TY  - THES
T1  - Comprehensive analyses of DNA methylation profile, regulation on flowering, and seed mineral accumulation in Arabidopsis thaliana in response to zinc deficiency
A1  - Chen Xiaochao
Y1  - 2017/02/24
N2  - Zinc (Zn) is an essential micronutrient for plant growth and development, which plays important roles in DNA binding, metabolic, catalytic and transcriptional regulator activities. However, Zn deficiency is a worldwide problem due to its limited bioavailability in soils in many agricultural areas, often as a result of high CaCO3 content and high pH. In addition, phytic acid is able to strongly chelate cations, such as Zn2+, Fe2+, Ca2+ and Mg2+ to form the phytate salts. Phytate cannot be digested by human beings or other monogastric animals due to lack of phytase, an enzyme that can hydrolyze phytate. Therefore, Zn bioavailability in seeds (or grains) is restricted by phytate. Moreover, seed Zn concentration is also reduced by elevated CO2, especially in C3 plants, such as wheat, rice and soybean. Regarding to the crucial roles but limited bioavailability of Zn, here I present a comprehensive analysis on roots, leaves (and flowering) and seeds in response to Zn deficiency in the model plant Arabidopsis thaliana via three experiments. 
First, I investigated the transcriptional response and whole-genome DNA methylation profile upon Zn deficiency in roots using next-generation sequencing. Ionome analysis on shoots showed that Zn concentration was strongly reduced in Zn deficiency, whereas other nutrients were not affected. Microarray Analysis identified several known Zn-deficiency responsive genes, confirming the effectiveness of Zn deficiency in this work. However, bisulfite sequencing results revealed that DNA methylation was eliminated by Zn deficiency in transposable elements and slightly in gene bodies as well. The DNA demethylation response to nutrient stress was a novel finding, as reversed to previous reports about phosphate stress which accumulated methylation. Surprisingly, further analysis suggested that DNA methylation occurred independent of gene transcription. Nevertheless, non-CpG methylation has a potential impact on flower development in response to Zn deficiency. 
The second experiment investigated the relationship between rosette size and flowering, and how rosette size and flowering time were regulated by Zn deficiency. Using natural variation population (168 Arabidopsis accessions), I found that flowering time was positively correlated with rosette size in early-flowering accessions but not in late-flowering accessions. Intriguingly, the flowering time was delayed by Zn deficiency in these early-flowering plants and resulting in promotion of vegetative biomass. However, Zn-regulated flowering time was independent of previously reported flowering pathways. Then genome-wide association study identified the underlying candidate gene was FLOWERING LOCUS T (FT) which was strongly inhibited by Zn deficiency in all accessions. Detailed genetic analysis confirmed this result as well. Furthermore, the promotion of leaf size in Zn deficiency was found being contributed by cell proliferation (cell number) but not cell size. 
Lastly, in the third experiment I was interested in the natural genetic variation in seed Zn concentration, together with iron (Fe) and manganese (Mn), in response to Zn deficiency. Across around 100 accessions, average seed Zn concentration decreased from 47.4 µg g-1 to 31.3 µg g-1 due to Zn deficiency. To identify candidate genes affecting seed Zn, Fe and Mn concentrations, genome-wide association mapping was performed. A candidate gene, inositol 1,3,4-trisphosphate 5/6-kinase 3 gene (ITPK3), was associated which is involved in phytate synthesis pathways. However, loss of this gene in itpk3-1 did neither affect phytate seed levels nor seed Zn, Fe and Mn. Nevertheless, large natural variance of micronutrient seed levels was identified in the population and several accessions maintained high seed Zn despite growth in Zn-deficient conditions. 
Altogether, this study presents comprehensive analyses in how Arabidopsis adapts to Zn deficiency in regard of root transcription and DNA methylation, flowering and leaf regulation, and seed mineral accumulation. I provided new possibilities of correlation between DNA methylation and gene transcription, which is much more complex than previously reported. I also opened a novel insight into flowering regulation on leaf size, resulting in promotion of vegetative biomass in nutrient deficiency. Substantial natural variation of seed experiment indicated that the evolution process was involved in seed mineral accumulation in Arabidopsis, especially those accessions maintaining Zn concentration in Zn-deficient soils are valuable for further investigations. I believe these findings in Arabidopsis also provide precious knowledge for plant breeders and agronomists who work on crops. 

KW  - Zinc; DNA methylation; Flowering; Seed; Assoiation mapping
CY  - Hohenheim
PB  - Kommunikations-, Informations- und Medienzentrum der Universität Hohenheim
AD  - Garbenstr. 15, 70593 Stuttgart
UR  - http://opus.uni-hohenheim.de/volltexte/2017/1323
ER  -