The PROTEOLYSIS 6 (PRT6) branch of the N-end rule pathway is a well-characterized negative regulator of flooding and low oxygen tolerance in plants. This study investigated the role of this pathway in adaptation to salinity stress in Arabidopsis and maize via physiological and molecular characterization of Arabidopsis prt6-1 and maize prt6 MU insertion mutants, respectively. Our study demonstrated that the loss of function mutation of prt6 in Arabidopsis activated hormonal and transcriptional responses associated with adaptation to salinity stress, enhancing high salt tolerance at seed germination, seedling, and adult plant stages. Our data also indicated that salinity tolerance conferred by the prt6 mutation is attributed to increased mRNA abundance of key transcriptional factors in ABA-dependent (AREB/ABFs) and independent (DREBs) pathways, together with the dominant expression of downstream dehydrins. Furthermore, this study revealed that the prt6 mutation enhances ethylene and brassinosteroid responses, resulting in restricted Na+ accumulation in roots and shoots as well as increased expression of dehydrin genes such as RD29A and RD29B. Maize prt6 mutant plants, contrary to our observation in Arabidopsis, showed lower seed germination, primary root elongation, and shoot biomass growth along with increased malondialdehyde (MDA) accumulation under high salt. Moreover, maize prt6 mutants exhibited reduced grain yield and yield-related components under high salt. These results indicate that PRT6 functions as a negative regulator for salinity tolerance in Arabidopsis, whereas this gene plays a positive role in salinity tolerance in maize. In wheat, we compared two genotypes with contrasting nitrogen-use-efficiency (NUE), VA08MAS-369 and VA07W-415, to dissect physiological and molecular mechanisms underlying NUE regulation. Our agronomic data revealed that line 369 maintained yield and yield-related parameters and exhibited greater NUE indexes relative to line 415 under N deficient conditions. Furthermore, our analyses suggested that the significantly higher nitrogen use efficiency (NUE) in line 369 could be attributed to the greater N uptake efficiency in this genotype. In fact, line 369 was able to maintain the development of root systems under N limitation. Consistently, genes encoding high-affinity nitrate transporters such as TaNRT2.1 and TaNRT2.2 were expressed more abundantly in the roots of line 369 than line 415 at limited N. Overall, the results of this study characterized physiological and molecular phenotypes associated with high N uptake efficiency in line 369. This is useful information for the development of new wheat accessions with improved NUE. / Doctor of Philosophy / In coastal areas, sea-level rise increases the chances of saltwater intrusion into cultivable lands, making a hostile environment for crop growth and production by imposing flooding and salinity stresses simultaneously. Identification of central regulators that regulate the adaptation to both flooding and salinity is a critical step for the development of new crop genotypes with enhanced tolerance to these stresses. Previous studies have characterized the function of the PROTEOLYSIS 6 (PRT6) gene in adaptation to flooding stress in plants. This study assessed whether this gene is involved in adaptation to salinity stress in Arabidopsis and maize by evaluating the growth and survival of their respective prt6 mutants under high salt. Consistent with the flooding tolerance data, our study showed that the PRT6 gene also functions as a negative regulator of salinity stress tolerance in Arabidopsis. The prt6 mutation in Arabidopsis activated the key transcriptional and hormone response pathways associated with adaptation to both salinity/osmotic stress and sodium toxicity, expressed as enhanced tolerance to excess salt at seed germination, seedling, and adult plant stages. In maize, disruption of the PRT6 gene decreased seed germination, primary root elongation, and shoot biomass growth under high salt, which is opposite to our observations in Arabidopsis. Additionally, the maize mutant plants encountered more oxidative stress, as demonstrated by the higher accumulation of malondialdehyde (MDA) under high salt. Moreover, maize prt6 mutants exhibited reduced grain yield under high salt. Overall, these results indicate that disruption of the PRT6 gene confers increased tolerance to high salt in Arabidopsis, whereas it conversely reduced salinity tolerance in maize. In wheat, we compared two genotypes with distinct nitrogen use efficiency (NUE), VA08MAS-369 and VA07W-415, to determine critical traits involved in NUE regulation. Our study showed that grain yield and yield-related parameters were significantly higher in line 369 than line 415 under low N. Moreover, high NUE in line 369 was attributed to efficient N uptake in this genotype under limited N. Our root architecture analysis demonstrated that line 369 was able to maintain root depth, volume, and thickness even under N limitation. Consistently, line 369 highly induced expression of genes associated with nitrogen transport at low N. Altogether, this study identified key traits involved in high NUE in wheat, facilitating the breeding of new wheat genotypes with enhanced NUE.

A better way to improve understanding and quantification of nitrous oxide (N₂O) emitted from intensive maize cropping systems is to develop an advanced emissions measurement method This study developed an open path (OP) method to measure N₂O emissions from four adjacent maize plots managed by tillage practices of no-till (NT) and chisel plow (ChP), and different nitrogen (N) treatments from 2014 to 2016. Anhydrous ammonia (220 kg NH₃-N ha^-1) was applied in once or equally split (full vs. split rate) and applied in different timing (Fall vs. Spring). The spring N application occurred either before planting (pre-plant) or in season (side-dress). Emissions measurements were conducted by using the OP method (the scanning OP Fourier transform infrared spectrometry (OP-FTIR) + the gas point-sampling system + a backward Lagrangian stochastic (bLS) dispersion model) and static closed chamber methods. The performance and feasibility of the OP measurements were assessed by a sensitivity analysis, starting with errors associated with the OP-FTIR for calculating N₂O concentrations, and then errors associated with the bLS model for estimating N₂O emissions. The quantification of N₂O concentrations using the OP-FTIR spectrum was influenced by ambient humidity, temperature, and the path length between a spectrometer and a retro-reflector. The optimal quantitative method mitigated these ambient interference effects on N₂O quantification. The averaged bias of the calculated N₂O concentrations from the spectra acquired from wide ranges of humidity (0.5 – 2.0 % water vapor content), temperature (10 – 35 °C), and path length (100 – 135 meters) was 1.4 %. The precision of the OP-FTIR N₂O concentrations was 5.4 part per billion(3σ) in a stationary flow condition for a 30-minute averaging period. The emissions measurement from multiple sources showed that the field of interest was likely interfered by adjacent fields. Fields with low emission rates were more sensitive to the adjacent fields with high emissions, resulting in substantial biases and uncertainties. The minimum detection limit of the N₂O emission rates was 1.2 µg m^-2 s^-1 (MDL; 3σ). The OP measurements showed that the NT practice potentially reduced N₂O emission compared with ChP. Under the long-term NT treatments, the split-N rate application (110 kg NH₃-N ha^-1 in the fall and spring) resulted in lower N₂O emissions than the full application (220 kg NH₃-N ha^-1 in the fall). The management of NT coupled with split-N rate application minimized N₂O emissions among treatments in this study, resulting in N₂O-N losses of 3.8, 13.2, and 6.6 N kg ha^-1 over 9-, 35-, and 20-days after the spring NH₃ application in 2014, 2015, and 2016, respectively. The spring pre-plant N application in 2015 also resulted in higher N₂O emissions than the spring side-dress application in 2016, and the increased N₂O-N loss was corresponding to lower N recovery efficiency in 2015 measurements. A comparison of chamber and OP measurements showed that soil N₂O emissions were likely underestimated by 10x without considering the wind-induced effect on gas transport at the ground-atmospheric interface. This study showed that the OP method provides a great opportunity to study agricultural N₂O emissions as well as management optimization for the sustainability of the agroecosystems.