Ancient plant DNA to the rescue: unlocking crop genetic diversity from the past Oscar Andres Estrada Santamaria Australian Centre for Ancient DNA (ACAD) School of Biological Sciences Faculty of Sciences The University of Adelaide AUSTRALIA Thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy March 2019 Ancient plant DNA to the rescue: unlocking crop genetic diversity from the past A Thesis Submitted By Oscar Andres Estrada Santamaria B.Sc. (Hons), M.Sc. For the Degree Of Doctor of Philosophy (Ph.D.) March 2019 Australian Centre for Ancient DNA (ACAD) School of Biological Sciences Faculty of Sciences The University of Adelaide Supervisors: Prof. Alan Cooper Dr James Breen Dr Stephen M Richards ii iii Table of Contents ABSTRACT ................................................................................................................................................ VI DECLARATION OF AUTHORSHIP ....................................................................................................... VII ACKNOWLEDGEMENTS ...................................................................................................................... VIII CHAPTER 1: INTRODUCTION ................................................................................................................. 1 REFERENCES ....................................................................................................................................................... 9 CHAPTER 2: LIMITATIONS, PROGRESS AND PROSPECTS OF ANCIENT PLANT DNA .............. 12 STATEMENT OF AUTHORSHIP ............................................................................................................................ 13 ABSTRACT ........................................................................................................................................................ 15 INTRODUCTION ................................................................................................................................................. 16 ANCIENT DNA ................................................................................................................................................. 17 ANCIENT PLANT DNA STUDIES ........................................................................................................................ 20 SOURCES OF ANCIENT PLANT DNA .................................................................................................................. 26 MOLECULAR BIOLOGY OF ANCIENT PLANT DNA .............................................................................................. 28 CONCLUDING REMARKS AND FUTURE DIRECTIONS ........................................................................................... 32 REFERENCES ..................................................................................................................................................... 34 CHAPTER 3: DNA ISOLATION FROM SINGLE SEEDS: APPLICATIONS IN HIGH-THROUGHPUT SEQUENCING AND DEGRADED PLANT DNA ..................................................................................... 47 STATEMENT OF AUTHORSHIP ............................................................................................................................ 48 ABSTRACT ........................................................................................................................................................ 50 INTRODUCTION ................................................................................................................................................. 51 MATERIALS AND METHODS .............................................................................................................................. 53 RESULTS ........................................................................................................................................................... 62 DISCUSSION ...................................................................................................................................................... 71 REFERENCES ..................................................................................................................................................... 72 SUPPLEMENTARY INFORMATION ...................................................................................................................... 76 CHAPTER 4: TARGET ENRICHMENT UNCOVERS THE GENETIC VARIABILITY OF HISTORICAL POLYPLOID WHEAT SPECIES FROM GEORGIA ...................................................... 96 STATEMENT OF AUTHORSHIP ............................................................................................................................ 97 ABSTRACT ........................................................................................................................................................ 99 INTRODUCTION ............................................................................................................................................... 100 MATERIALS AND METHODS ............................................................................................................................ 104 DATA ANALYSIS ............................................................................................................................................. 116 RESULTS ......................................................................................................................................................... 119 iv DISCUSSION .................................................................................................................................................... 131 CONCLUSION .................................................................................................................................................. 133 REFERENCES ................................................................................................................................................... 133 SUPPLEMENTARY INFORMATION .................................................................................................................... 139 CHAPTER 5: ANCIENT CHLOROPLAST AND NUCLEAR GENOMES PROVIDE INSIGHTS INTO THE EVOLUTIONARY HISTORY OF QUINOA (CHENOPODIUM QUINOA WILLD.) ................... 150 STATEMENT OF AUTHORSHIP .......................................................................................................................... 151 ABSTRACT ...................................................................................................................................................... 153 INTRODUCTION ............................................................................................................................................... 154 MATERIALS AND METHODS ............................................................................................................................ 156 DATA ANALYSIS ............................................................................................................................................. 159 RESULTS ......................................................................................................................................................... 163 DISCUSSION .................................................................................................................................................... 174 REFERENCES ................................................................................................................................................... 176 SUPPLEMENTARY INFORMATION .................................................................................................................... 181 CHAPTER 6: CONCLUSIONS ............................................................................................................... 188 ANCIENT PLANT DNA RECOVERY .................................................................................................................. 189 USING MODERN AGRICULTURAL INFORMATION TO STUDY ANCIENT PLANT MATERIAL ................................... 191 ALLELE-MINING, AND UTILISING ANCIENT GENOMIC INFORMATION TO IMPROVE CROP YIELDS ...................... 193 REFERENCES ................................................................................................................................................... 195 APPENDIX 1: PERSPECTIVES: ANCIENT PLANT DNA IN THE GENOMIC ERA ......................... 200 STATEMENT OF AUTHORSHIP .......................................................................................................................... 201 ANCIENT PLANT DNA IN THE GENOMIC ERA ................................................................................ 203 v The University of Adelaide Abstract Australian Centre for Ancient DNA (ACAD) School of Biological Sciences Faculty of Sciences Doctor of Philosophy Ancient plant DNA to the rescue: unlocking crop genetic diversity from the past By Oscar Andres Estrada Santamaria The domestication of animals and plants around 12,000 years ago triggered one of the most transcendental revolutions in human society; from a hunter-gatherer lifestyle to a sedentary, agricultural-based society. Since that time, it is estimated that almost 2,500 species of plants have been subject to domestication. However, the domestication history of most of these species remains unclear, with fundamental questions about the identity of wild ancestors, selected phenotypes (domestication traits), and timing and