Natural variation in LONELY GUY-Like 1 regulates rice grain weight under warmer night conditions.

Global nighttime temperatures are rising at twice the rate of daytime temperatures and pose a challenge for rice (Oryza sativa) production. High nighttime temperature (HNT) stress affects rice yield by reducing grain weight, size, and fertility. Although the genes associated with these yield parameters have been identified and characterized under normal temperatures, the genetic basis of grain weight regulation under HNT stress remains less explored. We examined the natural variation for rice single grain weight (SGW) under HNT stress imposed during grain development. A genome-wide association analysis identified several loci associated with grain weight under HNT stress. A locus, single grain weight 1 (SGW1), specific to HNT conditions resolved to LONELY GUY-Like 1 (LOGL1), which encodes a putative cytokinin activation enzyme. We demonstrated that LOGL1 contributes to allelic variation at SGW1. Accessions with lower LOGL1 transcript abundance had higher grain weight under HNT. This was supported by higher grain weight of logl1 mutants relative to the wild type under HNT. Compared to logl1 mutants, LOGL1 over-expressers showed increased sensitivity to HNT. We showed that LOGL1 regulates the thiamine biosynthesis pathway, which is under circadian regulation, which in turn is likely perturbed by HNT stress. These findings provide a genetic source to enhance rice adaptation to warming night temperatures and improve our mechanistic understanding of HNT stress tolerance pathways.

Alternative pathways leading to ascorbate biosynthesis in plants: lessons from the last 25 years.

l-Ascorbic acid (AsA) is an antioxidant with important roles in plant stress physiology, growth, and development. AsA also plays an essential role in human health, preventing scurvy. Humans do not synthesize AsA, which needs to be supplied via a diet rich in fresh produce. Research efforts have provided progress in the elucidation of a complex metabolic network with at least four routes leading to AsA formation in plants. In this review, three alternative pathways, namely the d-galacturonate, the l-gulose, and the myo-inositol pathways, are presented with the supporting evidence of their operation in multiple plant species. We critically discuss feeding studies using precursors and their conversion to AsA in plant organs, and research where the expression of key genes encoding enzymes involved in the alternative pathways showed >100% AsA content increase in the transgenics and in many cases accompanied by enhanced tolerance to multiple stresses. We propose that the alternative pathways are vital in AsA production in response to stressful conditions and to compensate in cases where the flux through the d-mannose/l-galactose pathway is reduced. The genes and enzymes that have been characterized so far in these alternative pathways represent important tools that are being used to develop more climate-tolerant crops.

Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice.

High night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.

Chlorophyll Fluorescence and Reflectance-Based Non-Invasive Quantification of Blast, Bacterial Blight and Drought Stresses in Rice.

Response of rice (Oryza sativa) exposed to both biotic and abiotic stresses can be quantified by employing fast and accurate optical methods. In this study, the overall stress responses of (i) 12 near-isogenic lines (NILs) in the genetic background of the rice blast-susceptible cultivar Lijiangxintuanheigu (LTH) and (ii) four NILs in the genetic background of the bacterial blight-susceptible cultivar IR24, were inspected by means of Chl fluorescence (Chl-F) imaging. The distribution of the maximum and effective quantum yield of PSII (Fv/FM and QY) and steady-state Chl-F (Ft) were found to be effective in differentiating symptomatic leaf tissue for both rice blast and bacterial blight, which correlated well with 30 cycles of rice blast and six cycles of bacterial blight previously screened using classical (manual) approaches. Subsequently, identified Chl-F parameters allowing detection under ambient light (QY and Ft) were tested across both biotic and abiotic (drought) stress experiments, for rice cultivars contrasting for drought stress response (N22, IR64 and NSIC Rc 222). Their applicability has been proven for both rice blast and bacterial blight; however, QY failed to detect the effect of drought. In addition to Chl-F, the usefulness of 11 selected vegetation indices (Vis) was tested on these three cultivars exposed to particular stresses: (i) rice blast was detectable by Vis calculated from the visible spectrum; (ii) bacterial blight by near-infrared-related Vis; and (iii) drought by Vis calculated from the visible spectrum. The key Chl-F parameters and/or Vis have been summarized and discussed.

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.

Effect of carbohydrates and night temperature on night respiration in rice.

Global warming causes night temperature (NT) to increase faster than day temperature in the tropics. According to crop growth models, respiration incurs a loss of 40-60% of photosynthate. The thermal sensitivity of night respiration (R(n)) will thus reduce biomass. Instantaneous and acclimated effects of NT on R(n) of leaves and seedlings of two rice cultivars having a variable level of carbohydrates, induced by exposure to different light intensity on the previous day, were investigated. Experiments were conducted in a greenhouse and growth chambers, with R(n) measured on the youngest fully expanded leaves or whole seedlings. Dry weight-based R(n) was 2.6-fold greater for seedlings than for leaves. Leaf R(n) was linearly related to starch (positive intercept) and soluble sugar concentration (zero intercept). Increased NT caused higher R(n) at a given carbohydrate concentration. The change of R(n) at NT increasing from 21 °C to 31 °C was 2.4-fold for the instantaneous response but 1.2- to 1.7-fold after acclimation. The maintenance component of R(n) (R(m)'), estimated by assimilate starvation, averaged 28% in seedlings and 34% in leaves, with no significant thermal effect on this ratio. The acclimated effect of increased NT on R(m)' across experiments was 1.5-fold for a 10 °C increase in NT. No cultivar differences were observed in R(n) or R(m)' responses. The results suggest that the commonly used Q10=2 rule overestimates thermal response of respiration, and R(n) largely depends on assimilate resources.

High night temperature induces contrasting responses for spikelet fertility, spikelet tissue temperature, flowering characteristics and grain quality in rice.

Climate change is increasing night temperature (NT) more than day temperature (DT) in rice-growing areas. Effects of combinations of NT (24-35°C) from microsporogenesis to anthesis at one or more DT (30 or 35°C) at anthesis on rice spikelet fertility, temperature within spikelets, flowering pattern, grain weight per panicle, amylose content and gel consistency were investigated in contrasting rice cultivars under controlled environments. Cultivars differed in spikelet fertility response to high NT, with higher fertility associated with cooler spikelets (P<0.01). Flowering dynamics were altered by high NT and a novel high temperature tolerance complementary mechanism, shorter flower open duration in cv. N22, was identified. High NT reduced spikelet fertility, grain weight per panicle, amylose content and gel consistency, whereas high DT reduced only gel consistency. Night temperature >27°C was estimated to reduce grain weight. Generally, high NT was more damaging to grain weight and selected grain quality traits than high DT, with little or no interaction between them. The critical tolerance and escape traits identified, i.e. spikelet cooling, relatively high spikelet fertility, earlier start and peak time of anthesis and shorter spikelet anthesis duration can aid plant breeding programs targeting resilience in warmer climates.