X-ray driven peanut trait estimation: computer vision aided agri-system transformation.

BACKGROUND: In India, raw peanuts are obtained by aggregators from smallholder farms in the form of whole pods and the price is based on a manual estimation of basic peanut pod and kernel characteristics. These methods of raw produce evaluation are slow and can result in procurement irregularities. The procurement delays combined with the lack of storage facilities lead to fungal contaminations and pose a serious threat to food safety in many regions. To address this gap, we investigated whether X-ray technology could be used for the rapid assessment of the key peanut qualities that are important for price estimation. RESULTS: We generated 1752 individual peanut pod 2D X-ray projections using a computed tomography (CT) system (CTportable160.90). Out of these projections we predicted the kernel weight and shell weight, which are important indicators of the produce price. Two methods for the feature prediction were tested: (i) X-ray image transformation (XRT) and (ii) a trained convolutional neural network (CNN). The prediction power of these methods was tested against the gravimetric measurements of kernel weight and shell weight in diverse peanut pod varieties1. Both methods predicted the kernel mass with R2 > 0.93 (XRT: R2 = 0.93 and mean error estimate (MAE) = 0.17, CNN: R2 = 0.95 and MAE = 0.14). While the shell weight was predicted more accurately by CNN (R2 = 0.91, MAE = 0.09) compared to XRT (R2 = 0.78; MAE = 0.08). CONCLUSION: Our study demonstrated that the X-ray based system is a relevant technology option for the estimation of key peanut produce indicators (Figure 1). The obtained results justify further research to adapt the existing X-ray system for the rapid, accurate and objective peanut procurement process. Fast and accurate estimates of produce value are a necessary pre-requisite to avoid post-harvest losses due to fungal contamination and, at the same time, allow the fair payment to farmers. Additionally, the same technology could also assist crop improvement programs in selecting and developing peanut cultivars with enhanced economic value in a high-throughput manner by skipping the shelling of the pods completely. This study demonstrated the technical feasibility of the approach and is a first step to realize a technology-driven peanut production system transformation of the future.

Quantitative trait loci (QTLs) for water use and crop production traits co-locate with major QTL for tolerance to water deficit in a fine-mapping population of pearl millet (Pennisetum glaucum L. R.Br.).

KEY MESSAGE: Four genetic regions associated with water use traits, measured at different levels of plant organization, and with agronomic traits were identified within a previously reported region for terminal water deficit adaptation on linkage group 2. Close linkages between these traits showed the value of phenotyping both for agronomic and secondary traits to better understand plant productive processes. Water saving traits are critical for water stress adaptation of pearl millet, whereas maximizing water use is key to the absence of stress. This research aimed at demonstrating the close relationship between traits measured at different levels of plant organization, some putatively involved in water stress adaptation, and those responsible for agronomic performance. A fine-mapping population of pearl millet, segregating for a previously identified quantitative trait locus (QTL) for adaptation to terminal drought stress on LG02, was phenotyped for traits at different levels of plant organization in different experimental environments (pot culture, high-throughput phenotyping platform, lysimeters, and field). The linkages among traits across the experimental systems were analysed using principal component analysis and QTL co-localization approach. Four regions within the LG02-QTL were found and revealed substantial co-mapping of water use and agronomic traits. These regions, identified across experimental systems, provided genetic evidence of the tight linkages between traits phenotyped at a lower level of plant organization and agronomic traits assessed in the field, therefore deepening our understanding of complex traits and then benefiting both geneticists and breeders. In short: (1) under no/mild stress conditions, increasing biomass and tiller production increased water use and eventually yield; (2) under severe stress conditions, water savings at vegetative stage, from lower plant vigour and fewer tillers in that population, led to more water available during grain filling, expression of stay-green phenotypes, and higher yield.

Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome.

BACKGROUND: Terminal drought stress leads to substantial annual yield losses in chickpea (Cicer arietinum L.). Adaptation to water limitation is a matter of matching water supply to water demand by the crop. Therefore, harnessing the genetics of traits contributing to plant water use, i.e. transpiration rate and canopy development dynamics, is important to design crop ideotypes suited to a varying range of water limited environments. With an aim of identifying genomic regions for plant vigour (growth and canopy size) and canopy conductance traits, 232 recombinant inbred lines derived from a cross between ICC 4958 and ICC 1882, were phenotyped at vegetative stage under well-watered conditions using a high throughput phenotyping platform (LeasyScan). RESULTS: Twenty one major quantitative trait loci (M-QTLs) were identified for plant vigour and canopy conductance traits using an ultra-high density bin map. Plant vigour traits had 13 M-QTLs on CaLG04, with favourable alleles from high vigour parent ICC 4958. Most of them co-mapped with a previously fine mapped major drought tolerance "QTL-hotspot" region on CaLG04. One M-QTL was found for canopy conductance on CaLG03 with the ultra-high density bin map. Comparative analysis of the QTLs found across different density genetic maps revealed that QTL size reduced considerably and % of phenotypic variation increased as marker density increased. CONCLUSION: Earlier reported drought tolerance hotspot is a vigour locus. The fact that canopy conductance traits, i.e. the other important determinant of plant water use, mapped on CaLG03 provides an opportunity to manipulate these loci to tailor recombinants having low/high transpiration rate and plant vigour, fitted to specific drought stress scenarios in chickpea.

Component traits of plant water use are modulated by vapour pressure deficit in pearl millet (Pennisetum glaucum (L.) R.Br.).

Traits influencing plant water use eventually define the fitness of genotypes for specific rainfall environments. We assessed the response of several water use traits to vapour pressure deficit (VPD) in pearl millet (Pennisetum glaucum (L.) R.Br.) genotypes known to differ in drought adaptation mechanisms: PRLT 2/89-33 (terminal drought-adapted parent), H 77/833-2 (terminal drought-sensitive parent) and four near-isogenic lines introgressed with a terminal drought tolerance quantitative trait locus (QTL) from PRLT 2/89-33 (ICMR01029, ICMR01031, ICMR02042, and ICMR02044). Plant water use traits at various levels of plant organisation were evaluated in seven experiments in plants exposed either transiently or over the long term to different VPD regimes: biomass components, transpiration (water usage per time unit) and transpiration rate (TR) upon transient VPD increase (gH2Ocm-2h-1)), transpiration efficiency (g dry biomass per kg H2O transpired), leaf expansion rate (cm per thermal time unit) and root anatomy (endodermis dimensions)). High VPD decreased biomass accumulation by reducing tillering, the leaf expansion rate and the duration of leaf expansion; decreased root endodermis cell size; and increased TR and the rate of TR increase upon gradual short-term VPD increases. Such changes may allow plants to increase their water transport capacity in a high VPD environment and are genotype-specific. Some variation in water use components was associated with terminal drought adaptation QTL. Knowledge of water use traits' plasticity in growth environments that varied in evaporative demand, and on their genetic determinacy, is necessary to develop trait-based breeding approaches to complex constraints.

Higher flower and seed number leads to higher yield under water stress conditions imposed during reproduction in chickpea.

The reproductive phase of chickpea (Cicer arietinum L.) is more sensitive to water deficits than the vegetative phase. The characteristics that confer drought tolerance to genotypes at the reproductive stage are not well understood; especially which characteristics are responsible for differences in seed yield under water stress. In two consecutive years, 10 genotypes with contrasting yields under terminal drought stress in the field were exposed to a gradual, but similar, water stress in the glasshouse. Flower number, flower+pod+seed abortion percentage, pod number, pod weight, seed number, seed yield, 100-seed weight (seed size), stem+leaf weight and harvest index (HI) were recorded in well watered plants (WW) and in water-stressed plants (WS) when the level of deficit was mild (phase I), and when the stress was severe (phase II). The WS treatment reduced seed yield, seed and pod number, but not flower+pod+seed abortion percentage or 100-seed weight. Although there were significant differences in total seed yield among the genotypes, the ranking of the seed yield in the glasshouse differed from the ranking in the field, indicating large genotype×environment interaction. Genetic variation for seed yield and seed yield components was observed in the WW treatment, which also showed differences across years, as well as in the WS treatment in both the years, so that the relative seed yield and relative yield components (ratio of values under WS to those under WW) were used as measures of drought tolerance. Relative total seed yield was positively associated with relative total flower number (R2=0.23 in year 2) and relative total seed number (R2=0.83, R2=0.79 in years 1 and 2 respectively). In phase I (mild stress), relative yield of seed produced in that phase was found to be associated with the flower number in both the years (R2=0.69, R2=0.76 respectively). Therefore, the controlled drought imposition that was used, where daily water loss from the soil was made equal for all plants, revealed genotypic differences in the sensitivity of the reproductive process to drought. Under these conditions, the seed yield differences in chickpea were largely related to the capacity to produce a large number of flowers and to set seeds, especially in the early phase of drought stress when the degree of water deficit was mild.

Changes in timing of water uptake and phenology favours yield gain in terminal water stressed chickpea AtDREB1A transgenics.

Terminal drought causes major yield loss in chickpea, so it is imperative to identify genotypes with best suited adaptive traits to secure yield in terminal drought-prone environments. Here, we evaluated chickpea (At) rd29A:: (At) DREB1A transgenic events (RD2, RD7, RD9 and RD10) and their untransformed C235 genotype for growth, water use and yield under terminal water-stress (WS) and well-watered (WW) conditions. The assessment was made across three lysimetric trials conducted in contained environments in the greenhouse (2009GH and 2010GH) and the field (2010F). Results from the greenhouse trials showed genotypic variation for harvest index (HI), yield, temporal pattern of flowering and seed filling, temporal pattern of water uptake across crop cycle, and transpiration efficiency (TE) under terminal WS conditions. The mechanisms underlying the yield gain in the WS transgenic events under 2009GH trial was related to conserving water for the reproductive stage in RD7, and setting seeds early in RD10. Water conservation also led to a lower percentage of flower and pod abortion in both RD7 and RD10. Similarly, in the 2010GH trial, reduced water extraction during vegetative stage in events RD2, RD7 and RD9 was critical for better seed filling in the pods produced from late flowers in RD2, and reduced percentage of flower and pod abortion in RD2 and RD9. However, in the 2010F trial, the increased seed yield and HI in RD9 compared with C235 came along only with small changes in water uptake and podding pattern, probably not causal. Events RD2 (2010GH), RD7 (2010GH) and RD10 (2009GH) with higher seed yield also had higher TE than C235. The results suggest that DREB1A, a transcription factor involved in the regulation of several genes of abiotic stress response cascade, influenced the pattern of water uptake and flowering across the crop cycle, leading to reduction in the percentage of flower and pod abortion in the glasshouse trials.

Modelling the effect of plant water use traits on yield and stay-green expression in sorghum.

Post-rainy sorghum (Sorghum bicolor (L.) Moench) production underpins the livelihood of millions in the semiarid tropics, where the crop is affected by drought. Drought scenarios have been classified and quantified using crop simulation. In this report, variation in traits that hypothetically contribute to drought adaptation (plant growth dynamics, canopy and root water conducting capacity, drought stress responses) were virtually introgressed into the most common post-rainy sorghum genotype, and the influence of these traits on plant growth, development, and grain and stover yield were simulated across different scenarios. Limited transpiration rates under high vapour pressure deficit had the highest positive effect on production, especially combined with enhanced water extraction capacity at the root level. Variability in leaf development (smaller canopy size, later plant vigour or increased leaf appearance rate) also increased grain yield under severe drought, although it caused a stover yield trade-off under milder stress. Although the leaf development response to soil drying varied, this trait had only a modest benefit on crop production across all stress scenarios. Closer dissection of the model outputs showed that under water limitation, grain yield was largely determined by the amount of water availability after anthesis, and this relationship became closer with stress severity. All traits investigated increased water availability after anthesis and caused a delay in leaf senescence and led to a 'stay-green' phenotype. In conclusion, we showed that breeding success remained highly probabilistic; maximum resilience and economic benefits depended on drought frequency. Maximum potential could be explored by specific combinations of traits.