IC4R004-Phenomics-2015-26111541

Project Title

Integrating Image-Based Phenomics and Association Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice

The Background of This Project

• Nearly one-third of the 54 million ha of the highly saline soils in the world are located in South and Southeast Asia. Rice (Oryza sativa), which is the pri- mary source of calories and protein for these two regions, is very sensitive to salinity stress, with even moderate salinity levels known to decrease yields by 50% (Zeng et al., 2002). Projected sea level rise due to climate change is expected to increase saltwater in-gress in coastal rice-growing regions of South and Southeast Asia. Therefore, development of salt-tolerant rice cultivars is essential to maintain rice productivity in the salinity-affected regions globally.
• However, to date, no studies have implemented an association mapping approach using image-derived phenotypes to address the genetic basis of dynamic stress responses in plants. Image-based phenotyping offers several advantages over conventional phenotyping: (1) quantitative mea- surements can be recorded over discrete time points to capture morphological and physiological responses in a nondestructive manner, and (2) the use of various types of spectral imaging address phenotypes that are not detectable to the human eye such as chlorophyll fluorescence and leaf water content. Integrating dynamic phenotypic data and association mapping has the potential to query genetic diversity across hundreds of accessions for complex traits and provides much higher resolution compared with conventional linkage mapping.
• In this project, the researchers explored the dynamic growth and chlorophyll responses to salinity of a diverse set of rice accessions using high-throughput visible and fluorescence imaging. To assess the genetic basis of plant growth in saline conditions, a logistic model was used to describe the temporal growth responses and was incorporated into the statistical framework necessary for association mapping. Coupled with temporal fluorescence imaging, we present, to our knowledge, new insights into the genetic architecture of osmotic and ionic responses during salinity. stress in rice.

Plant Culture & Treatment

Greenhouse Conditions

• Seeds from 373 genotypes from the rice (Oryza sativa) diversity panel were surface sterilized with fungicide, thiram, and germinated on moist paper towels in plastic boxes for 3 d (Famoso et al., 2011; Zhao et al., 2011). Three uniformly germinated seeds of each genotype were transplanted to pots (150-mm diameter 3 200-mm height) filled with 2.6 kg of UC Mix and placed into square containers to allow for water to collect. Plants were thinned to one seedling per pot 6 d after transplanting (DAT). For the first 7 DAT, each pot was watered daily with approximately 150 mL from the top of the pot. Over the course of the three experiments, the greenhouse temperatures during the day averaged 28.8°C (62.02°C, SD ) and 26.0°C (61.01°C, SD ) at night. Relative humidity was maintained at 63.4% (69.04%, SD ) during the day and 69.7% (61.73%, SD ) at night (Rotation Atomizer Defensor ABS3, Condair).

Salt Treatment

• Eight DAT, each pot was watered to a uniform weight so that approxi- mately 600 mL of water was maintained in the soil. For the salt-stressed plants, 100 mL of NaCl solution (270 m M NaCl:9.9 m M CaCl b ) was applied to the square dish, and small holes in the bottom of the pots allowed for the infiltration of salt into the soil through capillary action. Salt treatment was applied in two steps of 45 m M to reach a final concentration of 90 m M at 10 and 13 DAT. Control plants received 100 mL of water on days 10 and 13.

Research Findings

• Figure 1 shows illustrates the salinity-induced growth responses in a rice diversity panel. A to C, Relationship between PSA and conventional biomass metrics. Pearson correlation analyses were performed between PSA and shoot area (A), shoot fresh mass (B), and shoot dry mass (C). D, Comparisons of PSA between treatments at each of the 18 d of imaging. Differences between treatments at each time point were determined using a one-way blocked ANOVA, where accession is considered as a block (P , 0.0027).E, Comparison of salinity-induced growth response models between each of the five subpopulations defined by Zhao et al. (2011). The salinity-induced growth response was modeled with a decreasing logistic curve, and pairwise comparisons were made between each subpopulation. Aromatic accessions were excluded due to low n. Mean growth responses for each subpopulation are denoted by solid lines, while the SE for each subpopulation is indicated by shadows. TRJ, Tropical japonica; TEJ, temperate japonica; IND, indica; ADM, admix.
  
  

Figure 1. The salinity-induced growth responses in a rice diversity panel.

Labs working on this Project

• Department of Agronomy and Horticulture (M.T.C., H.W.), Holland Computing Center (A.C.K.), and
• Department of Statistics (D.W.), University of Nebraska, Lincoln, Nebraska 68583; The Plant Accelerator,
• Australian Plant Phenomics Facility, University of Adelaide, Urrbrae, South Australia 5064, Australia (B.B.);
• Phenomics and Bioinformatics Research Centre, University of South Australia, Adelaide, South Australia 5001, Australia (C.J.B.)

Corresponding Author

Harkamal Walia (hwalia2@unl.edu).