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Genetic Architecture of Hybrid Fitness and Wood Quality Traits in a Wide Interspecific Cross of Eucalyptus Tree Species

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Genetic Architecture of Hybrid Fitness and Wood Quality Traits in a Wide Interspecific Cross of Eucalyptus Tree Species ABSTRACT MYBURG, ALEXANDER ANDREW. Genetic Architecture of Hybrid Fitness and Wood Quality Traits in a Wide Interspecific Cross of Eucalyptus Tree Species. (Under the supervision of Ross W. Whetten and Ronald R. Sederoff.) The genetic architecture of interspecific differentiation plays a key role in the evolution of reproductive isolating barriers in plants, and has important implications for hybrid breeding programs. Interspecific hybridization is an important approach towards the genetic improvement of Eucalyptus tree plantations. However, incompatibilities between diverged eucalypt genomes often lead to reduced fitness of interspecific hybrids and decrease the efficiency of hybrid breeding programs. Furthermore, very little information is available on the genetic control of quantitative traits in interspecific hybrids of Eucalyptus tree species. The aim of this project was to obtain a detailed description of the genetic architecture of hybrid fitness and wood property traits in an interspecific cross between two commercially important hardwood tree species, E. grandis and E. globulus spp. globulus. This cross combines the superior growth and adaptability of E. grandis with the excellent wood properties of E. globulus. The two species are members of different sections of the subgenus Symphyomyrtus and hybrid generations of this wide cross are characterized by large amounts of F1 hybrid inviability and F2 hybrid breakdown. Two interspecific backcross families of E. grandis × E. globulus were each genotyped with more than 800 amplified fragment length polymorphism (AFLP) markers using a new high- throughput protocol for AFLP analysis on automated DNA sequencers. A pseudo-backcross mapping approach was used to generate detailed comparative genetic maps of a single superior F1 hybrid tree and of two backcross parents. The genetic maps of the two pure species parents and the F1 hybrid were colinear and 11 comparative synteny groups were characterized. Overall recombination rates did not differ significantly, although heterogeneity in recombination rates was observed in several map regions. Approximately 30% of the AFLP markers were significantly distorted from expected segregation ratios. The distorted markers were located in specific map regions and distortion was highly directional in these regions. A Bayesian Markov chain Monte Carlo approach was used to estimate the position and effect of genetic factors that cause segregation distortion. At least six segregation distorting loci (SDL) were located in the genetic maps of the F1 hybrid. Two SDL were detected in the genome of the E. grandis backcross parent and one SDL in the map of the E. globulus backcross parent. Donor alleles were found to be favored in the recurrent genetic background at several SDL in the maps of the F1 hybrid. Marker-assisted breeding based on detailed, whole-genome genotypes of hybrids may be useful to minimize the effect of hybrid breakdown factors in further generations of this cross. Near-infrared (NIR) analysis was used to predict wood property trait values for approximately 270 individuals of each backcross family after two years of growth in a field site. The trait data and AFLP genotypes were used for QTL detection and analysis in the parental genetic maps. In addition, a principal component analysis was performed on the NIR spectral data of each backcross family and the data used to map QTLs for NIR spectral variation. A total of 18 QTLs for NIR predicted wood properties and NIR spectral variation were characterized in the parental maps of the E. globulus BC family, while 13 QTLs were detected in the E. grandis BC family. Many of the QTLs had effects on multiple, correlated wood property traits and on raw NIR spectral variation. Individual principal components of NIR spectral variation were correlated with groups of chemical and physical wood properties, and shared several large-effect QTLs with the individual wood properties. These QTL may represent key genetic loci that are involved in the genetic differentiation of wood properties between these two species. ii GENETIC ARCHITECTURE OF HYBRID FITNESS AND WOOD QUALITY TRAITS IN A WIDE INTERSPECIFIC CROSS OF EUCALYPTUS TREE SPECIES by ALEXANDER ANDREW MYBURG A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy FORESTRY and GENETICS Raleigh 2001 APPROVED BY: Michael D. Purugganan Ross W. Whetten Trudy F.C. Mackay Ronald R. Sederoff To Chrisné, Rikkert and Berno ii BIOGRAPHY I was born on June 18th, 1969 in Bloemfontein, South Africa, 300 years after the first member of my family arrived from the Netherlands and settled in the “Cape of Good Hope” as a farmer. All eight of the subsequent generations made a living as farmers in different parts of South Africa. My parents, Frederick Jacobus Myburg and Anna-Marietta Myburg, own a farm on the banks of the Orange River in the North Eastern Cape Province near the town of Aliwal North. This is where my two sisters and I grew up and went to school. During school weeks, we lived in a boarding house with all the other farm children in the area. Weekends and vacations were spent on the farm, which is where I developed a love for agriculture and biology. I excelled in leadership roles from an early age, owing to positive role models of my parents and a keen sense of independence developed while learning to fend for myself in boarding house. Academic achievement came naturally, mostly due to the regimented student life in the boarding house, and an early realization that this would open many doors for me in later life. I finished high school in 1987 and spent the next two years performing compulsory military service. During 1988 and 1989 I was trained as an officer in the Anti-Aircraft Corps of the South African Army. From 1990 to 1994, I completed the B.Sc and B.Sc. Hons. degree programs in Botany and Genetics at the University of the Orange Free State (UOFS, now University of the Free State). I was heavily involved in student leadership development activities and was elected to the Student Representative Council (SRC) of the UOFS in 1992. I met my future wife, Chrisné, at the UOFS and we were fortunate to serve together on the SRC. This was a wonderful opportunity because it allowed us to meet many political, business and student leaders in South Africa, Zimbabwe and Zambia. We were exposed to the political turmoil that our country was going through at the time and developed a thorough appreciation for the great potential and serious challenges of life in Southern Africa. During 1993, I was very fortunate to be awarded the prestigious Abe Bailey Travel Bursary and spent a month exploring our colonial roots in England and Scotland with student representatives of other South African universities. Afterwards, I traveled through parts of Europe, and proposed to Chrisné in the small town of Konstanz in Germany. We were married in 1994. From 1994 to 1996 I completed a research project on the genetic mapping of Russian wheat aphid resistance in South African wheat cultivars as part of my M.Sc. degree program at UOFS. I Biography iii applied for and was awarded the Fulbright Scholarship for doctoral studies in the US in 1996, and received a scholarship for doctoral studies abroad from the National Research Foundation of South Africa. We moved to Raleigh, NC in August of 1996 where I was to pursue a doctoral program in Forestry and Genetics at North Carolina State University. I joined the Forest Biotechnology Group in 1996 and conducted the Ph.D. research project described in this dissertation under the supervision of Ross Whetten from 1997 to 2001. During our stay in Raleigh we became the parents of two beautiful boys, Rikkert and Berno. We are planning to return to South Africa and hope to contribute in a positive way to the various communities that we will be guided to serve. Biography iv AKNOWLEDGEMENTS I am truly grateful for wonderful opportunities that were granted to me throughout my university career and for the hard work, friendship and generosity of many people that made it possible and enjoyable to follow my dreams and ambitions. I especially want to thank the following people and institutions: My major advisor, Ross Whetten, and Committee Co-Chair, Ron Sederoff, for the opportunity to become part of the Forest Biotechnology Group, for guidance of my Ph.D. program, and for allowing me the freedom to do independent research on a topic that would ultimately benefit my own career. I am particularly grateful for the financial support provided by the Forest Biotechnology Group, without which life would have been much harder as a graduate student. Other members of my Advisory Committee, Trudy Mackay and Michael Purugganan, for their support, encouragement, and kindness during the difficult process of preparing this dissertation. Dave O’Malley for many stimulating discussions on molecular marker work and on life in general, and for his hard work to obtain the very best technology for molecular marker analysis. Arthur Johnson and previous members of the NCSU Sequencing Facility for help and access to equipment and software for AFLP analysis. David Remington for his wonderful example of scholarly research, many helpful discussions, and for assistance with AFLP analysis and mapping procedures. Cristina Marques for helping us to settle in Raleigh, for her friendship and enthusiasm, and for help to get the AFLP analysis optimized for Eucalyptus. Derek Harkins for being a very good friend, sharing the burden of graduate coursework, and celebrating with me countless milestones in our graduate careers. Also for years of help and advice in the lab. Ying-Hsuan Sun for always making time to help with computer problems, and always being friendly and gracious in doing so.
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