Relative Performance of Ontario Soybean Cultivars and Differential Selection of Early Soybean Breeding Lines in Organic versus Conventional Production Systems by Torin Dylan Boyle A Thesis Presented to The University of Guelph In partial fulfillment of requirements for the degree of Masters of Science in Plant Agriculture Guelph, Ontario, Canada © Torin Dylan Boyle, September, 2016 i ABSTRACT RELATIVE PERFORMANCE OF ONTARIO SOYBEAN CULTIVARS AND DIFFERENTIAL SELECTION OF EARLY SOYBEAN BREEDING LINES IN ORGANIC VERSUS CONVENTIONAL PRODUCTION SYSTEMS Torin Dylan Boyle Advisor: University of Guelph, 2016 Professor Istvan Rajcan Organic production systems differ from the conventional for insect pest, weed, disease, and nutrient management. The objective of this thesis was to determine if soybean cultivars and breeding lines responded differently in organic vs. conventional production systems. An F5/F6 generation breeding trial from two bi-parental soybean crosses and a replicated cultivar trials were conducted on an organic farm and conventional research station in the maturity group 0 zone of Southern Ontario. When thirty and thirty-three cultivars were tested in 2014 and 2015, respectively, significant crossover effects between environments indicated a differential cultivar performance between the production systems. GxT Biplots showed that the traits related to resource acquisition were associated with yield in the organic environment rather than nutrient re-mobilization. It was concluded that setting up a separate breeding program targeting an organic production system may lead to the development of a greater number of high yielding organic-adapted cultivars. ii Dedication I dedicate this thesis to the international organic agriculture movement. May we never forget the reasons why we work to foster a brighter future for healthy farms, food, people and communities. iii Acknowledgements Firstly, I would like to acknowledge my advisor Dr. Istvan Rajcan who has been a constant source of guidance, knowledge and encouragement, truly everything an advisor should be. I would also like to acknowledge and thank Dr. Ralph Martin for his enthusiasm and cooperation around the project as well. Dr. Rene Van Acker your input and insight has been a constant source of enlightenment, thank you. The soybean crew will always hold a special place in my heart Colbey Templeman, Chris Grainger, Lin Lao, Yesenia Salazar, Mei Wu, Martha Jimenez, Tim Currie, and the late Wade Montminy, thank you all for the constant support and help. My fellow graduate students, thank you for all the collaborations in classes and good times at the grad lounge. I received advice from numerous professors in the department and beyond about my project’s content and direction in both the planning and execution phase, thank you all. My family, thank you for constantly inspiring me throughout my education and beyond you have been the tightly knit support network that I could always rely upon. Your contributions as a whole have led me to where I am today and will continue to shape who I am into the future. Thank you: Laura, Doug, Pat and Calan Boyle. Finally, thank you Guelph and all the people who I have met and become friends with here. There are not a lot of places where social and environmental consciousness met a spirit of progress and entrepreneurism like they do in Guelph. Thank you for the everyday inspirations. iv Table of Contents CHAPTER 1: LITERATURE REVIEW: DEVELOPING AN ORGANIC SOYBEAN IDEOTYPE ......................... 1 1.1: INTRODUCTION ....................................................................................................................... 2 1.2: ORGANIC CROP BREEDING ...................................................................................................... 5 1.3: ORGANIC SOYBEAN IDEOTYPE DEVELOPMENT ........................................................................ 9 1.3.1: Biologically active organic matter fractions and nutrient dynamics .......................................................... 9 1.3.2: Phosphorus deficits and use efficiency ................................................................................................... 11 1.3.3: Potassium deficits and use efficiency...................................................................................................... 17 1.3.4: Symbiotic relationships and rhizosphere exudates ................................................................................. 19 1.3.5: Weed management, competition and suppressive ability ...................................................................... 25 1.3.6: Protein content, quality and processing factors ...................................................................................... 32 1.3.7: Implications for an organic soybean ideotype ........................................................................................ 35 1.4: HYPOTHESIS AND OBJECTIVES ............................................................................................... 37 CHAPTER 2: ASSESSMENT OF MG 0 SOYBEAN (GLYCINE MAX L.) CULTIVARS IN BOTH AN ORGANIC AND CONVENTIONAL ENVIRONMENT FOR EARLY SEASON CANOPY DEVELOPMENT, ROOT MORPHOLOGY, NUTRIENT USE EFFICIENCY AND OTHER AGRONOMIC TRAITS .............................. 38 2.1: ABSTRACT .............................................................................................................................. 39 2.2: INTRODUCTION ..................................................................................................................... 39 2.3: MATERIALS AND METHODS ................................................................................................... 45 2.4- RESULTS ................................................................................................................................ 55 2.4.1- Canopy Development Traits ................................................................................................................... 55 2.4.2- Root Morphology and Nodule Mass ....................................................................................................... 56 2.4.3- Nutrient Content and Use Efficiency ....................................................................................................... 56 v 2.4.4- Agronomic Traits .................................................................................................................................... 57 2.4.5: Relationships between traits of interest ................................................................................................. 58 2.5: DISCUSSION ........................................................................................................................... 60 2.5.1: Canopy Development Traits ................................................................................................................... 60 2.5.2: Root Morphology and Nodule Mass ....................................................................................................... 63 2.5.3: Nutrient Content and Use Efficiency ....................................................................................................... 67 2.5.4: Agronomic Traits .................................................................................................................................... 68 2.6: CONCLUSION ......................................................................................................................... 72 CHAPTER 3: ASSESSMENT OF EARLY GENERATION SELECTION IN ORGANIC VS CONVENTIONAL ENVIRONMENTS USING TWO DIFFERENT SOYBEAN POPULATIONS ............................................... 93 3.1: ABSTRACT .............................................................................................................................. 94 3.2: INTRODUCTION ..................................................................................................................... 95 3.3: MATERIALS AND METHODS ................................................................................................... 98 3.4: RESULTS .............................................................................................................................. 104 3.4.1: F5 yield data .......................................................................................................................................... 104 3.4.2: F6 yield data .......................................................................................................................................... 105 3.4.3: SSR Marker Data ................................................................................................................................... 108 3.5: DISCUSSION ......................................................................................................................... 109 3.6: CONCLUSION ....................................................................................................................... 116 GENERAL DISCUSSION AND CONCLUSIONS .................................................................................. 117 REFERENCES ................................................................................................................................ 135 vi List of Tables Table 2.1: List of genotypes in the replicated yield trials including their genotype number and release year……………………………………………………………………………………75 Table 2.2: Results of soil nutrient tests including Potassium, Available P, Organic P, Fixed P, pH and Organic Matter from each location year