Performing Department
(N/A)
Non Technical Summary
Rice is a staple crop for most of the world and a common grain consumed in the United States.Rice export from the U.S. is valued at nearly $2 billion per year. Rice yield and grain quality are sensitive to higher nighttime temperatures (HNT) stress, especially during grain development. This problem is further exacerbated due to continued asymmetric increase in nighttime temperatures relative to daytime temperatures due to climate change. We have recently discovered three rice genes that contribute towards the natural variation for grain size/weight in rice germplasm under HNT. In this project, we aim to leverage these findings and associated genetic resources to elucidate the physiological and molecular basis of HNT tolerance for grain yield and quality parameters. This research will generate the foundational knowledge needed for developing rice cultivars that are not only resilient to HNT for grain yield but are also able to mitigate some of the rice losses due to poor grain quality. Successful outcome from this research will elucidate mechanisms for HNT tolerance in rice and create new molecular insights for higher yield and quality in rice.
Animal Health Component
0%
Research Effort Categories
Basic
30%
Applied
50%
Developmental
20%
Goals / Objectives
This project will generate the foundational knowledge needed for developing rice cultivars that are not only resilient to HNT for grain yield but are also able to mitigate some of the rice losses due to poor grain quality. To accomplish this, through the following specific objectives:Obj. 1. Characterize panicle-level morphological responses to HNT stress in wildtype and mutants.Obj. 2. Examine the differential physiological responses of panicles and foliar tissue to HNT stress.Obj. 3.Molecular characterization of differential HNT response between wildtype and mutants.
Project Methods
We propose to use this methodology framework for pursuing the following specific objectives:Obj. 1. Characterize panicle-level morphological responses to HNT stress in wildtype and mutants.Panicle Imaging.In this objective, we will examine the spatiotemporal dynamics of panicle morphology from mutant and WT plants under HNT stress to identify differences in response to stress and among genotypes. For this we will perform panicle level phenotyping ofLOGL1, FIE1andHXK7mutants (three independent KO and OE lines) under HNT to determine their impact on sink capacity (measured as panicle volume/voxel count) and panicle maturation (using pixel colors). This RGB camera system will enable us to collect 120 side-view images every 2 days, starting from panicle tagging. We will impose the control and HNT stress treatment in greenhouse conditions.Mature grain phenotyping. We will use scanned grain images to extract size and color parameters from an open-source GUI calledGrain Extractordeveloped by Yu and Walia (65). The R/G ratio based on pixel level analysis of rice grains by theGrain Extractorapplication is sensitive to HNT treatment. We will determine if the grain image-derived R/G ratio diverges between the wildtype and mutants of the four target genes at a whole panicle level as well as for grains collected from the middle, upper, and basal branches of the primary panicle.Our second approach for grain quality assessment will be to use our customized hyperspectral (550-1700 nm) grain imaging set-up for scanning grain collected from panicle segments (upper, middle, and basal third) of WT and mutants under control and HNT stress.Foliar Imaging.Image-based foliar phenotyping.To compare the panicle HNT responses with foliar (source tissue) responses, we will image the same set of plants used for panicle imaging using the automated, RGB and fluorescence imaging systems at the UNL Phenotyping facility. This greenhouse facility has two separate greenhouses that have independent temperature settings (for HNT and control treatments) and are connected via an automated conveyor belt system for imaging. We will analyze the RGB and fluorescence images for detecting changes in shoot biomass accumulation, heat-induced senescence (chlorophyll pigmentation), and differences in plant architecture due to genetic and temperature perturbations.Obj. 2. Examine the differential physiological responses of panicles and foliar tissue to HNT stress.We will measure carbon assimilation rates from panicles using our non-destructive approaches and compare this information with foliar measurements for this parameter to gain insights into the source-sink dynamics.Foliar responses to heat stress.To compare thefoliar and non-foliarphotosynthetic responses to HNT over time, we will measure the gas exchange parameters (rate of carbon assimilation, transpiration), and chlorophyll fluorescence (for PSII sensitivity to heat stress) from the flag leaf and an older healthy leaf using the LI-6800 portable photosynthesis system at multiple time points Metabolomic analysis of panicle and flag leaves will be used to link sugar transport and sensing to the physiological measurements under HNT stress.Non-foliar responses to heat stress.We have a novel setup involving a cylinder gas exchange chamber that will enable us to take whole-panicle measurements from plants maintained under control and heat stress. We will combine these gas exchange measurements with thePI-Platconstructed 3D point-cloud to obtain estimates of surface area to correspond to each gas exchange measurement for normalization.Temporal carbon dynamics of source and sink tissue.We will examine the impact of HNT on WT and mutants (KO and OE lines) by estimating the level of assimilated and transported carbon in developing grains. We will measure starch, protein, lipids, sucrose, glucose, non-structural carbohydrate, trehalose and trehalose-6-phosphate content using the UNL metabolomics core facility.Obj. 3. Molecular characterization of differential HNT response between wildtype and mutants.Three of the novel candidate genes identified from these analyses will be tested for grain weight and quality under HNT stress by generating gene-edited and OE lines.Transcriptomic response of developing grains and differentiating panicles under HNT.[6 months; Yr 2] We will use two independent mutants (KO and OE) for each of the HNT genes (and WT) and collect developing grains for temporal transcriptome analysis under control and HNT stress. We will send samples to University of Illinois (Genomics Core) under an agreement between UNL and UIUC for RNA sequencing using standard protocols.Temporal gene network analysis to identify key genes for grain and panicle development under HNT.To identify novel genes that differentially modulate the transcriptome of mutants relative to WT under HNT stress and their interactions with panicle-level phenotypes, we will conduct temporal gene coexpression network analysis using a low-rank plus sparse framework that we have developed.Functional validation of three candidate genes.We will generate at least 4 independent gene edited and OE lines for these genes using protocols used previously for generating mutants forLOGL1, FIE1andHXK7in Kitaake background (life cycle of ~2 months). We will perform single grain level and whole plant level phenotyping of these mutants for vegetative and reproductive stages under control conditions and HNT stress imposed during the reproductive stage. High-resolution image analysis of these gene-edited and OE lines is outside the timeframe of this proposed project. Therefore, our priority will be to perform basic (non-imaging) phenotyping of mature grain weight and grain number per plant and grain quality assays to determine their impact on HNT responses in rice.