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Nitrogen (N) is an abundant element on earth. It is a crucial macro-element for plant growth and development. The lack of N causes reduced shoot growth and photosynthesis, early flowering, increased lateral/primary root ratio, and anthocyanin accumulation. Farmers apply N fertilizers to deal with N shortage, however, it causes adverse effects on the environment. Plants are adapted to live under low N supply and can still sustain growth and reproduction. N use efficiency (NUE), shoot dry matter per shoot N content, is used to measure the adaptation to the N depletion. This research investigates the candidate genes, which are responsible for sub-optimal N supply adaptation by using Arabidopsis thaliana, as a model organism. 354 diverse accessions of a natural population, called as HapMap population, are screened under sub-optimal (1 mM) and optimal (5 mM) N (in the form of ammonium/nitrate) conditions. NUE, related agronomic traits (NRATs), and phenotypic plasticity are used to map quantitative trait loci (QTLs). Genome-wide association study (GWAS) is used as a mapping technique and identifies 28 QTLs. 20 accessions from HapMap population are reassessed to confirm extreme accessions in the population. Besides, positive correlation is observed between NUE and relative growth rate and between shoot N concentration and water content. Br-0 and Col-0, two distinct accessions on NUE, are selected as parental accessions for further QTL investigation using bi-parental linkage mapping. QTL mapping reveals seven loci in Br-0 and Col-0 RIL population. One locus, associated with the phenotypic plasticity of water content in GWAS and the shoot fresh weight in the bi-parental linkage mapping, is found to be co-located in both mapping results. This research indicates that the natural genetic variation in Arabidopsis thaliana has a great potential for investigation of NUE improvement in plants. Both GWAS and bi-parental linkage mapping use the natural genetic variation to identify Q

Zn is an essential element for life and the second most abundant transition element in all organisms. Zn deficiency is one of most widespread micronutrient deficiencies in soils and plants need to cope with it. Plants are able to sense the shortage of Zn supply and adjust their Zn homeostasis accordingly. In this thesis, I explored the genetic architecture of the Zn deficiency response of Arabidopsis thaliana. I initiated functional analyses on some of the Zn transporter genes long known to be transcriptionally induced by Zn deficiency, but so far not investigated in much detail. Soon after the exposure to Zn deficiency the expression of these transporters is first induced in roots and later in shoots. Each Zn transporter gene is expressed in one, or more, specific root cell layer(s), which location may differ, depending on the root part. These transporters showed partial functional redundancy among them, which makes it difficult, if not impossible, to detect particular Zn deficiency phenotypes in single Zn transporter mutants. Considering that the effect of mutations on Zn transporter genes is difficult to detect, the Zn deficiency response can be studied from the perspective of their regulatory components. In the search of these regulators I found that the disruption of the N-ALPHA-TERMINAL ACETYLTRANSFERASE 25 (NAA25) gene, involved in N-terminal-acetylation of proteins, causes a strong Fe deficiency sensitivity and a slightly, but consistently, higher expression of several Zn deficiency responsive genes upon Zn sufficiency, when compared to wild-type plants. The causes for the unusual expression pattern of these genes still remain unknown. One hypothesis I postulate is that the lack of N-terminal acetylation of the Zn deficiency regulators bZIP19 and bZIP23, which are possible targets N-terminal acetylation, alters their regulatory activity. To identify more unconventional genetic players underlying the Zn deficiency response, that is not the known suspects invo