gains in the sustainable production of wheat (Triticum aestivum L.). Here we examine the hypothesis that past wheat breeding has led to changes in RSA and that future breeding efforts can focus directly on RSA to improve adaptation to target environments.

METHODS

We conducted field trials using diverse wheat varieties, including modern and historic UK varieties and non-UK landraces, tested under contrasting tillage regimes (non-inversion tillage versus conventional ploughing) for two trial years or different seeding rates (standard versus high rate) for one trial year. We used field excavation, washing and measurement of root crowns ('shovelomics') to characterise RSA traits, including: numbers of seminal, crown and nodal roots per plant, and crown root growth angle.

RESULTS

We found differences among genotypes for all root traits. Modern varieties generally had fewer roots per plant than historic varieties. On average, there were fewer crown roots and root angles were wider under shallow non-inversion tillage compared with conventional ploughing. Crown root numbers per plant also tended to be smaller at a high seeding rate compared with the standard. There were significant genotype-by-year, genotype-by-tillage and genotype-by-seeding-rate interactions for many root traits.

CONCLUSIONS

Smaller root systems are likely to be a result of past selection that facilitated historical yield increases by reducing below-ground competition within the crop. The effects of crop management practices on RSA depend on genotype, suggesting that future breeding could select for improved RSA traits in resource-efficient farming systems.

Phenotyping: New Windows into the Plant for Breeders

Plant phenotyping enables noninvasive quantification of plant structure and function and interactions with environments. High-capacity phenotyping reaches hitherto inaccessible phenotypic characteristics. Diverse, challenging, and valuable applications of phenotyping have originated among scientists, prebreeders, and breeders as they study the phenotypic diversity of genetic resources and apply increasingly complex traits to crop improvement. Noninvasive technologies are used to analyze experimental and breeding populations. We cover the most recent research in controlled-environment and field phenotyping for seed, shoot, and root traits. Select field phenotyping technologies have become state of the art and show promise for speeding up the breeding process in early generations. We highlight the technologies behind the rapid advances in proximal and remote sensing of plants in fields. We conclude by discussing the new disciplines working with the phenotyping community: data science, to address the challenge of generating FAIR (findable, accessible, interoperable, and reusable) data, and robotics, to apply phenotyping directly on farms.

Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big

The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometricand physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale.

Phenotypic variability in bread wheat root systems at the early vegetative stage

BACKGROUND

Understanding root system morphology in bread wheat is critical for identifying root traits to breed cultivars with improved resource uptake and better adaptation to adverse environments. Variability in root morphological traits at early vegetative stages was examined among 184 bread wheat genotypes originating from 37 countries grown in a semi-hydroponic phenotyping system.

RESULTS

At the onset of tillering (Z2.1, 35 days after transplanting), plants had up to 42 cm in shoot height and 158 cm long in root depth. Phenotypic variation existed for both shoot and root traits, with a maximal 4.3-fold difference in total root length and 5-fold difference in root dry mass among the 184 genotypes. Of the 41 measured traits, 24 root traits and four shoot traits had larger coefficients of variation (CV ≥ 0.25). Strong positive correlations were identified for some key root traits (i.e., root mass, root length, and these parameters at different depths) and shoot traits (i.e., shoot mass and tiller number) (P ≤ 0.05). The selected 25 global traits (at whole-plant level) contributed to one of the five principal components (eigenvalues> 1) capturing 83.0% of the total variability across genotypes. Agglomerative hierarchical clustering analysis separated the 184 genotypes into four (at a rescaled distance of 15) or seven (at a rescaled distance of 10) major groups based on the same set of root traits. Strong relationships between performance traits (dry mass) with several functional traits such as specific root length, root length intensity and root tissue density suggest their linkage to plant growth and fitness strategies.

CONCLUSIONS

Large phenotypic variability in root system morphology in wheat genotypes was observed at the tillering stage using established semi-hydroponic phenotyping techniques. Phenotypic differences in and trait correlations among some interesting root traits may be considered for breeding wheat cultivars with efficient water acquisition and better adaptation to abiotic stress.

Drying times: plant traits to improve crop water use efficiency and yield

Crop water use efficiency (WUE) has come into sharp focus as population growth and climate change place increasing strain on the water used in cropping. Rainfed crops are being challenged by an upward trend in evaporative demand as average temperatures rise and, in many regions, there is an increased irregularity and a downward trend in rainfall. In addition, irrigated cropping faces declining water availability and increased competition from other users. Crop WUE would be improved by, first, ensuring that as much water as possible is actually transpired by the crop rather than being wasted. Deeper roots and greater early crop vigour are two traits that should help achieve this. Crop WUE would also be improved by achieving greater biomass per unit water transpired. A host of traits has been proposed to address this outcome. Restricting crop transpiration through lower stomatal conductance is assessed as having limited utility compared with traits that improve carbon gain, such as enhancements to photosynthetic biochemistry and responsiveness, or greater mesophyll conductance. Ultimately, the most useful outcomes for improved crop WUE will probably be achieved by combining traits to achieve synergistic benefit. The potential utility of trait combinations is supported by the results of crop simulation modelling.

Transcriptome and GWAS analyses reveal candidate gene for seminal root length of maize seedlings under drought stress

Water deficits are a major constraint on maize growth and yield, and deep roots are one of the major mechanisms of drought tolerance. In this study, four root and shoot traits were evaluated within an association panel consisting of 209 diverse maize accessions under well-watered (WW) and water-stressed (WS) conditions. A significant positive correlation was observed between seminal root length (SRL) under WS treatment and the drought tolerance index (DI) of maize seedlings. The transcriptome profiles of maize seminal roots were compared between four drought-tolerant lines and four drought-sensitive lines under both water conditions to identify genes associated with the drought stress response. After drought stress, 343 and 177 common differentially expressed genes (DEGs) were identified in the drought-tolerant group and drought-sensitive group, respectively. In parallel, a coexpression network underlying SRL was constructed on the basis of transcriptome data, and 10 hub genes involved in two significant associated modules were identified. Additionally, a genome-wide association study (GWAS) of the SRL revealed 62 loci for the two water treatments. By integrating the results of the GWAS, the common DEGs and the coexpression network analysis, 7 promising candidate genes were prioritized for further research. Together, our results provide a foundation for the enhanced understanding of seminal root changes in response to drought stress in maize.

Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor

Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize (Zea mays) and sorghum (Sorghum bicolor), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe-quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa.

High throughput phenotyping dataset related to seed and seedling traits of sugar beet genotypes

Several seed and seedling traits are measured to evaluate germination and emergence potential in relation with environmental conditions. More generally, these traits are also measured in the field of ecology as simple traits that can be correlated to other adaptative traits more difficult to measure on adult plants, as for example traits of the rooting system. Methods were developed for deep high throughput phenotyping of hundreds of genotypes from dry seed to the end of heterotrophic growth. The present dataset comes from a project on genotyping and phenotyping of populations of genotypes, with different geographic and genetic origins so as to increase genotypic diversity of sugar beet in terms of germination and early growth traits, evaluated at low temperatures. Data were collected in relation to the creation of the first sugar beet crop ontology. This dataset corresponds to the first automated phenotyping of a population of 198 genotypes and 4 commercial control varieties and is hosted on INRAE public depository under the reference number doi.org/10.15,454/AKNF4Q. The equipment and methods presented here are available on a phenotyping platform opened to collaborative research and adaptable for specific services for characterizing thousands of genotypes on different crops or other species. The phenotyping values can also be linked to genomic information to study the genetic determinism of the trait values.

Soil strength influences wheat root interactions with soil macropores

Deep rooting is critical for access to water and nutrients found in subsoil. However, damage to soil structure and the natural increase in soil strength with depth, often impedes root penetration. Evidence suggests that roots use macropores (soil cavities greater than 75 μm) to bypass strong soil layers. If roots have to exploit structures, a key trait conferring deep rooting will be the ability to locate existing pore networks; a trait called trematotropism. In this study, artificial macropores were created in repacked soil columns at bulk densities of 1.6 g cm^-3 and 1.2 g cm^-3 , representing compact and loose soil. Near isogenic lines of wheat, Rht-B1a and Rht-B1c, were planted and root-macropore interactions were visualized and quantified using X-ray computed tomography. In compact soil, 68.8% of root-macropore interactions resulted in pore colonization, compared with 12.5% in loose soil. Changes in root growth trajectory following pore interaction were also quantified, with 21.0% of roots changing direction (±3°) in loose soil compared with 76.0% in compact soil. These results indicate that colonization of macropores is an important strategy of wheat roots in compacted subsoil. Management practices to reduce subsoil compaction and encourage macropore formation could offer significant advantage in helping wheat roots penetrate deeper into subsoil.

Soil strength influences wheat root interactions with soil macropores

Deep rooting is critical for access to water and nutrients found in subsoil. However, damage to soil structure and the natural increase in soil strength with depth, often impedes root penetration. Evidence suggests that roots use macropores (soil cavities greater than 75 μm) to bypass strong soil layers. If roots have to exploit structures, a key trait conferring deep rooting will be the ability to locate existing pore networks; a trait called trematotropism. In this study, artificial macropores were created in repacked soil columns at bulk densities of 1.6 g cm-3 and 1.2 g cm-3 , representing compact and loose soil. Near isogenic lines of wheat, Rht-B1a and Rht-B1c, were planted and root-macropore interactions were visualized and quantified using X-ray computed tomography. In compact soil, 68.8% of root-macropore interactions resulted in pore colonization, compared with 12.5% in loose soil. Changes in root growth trajectory following pore interaction were also quantified, with 21.0% of roots changing direction (±3°) in loose soil compared with 76.0% in compact soil. These results indicate that colonization of macropores is an important strategy of wheat roots in compacted subsoil. Management practices to reduce subsoil compaction and encourage macropore formation could offer significant advantage in helping wheat roots penetrate deeper into subsoil.

Chemical and physical influence of sodic soils on the coleoptile length and root growth angle of wheat genotypes

BACKGROUND AND AIMS

High exchangeable sodium percentage (ESP) and bulk density of sodic soils can reduce seedling emergence. This study examined variation in seedling coleoptile length and seminal root angle of wheat (Triticum aestivum. L) genotypes to determine whether these traits vary between genotypes that differ in their tolerance to sodic soils.

METHODS

Wheat genotypes were grown in three different experiments. First, four wheat genotypes were grown using soils of three ESPs (4, 10 and 17 %) and secondly in soils of three different bulk densities (1.2, 1.4 and 1.5 g cm-3) and ESP 10 %. Thirdly, seedling coleoptile length and seminal root angle were determined for 16 genotypes grown in a soil of ESP 10 % and bulk density 1.2 g cm-2. Seminal root angle and coleoptile length measurements from the current study were compared with seedling emergence rate and force measured previously.

KEY RESULTS

The seedling coleoptile length of all genotypes decreased with increasing soil ESP and bulk density, but with no significant differences between genotypes. In contrast, seminal root angles differed significantly between genotypes, but were not significantly affected by ESP or bulk density. There was an inverse relationship between the seminal root angle of the 16 genotypes and seedling emergence rate (R2 = 0.89) and also between seminal root angle and seedling emergence force (R2 = 0.61).

CONCLUSIONS

Lack of significant variation in coleoptile length between genotypes suggests that this may not be a suitable characteristic to identify wheat tolerance to sodic conditions. However, a narrower seminal root angle was correlated with rate and force of seedling emergence, traits likely to improve establishment. The mechanism underlying this correlation is not yet clear. Genotypes with a narrow root angle had greater root depth. One possible mechanism might be that genotypes with narrow root angles were able to take up more soil moisture at depth, leading to a higher proportion of seedling emergence.

Genetic Screening for Mutants with Altered Seminal Root Numbers in Hexaploid Wheat Using a High-Throughput Root Phenotyping Platform

Roots are the main channel for water and nutrient uptake in plants. Optimization of root architecture provides a viable strategy to improve nutrient and water uptake efficiency and maintain crop productivity under water-limiting and nutrient-poor conditions. We know little, however, about the genetic control of root development in wheat, a crop supplying 20% of global calorie and protein intake. To improve our understanding of the genetic control of seminal root development in wheat, we conducted a high-throughput screen for variation in seminal root number using an exome-sequenced mutant population derived from the hexaploid wheat cultivar Cadenza. The screen identified seven independent mutants with homozygous and stably altered seminal root number phenotypes. One mutant, Cadenza0900, displays a recessive extra seminal root number phenotype, while six mutants (Cadenza0062, Cadenza0369, Cadenza0393, Cadenza0465, Cadenza0818 and Cadenza1273) show lower seminal root number phenotypes most likely originating from defects in the formation and activation of seminal root primordia. Segregation analysis in F2 populations suggest that the phenotype of Cadenza0900 is controlled by multiple loci whereas the Cadenza0062 phenotype fits a 3:1 mutant:wild-type segregation ratio characteristic of dominant single gene action. This work highlights the potential to use the sequenced wheat mutant population as a forward genetic resource to uncover novel variation in agronomic traits, such as seminal root architecture.

Bambara groundnut: an exemplar underutilised legume for resilience under climate change

Bambara groundnut has the potential to be used to contribute more the climate change ready agriculture. The requirement for nitrogen fixing, stress tolerant legumes is clear, particularly in low input agriculture. However, ensuring that existing negative traits are tackled and demand is stimulated through the development of markets and products still represents a challenge to making greater use of this legume. World agriculture is currently based on very limited numbers of crops, representing a significant risk to food supplies, particularly in the face of climate change which is expected to increase the frequency of extreme events. Minor and underutilised crops can help to develop a more resilient and nutritionally dense future agriculture. Bambara groundnut [Vigna subterranea (L.) Verdc.[, as a drought resistant, nitrogen-fixing, legume has a role to play. However, as with most underutilised crops, there are significant gaps in knowledge and also negative traits such as 'hard-to-cook' and 'photoperiod sensitivity to pod filling' associated with the crop which future breeding programmes and processing methods need to tackle, to allow it to make a significant contribution to the well-being of future generations. The current review assesses these factors and also considers what are the next steps towards realising the potential of this crop.

Cortical Cell Diameter Is Key To Energy Costs of Root Growth in Wheat

Root growth requires substantial amounts of energy and thus carbohydrates. The energy costs of root growth are particularly high in both dry and compacted soil, due to high soil penetration resistance. Consequently, more carbon must be allocated from aboveground plant tissue to roots, which limits crop productivity. In this study, we tested the utility of root cortical cell diameter as a potential selection target to reduce the energy costs of root growth. Isothermal calorimetry was adopted for in situ quantification of the energy costs of root growth of 16 wheat (Triticum aestivum) genotypes under three levels of penetration resistance. We show that cortical cell diameter is a pivotal and heritable trait, which is strongly related to the energy costs of root growth. Genotypic diversity was found for cortical cell diameter and the energy costs of root growth. A large root cortical cell diameter correlated with reduced energy costs of root growth, particularly under high soil penetration resistance. Moreover, significant correlations were found between the ability to radially enlarge cortical cells upon greater penetration resistance (i.e. phenotypic plasticity) and the responsiveness in the energy costs of root growth. A higher degree of phenotypic plasticity in cortical cell diameter was associated with reduced energy costs of root growth as soil penetration resistance increased. We therefore suggest that genotypic diversity and phenotypic plasticity in cortical cell diameter should be harnessed to adapt crops to dry and compacted soils.

Genetic Dissection of the Seminal Root System Architecture in Mediterranean Durum Wheat Landraces by Genome-Wide Association Study

Roots are crucial for adaptation to drought stress. However, phenotyping root systems is a difficult and time-consuming task due to the special feature of the traits in the process of being analyzed. Correlations between root system architecture (RSA) at the early stages of development and in adult plants have been reported. In this study, the seminal RSA was analysed on a collection of 160 durum wheat landraces from 21 Mediterranean countries and 18 modern cultivars. The landraces showed large variability in RSA, and differences in root traits were found between previously identified genetic subpopulations. Landraces from the eastern Mediterranean region, which is the driest and warmest within the Mediterranean Basin, showed the largest seminal root size in terms of root length, surface, and volume and the widest root angle, whereas landraces from eastern Balkan countries showed the lowest values. Correlations were found between RSA and yield-related traits in a very dry environment. The identification of molecular markers linked to the traits of interest detected 233 marker-trait associations for 10 RSA traits and grouped them in 82 genome regions named marker-train association quantitative trait loci (MTA-QTLs). Our results support the use of ancient local germplasm to widen the genetic background for root traits in breeding programs.

Effects of ten years organic and conventional farming on early seedling traits of evolving winter wheat composite cross populations

Early vigour traits of wheat composite cross populations (CCPs) based on high yielding (Y) or high quality (Q) or Y*Q varietal intercross evolving under organic or conventional conditions in parallel populations were studied hydroponically. To eliminate storage and year effects, frozen F6, F10, F11 and F15 seeds were multiplied in one field, resulting in the respective Fx.1 generations. This eliminated generation and growing system effects on seed size for the F6.1 F10.1 and F15.1. Due to a severe winter kill affecting the F11, the generation effect persisted, leading to larger seeds and markedly different seedling traits in the F11.1 compared to the F10.1 and F15.1. Seedling traits were similar among parallel populations. Shoot length and weight increased in both systems until the F11.1 across farming systems and remained constant thereafter. Over time, seminal root length and root weight of organic CCPs increased and total- and specific- root length decreased significantly compared to the conventional CCPs. Rooting patterns under organic conditions suggests better ability to reach deeper soil nutrients. In both systems, Q and YQ CCPs were more vigorous than Y CCPs, confirming genetic differences among populations. Overall, heterogeneous populations appear very plastic and selection pressure was stronger in organic systems.