High-throughput phenotyping and genetic mapping of drought stress related traits in setaria (Setaria spp) and rice (Oryza spp)

Thathapalli Prakash, Parthiban

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Description

Title

High-throughput phenotyping and genetic mapping of drought stress related traits in setaria (Setaria spp) and rice (Oryza spp)

Author(s)

Thathapalli Prakash, Parthiban

Issue Date

2020-05-07

Director of Research (if dissertation) or Advisor (if thesis)

Leakey, Andrew

Doctoral Committee Chair(s)

Leakey, Andrew

Committee Member(s)

• Henry, Amelia
• Bollero, German
• Studer, Anthony

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Setaria
• Rice
• drought
• water-use efficiency
• phenotyping
• Genetic mapping

Abstract

Drought stress is one of the most important and complex abiotic stresses limiting crop yield. Therefore, it is essential to dissect this complex trait and understand mechanisms of drought resistance in the field. In this research, experiments were conducted in Setaria, a model C4 crop, and rice, a model C3 crop, in order to understand their response to managed water stress conditions. Chapters 2 and 3 are focused on phenotyping and genetic mapping for water-use efficiency (WUE) related traits in different Setaria populations. Chapter 4 is focused on phenotypic characterization of wild rice species for drought stress related traits. Mechanistic modeling indicates that stomatal conductance could be reduced to improve WUE in important C4 crops such as maize, sorghum and sugar cane. In Chapter 2, a novel image capture process was used to evaluate genetic variation in stomatal density, alongside canopy temperature as a proxy for canopy water use, in the model C4 plant, Setaria. An optical profilometer was used to generate a quantitative measurement of a patch of leaf surface to rapidly assess stomatal patterning. And the canopy temperature of the plots were measured using aerial infrared imaging. A population of 120 recombinant inbred lines (RIL) derived from an Setaria italica x Setaria viridis cross were grown with ample or limiting water supply under field conditions in Illinois. The total above-ground biomass was negatively correlated with canopy temperature and stomatal density whereas stomatal density and canopy temperature were positively correlated. These trait relationships suggests the an interaction is likely occurring between stomatal density and the other drivers of water use such as stomatal size and aperture. Multiple QTLs were identified for stomatal density and canopy temperature, including co-located QTLs on chromosomes 5 and 9. The direction of the additive effect of these QTLs on chromosome 5 and 9 were in accordance with the positive phenotypic relationship between these two traits. These identified QTLs could help us understand the genetic architecture of the trait and potentially be used in breeding programs develop plants with altered stomatal density. In the Chapter 3, a set of 208 Setaria accessions were screened under ample or limiting water supply under field conditions in Illinois. The traits and phenotyping methods were the same as described in Chapter 2. In contrast to the Chapter 2, the population screened is a diversity panel where the variation for traits arises due to the historical recombination events. Significant negative correlations were observed between midday canopy temperature and above-ground biomass, and between stomatal density and above-ground biomass. The stomatal density was higher in the dry treatment when compared to wet treatment. A total of 25 significant marker trait associations were identified in this study for stomatal density and midday canopy temperature under both wet and dry treatments. By scanning across the genomic regions of the 25 SNPs, 59 candidate genes were identified using the annotated Setaria viridis genome. Genetics resources for Setaria could now be used to functionally validate these candidate genes. Rice is the staple food for nearly half of the world’s population and consumes 24-30% of the freshwater resources. However, rice production is affected by water stress especially during seedling and reproductive stages of growth. Therefore, developing drought resistant and water use efficient rice varieties is essential to improve productivity in farmers’ fields that are affected by drought. Because drought resistance is a complex trait, identifying novel genetic regions responsible for drought resistance will be beneficial to the development of better drought resistant varieties. A potential source of novel genetic regions for drought resistance is wild rice. In this study, a panel of Oryza glumaepatula accessions from the genebank of International Rice Research Institute (IRRI) and National Institute of Genetics (NIG), Japan were screened for drought stress related traits (Chapter 4). O. glumaepatula is one of the 21 wild rice species originating from South America with a diploid AA genome similar to O. sativa and to date has received very little detailed study related to drought resistance. In this study, 69 accessions were screened along with O. sativa check lines S. Dhan (drought resistant) and IR64 (drought susceptible) for morphological and physiological traits under drought and well-watered conditions, in two different seasons, under screen house condition at IRRI. The traits that were measured include shoot dry weight, plant height, tiller number, chlorophyll content, canopy temperature, specific leaf area, leaf water and osmotic potential, crown root number, root length density at different depths and percent lateral roots. Six O. glumaepatula accessions showed lower shoot dry weight reduction due to drought than S.dhan in both seasons and were shortlisted as donors for drought resistance. In addition, these six genotypes had a greater deep root percentage and lower stomatal density than S.dhan in both seasons. Another set of experiments was conducted in lysimeters (cylindrical pots) under greenhouse condition with progenies of two F2 populations derived from crosses between Oryza sativa and O. glumaepatula, the corresponding parents and O. sativa checks. The two O. glumaepatula parental genotypes 105692 (Parent of Population 1) and 105672 (Parent of Population 2) had higher shoot dry weight, plant height, number of tillers, maximum root depth, and total root dry weights than all O. sativa checks. It was observed that water uptake rate was negatively correlated with deeper root dry weight in Population 1 (NSICRc222 x 105692), whereas water uptake rate was negatively correlated with leaf water and osmotic potential in Population 2 (NSICRc222 x 105672). These differences indicate that the two populations responded differently to drought stress conditions and Population 1 tended to express a conservative approach to water use when compared to Population 2. Thus these combined experiments successfully screened for water use and drought resistance related traits in two crops belonging to C3 and C4 system under well-watered and water limited conditions using different phenotypic techniques. Multiple QTL and candidate genes associated with water use related traits in the Setaria studies could be used in the crop improvement programs either through forward or reverse genetics approach. The accessions shortlisted as donors for drought resistance in the rice study could be used in breeding rice for drought conditions.

Graduation Semester

2020-05

Type of Resource

Thesis

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Copyright 2020 Parthiban Thathapalli Prakash

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