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Regulation of Postharvest Inflorescence Senescence in Arabidopsis Thaliana

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Regulation of Postharvest Inflorescence Senescence in Arabidopsis Thaliana Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. Regulation of postharvest inflorescence senescence in Arabidopsis thaliana A thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Science at Massey University, Palmerston North, New Zealand. Xi Xu 2020 Abstract Senescence is critical for plant survival and fitness as it ensures the most efficient use of nutrients for development and production of offspring. Senescence is a genetically controlled and hormone-mediated programme. Besides being induced in an age-dependent manner, senescence can also be initiated precociously from harvest-induced stress such as light- and sugar- deprivation. Understanding the biological mechanisms behind dark-mediated senescence is important as it helps to provide a new strategy for extending shelf life of crop plants. This project aims to understand the regulation of dark-induced inflorescence senescence in model plant Arabidopsis thaliana by using a forward genetic approach. Arabidopsis mutants showing accelerated and delayed inflorescence senescence (named ais and dis) were identified previously. Here, I rescreened 23 mutants and confirmed the altered time to senescence phenotype of nine mutants, including two ais and seven dis mutants. Of those, the dis2, dis9, dis15 and dis51 mutants were used for further analysis. The delayed degreening phenotype was also observed in detached dark-held leaves of dis2 and dis51 mutants, indicating that the causal mutations affected genes that regulate both leaf and inflorescence senescence. Segregation analysis was used to determine the genetic nature of dis traits in the dis2 and dis51 mutants. The dis2 trait was found to be monogenic recessive while the dis51 trait is dual- genic recessive. The dis2 mutant showed an extended “stay-green” phenotype and retained higher chlorophyll (Chl) b than Chl a. These findings were consistent with a lesion in the NON-YELLOW COLORING1 (NYC1) gene. Sequencing revealed a C/T transition in exon 8 of NYC1, which caused a highly conserved proline to be substituted by serine at amino acid position 360 of the NYC1 protein. By contrast, dis51 retained a similar amount of Chl a and Chl b. One of the genetic lesions in this mutant was mapped to a ~665 kb region at the top arm of chromosome 5 by using High Resolution Melt (HRM)-based mapping technology. The ETHYLENE INSENSITIVE2 (EIN2) gene was considered as a promising candidate because similar phenotypes were observed in ein2 mutants and dis51 seedlings did not show triple response I when treated with the ethylene precursor ACC in the dark. PCR-based sequencing showed a G to A mutation in exon 6 of EIN2, resulting in a premature stop codon, which thereby resulted in a truncated EIN2 protein missing part of the C-terminal region that is required for ethylene signal transduction. In addition, the dis51 mutant emitted a pleasant aroma, which is abnormal in Arabidopsis. Four compounds (benzaldehyde, benzyl alcohol, phenylacetaldehyde and phenylethanol) were detected by using GC-MS analysis. However, it is not clear if the mutation causing the aroma phenotype also contributed to the dis51 phenotype. The mutations in the dis9 and dis15 mutants were previously mapped to chromosome 3 and chromosome 2, respectively. Here, further HRM and whole genome sequencing (WGS) data analyses were used to identify the causal mutation in the dis9 mutant. The mutation changed a highly conserved Ser-97 to Phe in the active site of strigolactone (SL) receptor gene DWARF14 (D14), likely causing loss-of-activity. Since dis15 showed similar phenotypes to dis9, I hypothesised that the genetic lesion in dis15 may also have occurred in an SL pathway gene. The MORE AXIALLY GROWTH1 (MAX1) SL biosynthesis gene was present within the previously mapped region of this mutant. By using WGS data, I found a G/A mutation in the coding region of MAX1. The mutation in MAX1 substituted a highly conserved Gly-469 (G469) with Arg (R) in the haem- iron ligand signature of the Cytochrome P450 proteins. Using a N. benthamiana transient expression system, I found that the G469R substitution caused loss- of-activity of MAX1. In addition, the delayed sepal degreening of dis9 and dis15 was also observed in planta, suggesting a role of SL in regulation of both developmental and dark-induced sepal/inflorescence senescence. nCounter transcript counting technology was used to investigate the relationship between SL biosynthesis and signalling, sugar signalling and dark-induced senescence. There was no evidence of SL biosynthesis during the normal night in the inflorescences. During the extended night, the expression patterns of the SL biosynthetic gene MAX3 and signalling gene SUPPRESSOR OF MAX2-LIKE7 (SMXL7) best correlated with the sugar-responsive senescence regulatory genes [ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN92 (ANAC092) and NAC-LIKE, ACTIVATED BY AP3/PI (NAP)] and senescence marker gene II (SENESCENCE-ASSOCIATED GENE12; SAG12), suggesting an interaction between SL and sugar signalling in controlling dark-induced inflorescence senescence. ANAC092 and NAP were further induced in the max1 mutant by the SL analogue, GR24, suggesting they are SL-inducible genes. The overall findings in this project reflect a complex regulatory network, which involves multiple phytohormones and degradation pathways, during dark- induced inflorescence senescence in Arabidopsis. Here, I proposed a model in which prolonged darkness first causes sugar-starvation in the excised inflorescence; the plant hormones ethylene and SL subsequently work together to regulate inflorescence senescence, including NYC1-regulated Chl degradation. III Acknowledgements I would like to give my sincere thanks to my supervisors Associate Professor Paul Dijkwel, Dr. Donald Hunter and Associate Professor Andrew Sutherland- Smith for their useful advice and kind help in their own research areas during my PhD study. I thank Paul and Don for tolerating my arguments during academic discussions. Special thanks to Paul for his understanding, moral support and insightful advice during my PhD study, especially during thesis and manuscript writing. I am also very impressed by his intelligence on genetics, in which area I have learnt a lot from him. Special thanks to Don for offering Arabidopsis mutants, for every support when I did my work in Plant & Food Research (PFR) and for his brilliant advice on presentation of nCounter data. Also, I thank Don and his family for taking care of me when I was sick and for comforting me when my grandma passed away. I am grateful for Andrew’s guide and help for the protein structure analysis and his encouragement when I was stuck at my research. For the collaborative research, I acknowledge Prof. Harro Bouwmeester at the University of Amsterdam and everyone in his group, especially Yanting Wang, Kristyna Flokova, Lemeng Dong and Olka for hosting me and assisting me with the transient expression assay when I was in their lab. For technical support, I want to give my sincere thanks to Dr. Axel Heiser at AgReserch for all the support and kind help when I did nCounter experiment in his lab. I also appreciate Prof. Pilar Cubas at Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas for providing the D14 construct for genetic complementation. I also want to thank the following people for their help or advice: Dave Wheeler for help with WGS data analysis; Andrew McLachlan for the linear mixed model analysis; Martin Hunt for the GC-MS analysis; David Chagné for his advice and support on HRM analysis; Ian king for his kind help in the plant house; Huaibi Zhang and Nick Albert for their useful advice on some lab work; Kimberley Snowden and Bart Janssen for their useful feedback towards the manuscript. IV I thank Dave Brummell, Marian McKenzie, and Erin O’Donoghue, David Lewis for always being nice and friendly to me when I was in PFR. I thank Sheryl and Steve for their assistance in the lab. Also, I thank my colleagues and friends in PFR (Sarah, Lei, Chethi, Chris, Marzi, Evie, Zoe, Ronan) and in Massey (Tina, Nikolai, Meriem, Elva and Rama) for their friendship, company and moral support. Especially, I want to thank Sarah for her understanding and comfort during the hard time of my research and life, and to Nikolai for sharing experience with me for some bioinformatic analysis. I thank Flavia and Maria for their kind help in Torino when I attended the conference there. I thank Bea for her friendship, help and company when I was in Amsterdam. Special thanks to Ann Truter and Kathryn Stowell for all their support during my PhD study. I thank the Massey foundation, IFS department and NZSPB for their financial support to attend the international conference and to go to the Netherlands for conducting some work. I acknowledge Massey University Joint Graduate School of Horticulture and Food Enterprise for a doctoral scholarship and PFR SSIF funding: 1972 – “Breeding Technology Development” for financial assistance to conduct my research in PFR. Finally, but the most important, I want to thank my dearest parents for everything they did for me in my life. No word in this world can express my appreciation and love to them. Thank you so much for everything!!! All in all, thanks to everyone who helped and supported me in this project as well
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