Modeling branching in cereals

Segmentation of structural parts of rosebush plants with 3D point-based deep learning methods

BACKGROUND

Segmentation of structural parts of 3D models of plants is an important step for plant phenotyping, especially for monitoring architectural and morphological traits. Current state-of-the art approaches rely on hand-crafted 3D local features for modeling geometric variations in plant structures. While recent advancements in deep learning on point clouds have the potential of extracting relevant local and global characteristics, the scarcity of labeled 3D plant data impedes the exploration of this potential.

RESULTS

We adapted six recent point-based deep learning architectures (PointNet, PointNet++, DGCNN, PointCNN, ShellNet, RIConv) for segmentation of structural parts of rosebush models. We generated 3D synthetic rosebush models to provide adequate amount of labeled data for modification and pre-training of these architectures. To evaluate their performance on real rosebush plants, we used the ROSE-X data set of fully annotated point cloud models. We provided experiments with and without the incorporation of synthetic data to demonstrate the potential of point-based deep learning techniques even with limited labeled data of real plants.

CONCLUSION

The experimental results show that PointNet++ produces the highest segmentation accuracy among the six point-based deep learning methods. The advantage of PointNet++ is that it provides a flexibility in the scales of the hierarchical organization of the point cloud data. Pre-training with synthetic 3D models boosted the performance of all architectures, except for PointNet.

Alternative splicing of a barley gene results in an excess-tillering and semi-dwarf mutant

An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F₁, F₂, and F_2:3 populations showed that a single recessive gene controlled the excess-tillering semi-dwarf in htd. Using BSR-Seq and gene mapping, the Hvhtd gene was delimited within a 1.8 Mb interval on chromosome 2HL. Alignment of the RNA-Seq data with the functional genes in the interval identified a gene HORVU2Hr1G098820 with alternative splicing between exon2 and exon3 in the mutant, due to a G to A single-nucleotide substitution at the exon and intron junction. An independent mutant with a similar phenotype confirmed the result, with alternative splicing between exon3 and exon4. In both cases, the alternative splicing resulted in a non-functional protein. And the gene HORVU2Hr1G098820 encodes a trypsin family protein and may be involved in the IAA signaling pathway and differs from the mechanism of Green Revolution genes in the gibberellic acid metabolic pathway.

Modelling tiller growth and mortality as a sink-driven process using Ecomeristem: implications for biomass sorghum ideotyping

BACKGROUND AND AIMS

Plant modelling can efficiently support ideotype conception, particularly in multi-criteria selection contexts. This is the case for biomass sorghum, implying the need to consider traits related to biomass production and quality. This study evaluated three modelling approaches for their ability to predict tiller growth, mortality and their impact, together with other morphological and physiological traits, on biomass sorghum ideotype prediction.

METHODS

Three Ecomeristem model versions were compared to evaluate whether tillering cessation and mortality were source (access to light) or sink (age-based hierarchical access to C supply) driven. They were tested using a field data set considering two biomass sorghum genotypes at two planting densities. An additional data set comparing eight genotypes was used to validate the best approach for its ability to predict the genotypic and environmental control of biomass production. A sensitivity analysis was performed to explore the impact of key genotypic parameters and define optimal parameter combinations depending on planting density and targeted production (sugar and fibre).

KEY RESULTS

The sink-driven control of tillering cessation and mortality was the most accurate, and represented the phenotypic variability of studied sorghum genotypes in terms of biomass production and partitioning between structural and non-structural carbohydrates. Model sensitivity analysis revealed that light conversion efficiency and stem diameter are key traits to target for improving sorghum biomass within existing genetic diversity. Tillering contribution to biomass production appeared highly genotype and environment dependent, making it a challenging trait for designing ideotypes.

CONCLUSIONS

By modelling tiller growth and mortality as sink-driven processes, Ecomeristem could predict and explore the genotypic and environmental variability of biomass sorghum production. Its application to larger sorghum genetic diversity considering water deficit regulations and its coupling to a genetic model will make it a powerful tool to assist ideotyping for current and future climatic scenario.

Light Regulation of Axillary Bud Outgrowth Along Plant Axes: An Overview of the Roles of Sugars and Hormones

Apical dominance, the process by which the growing apical zone of the shoot inhibits bud outgrowth, involves an intricate network of several signals in the shoot. Auxin originating from plant apical region inhibits bud outgrowth indirectly. This inhibition is in particular mediated by cytokinins and strigolactones, which move from the stem to the bud and that respectively stimulate and repress bud outgrowth. The action of this hormonal network is itself modulated by sugar levels as competition for sugars, caused by the growing apical sugar sink, may deprive buds from sugars and prevents bud outgrowth partly by their signaling role. In this review, we analyze recent findings on the interaction between light, in terms of quantity and quality, and apical dominance regulation. Depending on growth conditions, light may trigger different pathways of the apical dominance regulatory network. Studies pinpoint to the key role of shoot-located cytokinin synthesis for light intensity and abscisic acid synthesis in the bud for R:FR in the regulation of bud outgrowth by light. Our analysis provides three major research lines to get a more comprehensive understanding of light effects on bud outgrowth. This would undoubtedly benefit from the use of computer modeling associated with experimental observations to deal with a regulatory system that involves several interacting signals, feedbacks, and quantitative effects.

WALTer: a three-dimensional wheat model to study competition for light through the prediction of tillering dynamics

BACKGROUND AND AIMS

Branching is a main morphogenetic process involved in the adaptation of plants to the environment. In grasses, tillering is divided into three phases: tiller emergence, cessation of tillering and tiller regression. Understanding and prediction of the tillering process is a major challenge to better control cereal yields. In this paper, we present and evaluate WALTer, an individual-based model of wheat built on simple self-adaptive rules for predicting the tillering dynamics at contrasting sowing densities.

METHODS

WALTer simulates the three-dimensional (3-D) development of the aerial architecture of winter wheat. Tillering was modelled using two main hypotheses: (H1) a plant ceases to initiate new tillers when a critical Green Area Index (GAIc) is reached, and (H2) the regression of a tiller occurs if its interception of light is below a threshold (PARt). The development of vegetative organs follows descriptive rules adapted from the literature. A sensitivity analysis was performed to evaluate the impact of each parameter on tillering and GAI dynamics. WALTer was parameterized and evaluated using an initial dataset providing an extensive description of GAI dynamics, and another dataset describing tillering dynamics under a wide range of sowing densities.

KEY RESULTS

Sensitivity analysis indicated the predominant importance of GAIc and PARt. Tillering and GAI dynamics of expt 1 were well fit by WALTer. Once calibrated based on the agronomic density of expt 2, tillering parameters allowed an adequate prediction of tillering dynamics at contrasting sowing densities.

CONCLUSIONS

Using simple rules and a small number of parameters, WALTer efficiently simulated the wheat tillering dynamics observed at contrasting densities in experimental data. These results show that the definition of a critical GAI and a threshold of PAR is a relevant way to represent, respectively, cessation of tillering and tiller regression under competition for light.

Estimating Sink Parameters of Stochastic Functional-Structural Plant Models Using Organic Series-Continuous and Rhythmic Development

Functional-structural plant models (FSPMs) generally simulate plant development and growth at the level of individual organs (leaves, flowers, internodes, etc.). Parameters that are not directly measurable, such as the sink strength of organs, can be estimated inversely by fitting the weights of organs along an axis (organic series) with the corresponding model output. To accommodate intracanopy variability among individual plants, stochastic FSPMs have been built by introducing the randomness in plant development; this presents a challenge in comparing model output and experimental data in parameter estimation since the plant axis contains individual organs with different amounts and weights. To achieve model calibration, the interaction between plant development and growth is disentangled by first computing the occurrence probabilities of each potential site of phytomer, as defined in the developmental model (potential structure). On this basis, the mean organic series is computed analytically to fit the organ-level target data. This process is applied for plants with continuous and rhythmic development simulated with different development parameter sets. The results are verified by Monte-Carlo simulation. Calibration tests are performed both in silico and on real plants. The analytical organic series are obtained for both continuous and rhythmic cases, and they match well with the results from Monte-Carlo simulation, and vice versa. This fitting process works well for both the simulated and real data sets; thus, the proposed method can solve the source-sink functions of stochastic plant architectures through a simplified approach to plant sampling. This work presents a generic method for estimating the sink parameters of a stochastic FSPM using statistical organ-level data, and it provides a method for sampling stems. The current work breaks a bottleneck in the application of FSPMs to real plants, creating the opportunity for broad applications.

Subtle variation in shade avoidance responses may have profound consequences for plant competitiveness

BACKGROUND AND AIMS

Although phenotypic plasticity has been shown to be beneficial for plant competitiveness for light, there is limited knowledge on how variation in these plastic responses plays a role in determining competitiveness.

METHODS

A combination of detailed plant experiments and functional-structural plant (FSP) modelling was used that captures the complex dynamic feedback between the changing plant phenotype and the within-canopy light environment in time and 3-D space. Leaf angle increase (hyponasty) and changes in petiole elongation rates in response to changes in the ratio between red and far-red light, two important shade avoidance responses in Arabidopsis thaliana growing in dense population stands, were chosen as a case study for plant plasticity. Measuring and implementing these responses into an FSP model allowed simulation of plant phenotype as an emergent property of the underlying growth and response mechanisms.

KEY RESULTS

Both the experimental and model results showed that substantial differences in competitiveness may arise between genotypes with only marginally different hyponasty or petiole elongation responses, due to the amplification of plant growth differences by small changes in plant phenotype. In addition, this study illustrated that strong competitive responses do not necessarily have to result in a tragedy of the commons; success in competition at the expense of community performance.

CONCLUSIONS

Together, these findings indicate that selection pressure could probably have played a role in fine-tuning the sensitive shade avoidance responses found in plants. The model approach presented here provides a novel tool to analyse further how natural selection could have acted on the evolution of plastic responses.

The Genetic Architecture of Barley Plant Stature

Plant stature in temperate cereals is predominantly controlled by tillering and plant height as complex agronomic traits, representing important determinants of grain yield. This study was designed to reveal the genetic basis of tillering at five developmental stages and plant height at harvest in 218 worldwide spring barley (Hordeum vulgare L.) accessions under greenhouse conditions. The accessions were structured based on row-type classes [two- vs. six-rowed] and photoperiod response [photoperiod-sensitive (Ppd-H1) vs. reduced photoperiod sensitivity (ppd-H1)]. Phenotypic analyses of both factors revealed profound between group effects on tiller development. To further verify the row-type effect on the studied traits, Six-rowed spike 1 (vrs1) mutants and their two-rowed progenitors were examined for tiller number per plant and plant height. Here, wild-type (Vrs1) plants were significantly taller and had more tillers than mutants suggesting a negative pleiotropic effect of this row-type locus on both traits. Our genome-wide association scans further revealed highly significant associations, thereby establishing a link between the genetic control of row-type, heading time, tillering, and plant height. We further show that associations for tillering and plant height are co-localized with chromosomal segments harboring known plant stature-related phytohormone and sugar-related genes. This work demonstrates the feasibility of the GWAS approach for identifying putative candidate genes for improving plant architecture.

Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690-710 mm) and water-limited (290-320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass-specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.

Optimizing tiller production and survival for grain yield improvement in a bread wheat × spelt mapping population

BACKGROUND AND AIMS

Tiller production and survival determine final spike number, and play key roles in grain yield formation in wheat (Triticum aestivum). This study aimed to understand the genetic and physiological basis of the tillering process, and its trade-offs with other yield components, by introducing genetic variation in tillering patterns via a mapping population of wheat × spelt (Triticum spelta).

METHODS

The dynamics of tillering and red/far-red ratio (R:FR) at the base of a canopy arising from neighbouring plants in a bread wheat (Triticum aestivum 'Forno') × spelt (Triticum spelta 'Oberkulmer') mapping population were measured in the field in two growing seasons. Additional thinning and shading experiments were conducted in the field and glasshouse, respectively. Yield components were analysed for all experiments, followed by identification of quantitative trait loci (QTL) associated with each trait.

KEY RESULTS

Large genetic variation in tillering was observed, and more fertile shoots per plant were associated with more total shoots initiated, faster tillering rate, delayed tillering onset and cessation, and higher shoot survival. A total of 34 QTL for tillering traits were identified, and analysis of allelic effects confirmed the above associations. Low R:FR was associated with early tillering cessation, few total shoots, high infertile shoot number and shoot abortion, and these results concurred with the thinning and shading experiments. These effects probably resulted from an assimilate shortage for tiller buds or developing tillers, due to early stem elongation and enhanced stem growth induced by low R:FR. More fertile tillers normally contributed to plant yield and grain number without reducing yield and grain set of individual shoots. However, there was a decrease in grain weight, partly because of smaller carpels and fewer stem water-soluble carbohydrates at anthesis caused by pleiotropy or tight gene linkages.

CONCLUSIONS

Tillering is under the control of both genetic factors and R:FR. Genetic variation in tillering and tolerance to low R:FR can be used to optimize tillering patterns for yield improvement in wheat.

Multiple pathways regulate shoot branching

Shoot branching patterns result from the spatio-temporal regulation of axillary bud outgrowth. Numerous endogenous, developmental and environmental factors are integrated at the bud and plant levels to determine numbers of growing shoots. Multiple pathways that converge to common integrators are most probably involved. We propose several pathways involving not only the classical hormones auxin, cytokinins and strigolactones, but also other signals with a strong influence on shoot branching such as gibberellins, sugars or molecular actors of plant phase transition. We also deal with recent findings about the molecular mechanisms and the pathway involved in the response to shade as an example of an environmental signal controlling branching. We propose the TEOSINTE BRANCHED1, CYCLOIDEA, PCF transcription factor TB1/BRC1 and the polar auxin transport stream in the stem as possible integrators of these pathways. We finally discuss how modeling can help to represent this highly dynamic system by articulating knowledges and hypothesis and calculating the phenotype properties they imply.

Canopy architectural and physiological characterization of near-isogenic wheat lines differing in the tiller inhibition gene tin

Tillering is a core constituent of plant architecture, and influences light interception to affect plant and crop performance. Near-isogenic lines (NILs) varying for a tiller inhibition (tin) gene and representing two genetic backgrounds were investigated for tillering dynamics, organ size distribution, leaf area, light interception, red: far-red ratio, and chlorophyll content. Tillering ceased earlier in the tin lines to reduce the frequencies of later primary and secondary tillers compared to the free-tillering NILs, and demonstrated the genetically lower tillering plasticity of tin-containing lines. The distribution of organ sizes along shoots varied between NILs contrasting for tin. Internode elongation commenced at a lower phytomer, and the peduncle was shorter in the tin lines. The flag leaves of tin lines were larger, and the longest leaf blades were observed at higher phytomers in the tin than in free-tillering lines. Total leaf area was reduced in tin lines, and non-tin lines invested more leaf area at mid-canopy height. The tiller economy (ratio of seed-bearing shoots to numbers of shoots produced) was 10% greater in the tin lines (0.73-0.76) compared to the free-tillering sisters (0.62-0.63). At maximum tiller number, the red: far-red ratio (light quality stimulus that is thought to induce the cessation of tillering) at the plant-base was 0.18-0.22 in tin lines and 0.09-0.11 in free-tillering lines at levels of photosynthetic active radiation of 49-53% and 30-33%, respectively. The tin lines intercepted less radiation compared to their free-tillering sisters once genotypic differences in tiller numbers had established, and maintained green leaf area in the lower canopy later into the season. Greater light extinction coefficients (k) in tin lines prior to, but reduced k after, spike emergence indicated that differences in light interception between NILs contrasting in tin cannot be explained by leaf area alone but that geometric and optical canopy properties contributed. The careful characterization of specifically-developed NILs is refining the development of a physiology-based model for tillering to improve understanding of the value of architectural traits for use in cereal improvement.