Genome-wide association reveals novel genomic loci controlling rice grain yield and its component traits under water-deficit stress during the reproductive stage

A diversity panel comprising of 296 indica rice genotypes was phenotyped under non-stress and water-deficit stress conditions during the reproductive stage in the 2013 and 2014 dry seasons (DSs) at IRRI, Philippines. We investigated the genotypic variability for grain yield, yield components, and related traits, and conducted genome-wide association studies (GWAS) using high-density 45K single nucleotide polymorphisms. We detected 38 loci in 2013 and 64 loci in 2014 for non-stress conditions and 69 loci in 2013 and 55 loci in 2014 for water-deficit stress. Desynchronized flowering time confounded grain yield and its components under water-deficit stress in the 2013 experiment. Statistically corrected grain yield and yield component values using days to flowering helped to detect 31 additional genetic loci for grain yield, its components, and the harvest index in 2013. There were few overlaps in the detected loci between years and treatments, and when compared with previous studies using the same panel, indicating the complexity of yield formation under stress. Nevertheless, our analyses provided important insights into the potential links between grain yield with seed set and assimilate partitioning. Our findings demonstrate the complex genetic architecture of yield formation and we propose exploring the genetic basis of less complex component traits as an alternative route for further yield enhancement

Using photorespiratory oxygen response to analyse leaf mesophyll resistance

Classical approaches to estimate mesophyll conductance ignore differences in resistance components for CO2 from intercellular air spaces (IAS) and CO2 from photorespiration (F) and respiration (Rd). Consequently, mesophyll conductance apparently becomes sensitive to (photo)respiration relative to net photosynthesis, (F + Rd)/A. This sensitivity depends on several hard-to-measure anatomical properties of mesophyll cells. We developed a method to estimate the parameter m (0 ≤ m ≤ 1) that lumps these anatomical properties, using gas exchange and chlorophyll fluorescence measurements where (F + Rd)/A ratios vary. This method was applied to tomato and rice leaves measured at five O2 levels. The estimated m was 0.3 for tomato but 0.0 for rice, suggesting that classical approaches implying m = 0 work well for rice. The mesophyll conductance taking the m factor into account still responded to irradiance, CO2, and O2 levels, similar to response patterns of stomatal conductance to these variables. Largely due to different m values, the fraction of (photo)respired CO2 being refixed within mesophyll cells was lower in tomato than in rice. But that was compensated for by the higher fraction via IAS, making the total re-fixation similar for both species. These results, agreeing with CO2 compensation point estimates, support our method of effectively analysing mesophyll resistance.</p

Hemp (Cannabis sativa L.) leaf photosynthesis in relation to nitrogen content and temperature: implications for hemp as a bio-economically sustainable crop

Hemp (Cannabis sativa L.) may be a suitable crop for the bio-economy as it requires low inputs while producing a high and valuable biomass yield. With the aim of understanding the physiological basis of hemp's high resource-use efficiency and yield potential, photosynthesis was analysed on leaves exposed to a range of nitrogen and temperature levels. Light-saturated net photosynthesis rate (Amax) increased with an increase in leaf nitrogen up to 31.2\uc2&nbsp;\uc2\ub1\uc2&nbsp;1.9\uc2&nbsp;\uce\ubcmol m\ue2\u88\u922 s\ue2\u88\u921 at 25\uc2&nbsp;\uc2\ub0C. The Amax initially increased with an increase in leaf temperature (TL), levelled off at 25\ue2\u80\u9335\uc2&nbsp;\uc2\ub0C and decreased when TL became higher than 35\uc2&nbsp;\uc2\ub0C. Based on a C3 leaf photosynthesis model, we estimated mesophyll conductance (gm), efficiency of converting incident irradiance into linear electron transport under limiting light (\uce\uba2LL), linear electron transport capacity (Jmax), Rubisco carboxylation capacity (Vcmax), triose phosphate utilization capacity (Tp) and day respiration (Rd), using data obtained from gas exchange and chlorophyll fluorescence measurements at different leaf positions and various levels of incident irradiance, CO2 and O2. The effects of leaf nitrogen and temperature on photosynthesis parameters were consistent at different leaf positions and among different growth environments except for \uce\uba2LL, which was higher for plants grown in the glasshouse than for those grown outdoors. Model analysis showed that compared with cotton and kenaf, hemp has higher photosynthetic capacity when leaf nitrogen is &lt;2.0\uc2&nbsp;g N m\ue2\u88\u922. The high photosynthetic capacity measured in this study, especially at low nitrogen level, provides additional evidence that hemp can be grown as a sustainable bioenergy crop over a wide range of climatic and agronomic conditions

Pollen germination and in vivo fertilization in response to high-temperature during flowering in hybrid and inbred rice

High-temperature during flowering in rice causes spikelet sterility and is a major threat to rice productivity in tropical and subtropical regions, where hybrid rice development is increasingly contributing to sustain food security. However, the sensitivity of hybrids to increasing temperature and physiological responses in terms of dynamic fertilization processes is unknown. To address these questions, several promising hybrids and inbreds were exposed to control temperature and high day-time temperature (HDT) in Experiment 1, and hybrids having contrasting heat tolerance were selected for Experiment 2 for further physiological investigation under HDT and high-night-time-temperature treatments. The day-time temperature played a dominant role in determining spikelet fertility compared with the night-time temperature. HDT significantly induced spikelet sterility in tested hybrids, and hybrids had higher heat susceptibility than the high-yielding inbred varieties. Poor pollen germination was strongly associated with sterility under high-temperature. Our novel observations capturing the series of dynamic fertilization processes demonstrated that pollen tubes not reaching the viable embryo sac was the major cause for spikelet sterility under heat exposure. Our findings highlight the urgent need to improve heat tolerance in hybrids and incorporating early-morning flowering as a promising trait for mitigating HDT stress impact at flowering.</p

Genetic control of plasticity in root morphology and anatomy of rice in response to water deficit

Elucidating the genetic control of rooting behavior under water-deficit stress is essential to breed climate-robust rice (Oryza sativa) cultivars. Using a diverse panel of 274 indica genotypes grown under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, mostly related to root morphology and anatomy, involving 45,000 root-scanning images and nearly 25,000 cross sections from the root-shoot junction. The phenotypic plasticity of these traits was quantified as the relative change in trait value under water-deficit compared with control conditions. We then carried out a genome-wide association analysis on these traits and their plasticity, using 45,608 high-quality single-nucleotide polymorphisms. One hundred four significant loci were detected for these traits under control conditions, 106 were detected under water-deficit stress, and 76 were detected for trait plasticity. We predicted 296 (control), 284 (water-deficit stress), and 233 (plasticity) a priori candidate genes within linkage disequilibrium blocks for these loci. We identified key a priori candidate genes regulating root growth and development and relevant alleles that, upon validation, can help improve rice adaptation to water-deficit stress. (Résumé d'auteur

Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements

Day respiration (Rd) is an important parameter in leaf ecophysiology. It is difficult to measure directly and is indirectly estimated from gas exchange (GE) measurements of the net photosynthetic rate (A), commonly using the Laisk method or the Kok method. Recently a new method was proposed to estimate Rd indirectly from combined GE and chlorophyll fluorescence (CF) measurements across a range of low irradiances. Here this method is tested for estimating Rd in five C3 and one C4 crop species. Values estimated by this new method agreed with those by the Laisk method for the C3 species. The Laisk method, however, is only valid for C3 species and requires measurements at very low CO2 levels. In contrast, the new method can be applied to both C3 and C4 plants and at any CO2 level. The Rd estimates by the new method were consistently somewhat higher than those by the Kok method, because using CF data corrects for errors due to any non-linearity between A and irradiance of the used data range. Like the Kok and Laisk methods, the new method is based on the assumption that Rd varies little with light intensity, which is still subject to debate. Theoretically, the new method, like the Kok method, works best for non-photorespiratory conditions. As CF information is required, data for the new method are usually collected using a small leaf chamber, whereas the Kok and Laisk methods use only GE data, allowing the use of a larger chamber to reduce the noise-to-signal ratio of GE measurements

Using a reaction‐diffusion model to estimate day respiration and reassimilation of (photo)respiredCO2in leaves

peer-reviewedMethods using gas exchange measurements to estimate respiration in the light (day respiration Rd) make implicit assumptions about reassimilation of (photo)respired CO2; however, this reassimilation depends on the positions of mitochondria. We used a reaction-diffusion model without making these assumptions to analyse datasets on gas exchange, chlorophyll fluorescence and anatomy for tomato leaves. We investigated how Rd values obtained by the Kok and the Yin methods are affected by these assumptions and how those by the Laisk method are affected by the positions of mitochondria. The Kok method always underestimated Rd. Estimates of Rd by the Yin method and by the reaction-diffusion model agreed only for nonphotorespiratory conditions. Both the Yin and Kok methods ignore reassimilation of (photo)respired CO2, and thus underestimated Rd for photorespiratory conditions, but this was less so in the Yin than in the Kok method. Estimates by the Laisk method were affected by assumed positions of mitochondria. It did not work if mitochondria were in the cytosol between the plasmamembrane and the chloroplast envelope. However, mitochondria were found to be most likely between the tonoplast and chloroplasts. Our reaction-diffusion model effectively estimates Rd, enlightens the dependence of Rd estimates on reassimilation and clarifies (dis)advantages of existing methods.KU Leuve