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Exploration of the Genetic Diversity of Cultivated Potato and Its Wild Progenitors (Solanum Sect

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Exploration of the Genetic Diversity of Cultivated Potato and Its Wild Progenitors (Solanum Sect EXPLORATION OF THE GENETIC DIVERSITY OF CULTIVATED POTATO AND ITS WILD PROGENITORS (SOLANUM SECT. PETOTA) WITH INSIGHTS INTO POTATO DOMESTICATION AND GENOME EVOLUTION By Michael Alan Hardigan A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Crop and Soil Sciences - Doctor of Philosophy 2016 ABSTRACT EXPLORATION OF THE GENETIC DIVERSITY OF CULTIVATED POTATO AND ITS WILD PROGENITORS (SOLANUM SECT. PETOTA) WITH INSIGHTS INTO POTATO DOMESTICATION AND GENOME EVOLUTION By Michael Alan Hardigan Cultivated potato (Solanum tuberosum L.) is a clonally propagated autotetraploid (2n=4x=48) with high potential for genetic improvement due to the expansive genetic diversity of its related germplasm. This diversity includes high levels of heterozygosity but also deleterious genetic load in cultivated clones, multiple groups of genetically distinct landrace sub-species, and over 100 related tuber-bearing species that can introduce heterosis and adaptation. To generate a better understanding of the landscape of potato genetic diversity, studies were conducted to (1) explore the genetic relationships between tuber-bearing Solanum species, landraces, and cultivars, (2) investigate the role of structural variation in cultivated potato genome evolution and diversity, and (3) identify key loci that were selected during domestication of potato. Phylogenetic analysis of tuber-bearing Solanum species was examined in the first application of genome-wide nuclear single nucleotide polymorphism (SNP) markers with a diversity panel of potato species from the USDA Potato Gene Bank core collection. Genotyping a panel of 75 accessions representing 25 species and 213 cultivated tetraploid clones using 5,023 polymorphic SNPs supported previous taxonomic placement of wild potato germplasm, while reinforcing the theory of a Peruvian domestication origin for potato. Several genes involved in carbohydrate metabolism or with potential roles in tuber development were found to contain diverging allele frequencies in the wild and cultivated potato groups suggesting they may have been key loci involved in domestication. A comprehensive analysis of genomic variation (sequence and structural variation) using 30- 70x sequence coverage in a panel of 12 monoploid/doubled monoploid potatoes derived from primitive South American diploid landraces was performed. Extensive copy number variation (CNV) was found to impact over 30% of the potato genome and nearly 30% of genes, with widespread deletion affecting lowly expressed sequences, and enriched duplication within gene families that function in adaptation and environmental response. This study revealed CNV is equally relevant to sequence-level variation (SNPs, insertions/deletions) in its contribution to deleterious mutation load and gene evolution in the potato genome. The study also demonstrated that the extensive structural heterogeneity present in tetraploid genotypes is present in their diploid progenitors, and thus, is not the result of polyploidy alone. A diversity panel was sequenced at 8x to 16x coverage to enable genome-wide comparison of allele composition in 23 tetraploid potato cultivars, 20 wild species and 20 landrace progenitors. Analysis of selection signatures including FST, Tajima’s D, reduced nucleotide diversity and allele frequency differences yielded a set of domestication candidate genes including several regulating carbohydrate pathways, glycoalkaloid biosynthesis and stress responses. Comparable levels of total sequence diversity were present in elite cultivars and South American landraces, yet significant genetic variance between landrace populations was re- partitioned as single-clone heterozygosity in cultivars, confirming the hypothesis that elite varieties represent a highly heterozygous group lacking significant population structure. These findings may assist the ability of potato breeders to exploit key performance-related loci and heterosis in the future. Dedicated to my best friend and brother, Christopher J. Hardigan. iv ACKNOWLEDGEMENTS I thank Dr. C. Robin Buell as a mentor during my post-graduate research. I thank the members of my graduate committee, Drs. C. Robin Buell, David Douches, James Hancock, Wayne Loescher, and Amy Iezzoni for dedicating their time and experience toward my development as a graduate student and young scientist. I thank my NSF potato vigor project collaborators Parker Laimbeer, Dr. Richard Veilleux and Dr. Jiming Jiang for their substantial contributions to my own published research, and members of the Buell lab for lending their expertise in support of these studies. I thank Kevin Childs and John Hamilton for providing mentorship during my early months of bioinformatics training. I thank my girlfriend Jane Ames for her patience during the last three years of my graduate research. I thank my parents for their life-long support of my education and happiness. I owe my greatest debt to the many great scientists whose knowledge and hard work laid the foundation upon which my own research was built. It is my hope that the work herein helps to raise this foundation a bit higher. v TABLE OF CONTENTS LIST OF TABLES ....................................................................................................................... ix LIST OF FIGURES ....................................................................................................................... x CHAPTER 1 ...................................................................................................................................1 INTRODUCTION .........................................................................................................................1 Tuber Bearing Solanum Species ..............................................................................................2 Origins of Cultivated Potatoes .................................................................................................3 Potential Limitations of the North American Cultivar Genetic Base ......................................5 Potato Breeding Challenges .....................................................................................................8 New Technologies to Improve Potato Breeding ....................................................................10 Diploid Breeding ................................................................................................................10 Genome Editing .................................................................................................................11 A Path Toward Deploying Germplasm Diversity in the Future Improvement of Potato ......12 Problem Definition .................................................................................................................14 Objective ................................................................................................................................14 Dissertation Outline ...............................................................................................................15 LITERATURE CITED ..........................................................................................................16 CHAPTER 2 .................................................................................................................................22 TAXONOMY AND GENETIC DIFFERENTIATION AMONG WILD AND CULTIVATED GERMPLASM OF SOLANUM SECT. PETOTA .........................................22 Abstract ..................................................................................................................................23 Introduction ............................................................................................................................24 Materials and Methods ...........................................................................................................27 Plant Materials ...................................................................................................................27 Single Nucleotide Polymorphism Genotyping ..................................................................34 Single Nucleotide Polymorphism Functional Annotation .................................................34 Phylogenetic Analysis and Estimates of Genetic Diversity ...............................................35 Functional Analysis of Single Nucleotide Polymorphisms and Associated Genes ...........36 Results and Discussion ..........................................................................................................37 Phylogeny Results ..............................................................................................................37 Genetic Diversity Within Solanum sect. Petota Accessions .............................................43 Heterozygosity and Genetic Diversity in Solanum Germplasm and Cultivated Potato .....46 Allele Frequency Divergence in Solanum sect. Petota Diversity Panel vs. Cultivated Tetraploid Panel Clones .....................................................................................................50 Conclusions ............................................................................................................................57 LITERATURE CITED ..........................................................................................................59 CHAPTER 3 .................................................................................................................................66 vi GENOME REDUCTION
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