Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1438 Understanding the genetic basis of complex traits YANJUN ZAN ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6206 ISBN 978-91-513-0260-7 UPPSALA urn:nbn:se:uu:diva-343174 2018 Dissertation presented at Uppsala University to be publicly examined in C8:301, BMC, Husargatan 3, Uppsala, Friday, 27 April 2018 at 09:15 for the degree of Doctor of Philosophy (Faculty of Medicine). The examination will be conducted in English. Faculty examiner: Professor Pär Ingvarsson. Abstract Zan, Y. 2018. Understanding the genetic basis of complex traits. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1438. 49 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0260-7. Recent advances in genetics and genomics have provided numerous opportunities to study the genetic basis of complex traits. Nevertheless, dissecting the genetic basis of complex traits is still challenged by the complex genetic architecture, in which many genes are involved, and many have small contributions to phenotypic variation, interactions with other genes or environmental factors. The aim of this thesis is to evaluate the genetic basis of the complex traits by exploring available genomic resources and analytical approaches. Four studies included in this thesis explore: the genetic basis of global transcriptome variation in natural population (Study I); the genetic basis of 8-week body weight in artificial selected chicken lines (Study II); the genetic basis of flowering time variation for Arabidopsis thaliana sampled from a wide range of ecological conditions (Study III and Study IV). Findings from this thesis show that the genetic architecture of complex traits involves many polymorphisms with variable effect sizes. Some of those polymorphisms are multi-allelic and have interactions with each other and environmental factors at the same time. The presence of many alleles with minor contributions to phenotypic variation in natural and artificially selected population demonstrates that response to natural and artificial selection has been achieved by polygenic adaptation. Furthermore, population- specific large-effect loci with long-range LD to QTL in functionally related pathways indicate that emergence and fixation of loci with large effects and co-evolution of loci in the related pathway is contributing to the local adaptation of Arabidopsis thaliana. Overall, this thesis shows the complexity of complex trait genetics and provides a few insights into study designs and analysis approaches for understanding the genetic basis of complex traits. Keywords: genetic architecture, complex traits, epistasis, multi-allelic, genotype by environment interaction, polygenic adaptation Yanjun Zan, Department of Medical Biochemistry and Microbiology, Box 582, Uppsala University, SE-75123 Uppsala, Sweden. © Yanjun Zan 2018 ISSN 1651-6206 ISBN 978-91-513-0260-7 urn:nbn:se:uu:diva-343174 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-343174) The more we learn the more we realize how little we know. R. Buckminster Fuller List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I. Zan Y, Shen X, Forsberg SK, Carlborg Ö. Genetic regulation of transcrip- tional variation in natural Arabidopsis thaliana accessions. G3, 2016, 6(8): 2319-2328. II. Zan Y*, Sheng Z*, Lillie M Rönnegård L, Honaker CF, Siegel PB, Carl- borg Ö. Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture. Molecular Biology and Evolu- tion, 2017, 2, 7–10 III. Zan Y, Carlborg Ö. A multi-locus association analysis method integrat- ing phenotype and expression data reveals multiple novel associations to flowering time variation in wild-collected Arabidopsis thaliana. Molecular Ecology Resources, 2018, 00, 1-11. IV. Zan Y, Carlborg Ö. Explorations of the polygenic genetic architecture of flowering time in the worldwide Arabidopsis thaliana population. BioRxiv, doi: https:// doi.org/10.1101/ 206706. Manuscript *These authors contributed equally Reprints were made with permission from the respective publishers. List of Papers (not included in this thesis) 1. Wang B, Li Z, Xu W, Feng X, Wan Q, Zan Y, et al. Bivariate genomic analysis identifies a hidden locus associated with bacteria hypersensitive response in Ara- bidopsis thaliana. Scientific report, 2017, 7:45281. Contents 1. Background and aim .................................................................................... 9 2. Complex trait genetics ............................................................................... 11 2.1. Theory ................................................................................................ 11 2.1.1. Terminologies mentioned in this thesis ...................................... 11 2.1.2. Genetic theory for modelling genotype to phenotype map ........ 11 2.1.3. Linear-mixed model based genome-wide association study ...... 13 2.2. Understanding the genetic architecture of complex traits .................. 15 2.2.1. Challenges in dissecting the genetic basis of complex traits ...... 15 2.2.2. Background of two populations used in this thesis .................... 16 3. Summary of studies ................................................................................... 19 3.1. Study I – Genetic basis of transcriptome variation in natural population ................................................................................................. 19 3.2. Study II – Dissecting the polygenetic genetic architecture underlying 16-fold response to long-term bi-directional selection ........... 21 3.3. Study III – Dissecting the genetic architecture of a polygenic trait in nature ............................................................................................. 25 3.4. Study IV – Polygenetic architecture and adaptation in natural population ................................................................................................. 27 4. Concluding remarks and future perspectives ............................................ 31 4.1. Complexity of the genetic basis of complex traits ............................. 31 4.1.1. Polygenicity ................................................................................ 31 4.1.2. Multi-allelic loci and bi-allelic SNP ........................................... 32 4.1.3. Additive model and Non-additivity ............................................ 33 4.2. Polygenetic architecture and selection response ................................ 35 4.2.1. Polygenetic response to artificial selection ................................ 35 4.2.2. Polygenetic adaptation to natural selection ................................ 36 4.2.3. Genetic architecture and evolvability ......................................... 37 4.3. Future developments in complex trait genetics ................................. 38 4.3.1. Studied resources and approaches .............................................. 38 4.3.2. Novel developments of analytical methods ................................ 39 4.4. From associations to biology ............................................................. 40 4.5. In the end ........................................................................................... 40 5. Acknowledgements ................................................................................... 41 6. References ................................................................................................. 44 Abbreviations RAPD Random amplification of polymorphic DNA RFLP Restriction fragment length polymorphism AFLP Amplified fragment length polymorphism SSR Simple sequence repeat SNP Single nucleotide polymorphism SV Structural variant G-P map Genotype to phenotype map QTL Quantitative trait locus GWAS Genome-wide association study LD Linkage disequilibrium GRM Genome-wide relationship matrix 1. Background and aim Just by looking around, we can find substantial variations among individuals. For instance, people that are short or tall, healthy or sick, blonde or brunette. If we look carefully, we could also notice some degree of resemblance with- in ethnic groups or inheritance of these features within families. Apart from human beings, such diversities can also be found in microbes, plants and animals. This makes us wonder what makes an individual different from each other. A deep understanding of this question is not only of fundamental importance to address the law of nature but also has abundant applications in improving diagnostics, prevention and treatment of diseases in public healthcare, improving the agronomic traits of animals and plants in agricul- ture and conservation of endangered species for a better world. Throughout the history of mankind, we have probably always wondered about these questions, and many pioneers have pursued these answers for centuries. Centuries of explorations have taught us a lot: i) We learned how discrete characteristics, such as shape of the pea and colour of the flower is inherited through the work of Gregor Mendel in the1860s [1]. ii) We gained many insights on the inheritance of continuous phenotype, for instance, hu- man height, and developed several methods to study them out of the inspira- tion from Francis Galton [2] and Ronald Fisher [3]. iii) We have discovered that DNA is the heritable molecule that is passed down from one generation to another [4] and variations in DNA sequences make us different. With the