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The Pennsylvania State University The Pennsylvania State University The Graduate School College of Agricultural Sciences NUTRITIONAL AND GENETIC ARCHITECTURE OF ROOT TRAITS IN RICE (Oryza sativa) A Dissertation in Horticulture by Phanchita Vejchasarn 2014 Phanchita Vejchasarn Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2014 The dissertation of Phanchita Vejchasarn was reviewed and approved* by the following: Kathleen Brown Professor of Plant Stress Biology Dissertation Advisor Chair of Committee Graduate Program Officer Jonathan Lynch Professor of Plant Nutrition Dawn Luthe Professor of Plant Stress Biology Yinong Yang Associate Professor of Plant Pathology *Signatures are on file in the Graduate School iii ABSTRACT As the global population continues to grow, especially in the developing nations, about 870 million people are food insecure and experiencing chronic malnutrition. Rice is the most important cereal crop of the developing world and a staple food source of more than half of the world’s population, providing 20-70% of total daily caloric intake. Rainfed lowland rice is the dominant rice production system in areas of greatest poverty: South Asia, parts of Southeast Asia, and essentially all of Africa, where its production is limited by multiple abiotic stresses, uncertain moisture supply and decreasing soil fertility. Phosphorus deficiency is considered to be one of the major constraints limiting rice production in those areas. Most farmers still plant traditional rice varieties that produce poor plant growth and low yields. Adding to the problem is that resource- poor farmers are largely unable to afford the cost of fertilizers, thus, they remain trapped in poverty. An alternative strategy is to develop phosphorus efficient varieties with enhanced genetic adaptation to phosphorus-stressed soils, defined as improved yield ability in low-input agricultural systems coupled with better phosphorus acquisition and use efficiency. Plant roots display a wide array of adaptations to low phosphorus stress, including changes in root anatomy, morphology and architecture as well as increased production and secretion of root exudates. Plastic root responses to low phosphorus availability show promising benefits to improve phosphorus acquisition efficiency. The first experiment was undertaken to investigate the effect of low phosphorus availability on root morphological, anatomical and architectural characteristics among diverse rice iv genotypes. This work serves as the basis of further understanding of various root traits controlled by low phosphorus availability in rice. Our results show that rice genotypes varied considerably in root traits. Low phosphorus availability has significant effects on the majority of root traits evaluated. Several root traits such as root hairs and root cortical aerenchyma are considered important in phosphorus acquisition. In addition, genetic mechanisms determining natural phenotypic variation of root hairs, lateral root branching, root anatomical features, and nodal root growth angle were studied. Traits were evaluated on ~335 accessions from the O. sativa diversity panel. To identify loci underlying such traits, genome-wide association (GWA) analyses were performed using 36,901 single nucleotide polymorphisms (SNPs). We identified significant associations for all root traits. Significant loci associated with these root traits would be useful for plant breeders by incorporating them into new rice cultivars. This study represents an essential step toward genetic improvement strategies with the final goal of producing improved cultivars that enhance acquisition efficiency of soil resources, especially phosphorus, in the low-input agricultural system. v TABLE OF CONTENTS List of Figures .............................................................................................................. viii List of Tables ............................................................................................................... xiii Chapter 1 Introduction ................................................................................................. 1 Low soil phosphorus availability: a major limiting factor for plant productivity .................................................................................................... 1 The importance of rice, rice production and ecosystems ..................................... 2 Structure of the rice root system ........................................................................... 3 Adaptive root traits for better phosphorus acquisition ......................................... 4 References ............................................................................................................. 8 Chapter 2 Effect of Phosphorus on Root Hairs and Anatomical and Architectural Traits in Rice Roots (Oryza sativa) ...................................................................... 14 Abstract ................................................................................................................. 14 Introduction ........................................................................................................... 15 Materials and Methods ......................................................................................... 17 Plant cultivation and phosphorus treatments ................................................. 17 Root and shoot growth measurements ........................................................... 18 Root hair measurement .................................................................................. 18 Lateral branching measurement .................................................................... 19 Root anatomical traits measurement ............................................................. 19 Tissue phosphorus content ............................................................................ 20 Experimental design and data analysis .......................................................... 20 Results................................................................................................................... 21 Phenotypic variation of root hair traits within the root systems .................... 21 Phenotypic variation of root cortical aerenchyma (RCA) within the root systems ................................................................................................... 22 Genotypic differences in root morphological and anatomical characteristics as affected by low phosphorus availability .................... 23 Discussion ............................................................................................................. 26 References ............................................................................................................. 67 Chapter 3 Genome-wide Association Mapping of Root Hair Traits in Rice (Oryza sativa) ................................................................................................................... 74 Abstract ................................................................................................................. 74 Materials and Methods ......................................................................................... 77 Plant cultivation ............................................................................................. 77 Root hair measurement .................................................................................. 78 Experimental design and data analysis .......................................................... 78 vi Genome-wide association (GWA) analysis ................................................... 79 Results................................................................................................................... 80 Phenotypic variation of root hair traits .......................................................... 80 Identification of loci underlying root hair traits through genome-wide association (GWA) study ....................................................................... 81 Discussion ............................................................................................................. 82 References ............................................................................................................. 95 Chapter 4 Genome-wide Association Mapping of Root Anatomical Traits in Rice (Oryza sativa) ....................................................................................................... 99 Abstract ................................................................................................................. 99 Introduction ........................................................................................................... 100 Materials and Methods ......................................................................................... 103 Plant cultivation ............................................................................................. 103 Root anatomical traits measurement ............................................................. 104 Experimental design and data analysis .......................................................... 105 Genome-wide association (GWA) analysis ................................................... 105 Results................................................................................................................... 106 Phenotypic variation of root anatomical traits ............................................... 106 Detecting loci controlling root anatomical traits
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