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Item Improving shallot (Allium cepa Aggregatum group) production in acidic soils in West Java, Indonesia : a dissertation presented in partial fulfilment of the requirements for the degree Doctor of Philosophy of Gina Aliya Sopha in Horticulture at Massey University, Manawatu, New Zealand(Massey University, 2022) Sopha, Gina AliyaIn the West Java region, Indonesia, the wide range of shallot (Allium cepa) bulb yields suggests that there is potential for productivity improvements, especially for smallholder farmers. This study, which involved a farmer and soil fertility survey, two field trials and a laboratory incubation study, aimed to improve the shallot productivity of smallholder farmers. The survey, conducted in four districts of West Java, identified that the Pacet District had the lowest average bulb yield of 5.4 t ha⁻¹ and also had a wide range of yields (2.3 to 11.8 t ha⁻¹). The two common soil fertility constraints were very low soil pH and low available soil phosphorus (P). The first field trial aimed to determine the optimal P fertiliser rates, when rates of up to 1 tonne of lime ha⁻¹ were applied, for three different farm sites in the Pacet District. These sites had strongly acidic soils with constraining exchangeable Al³⁺ and available soil P levels. The second field trial aimed to determine the response of shallot bulb yield to P fertiliser once exchangeable Al³⁺ had been decreased to a low level using high rates of lime. This field trial used a single farm site with a very low soil pHH₂O of 4.1, a high exchangeable Al³⁺ of 1.9 cmol (+) kg⁻¹ and a low Bray1-P of 10 mg P kg⁻¹. The incubation experiment assessed the effect of a range of liming materials, as well as rice husk biochar and zeolite, on soil pH, exchangeable Al³⁺ and cation exchange capacity (CEC). This study quantified the benefits of improved lime and P fertiliser practices and identified constraints to their implementation. Farmers should aim to ensure that soil exchangeable Al³⁺ levels are maintained < 0.5 cmol (+) kg⁻¹, which will be at soil pH levels of approximately > 4.7. Monitoring soil P status through soil testing and achieving Bray1-P levels above 28 kg ha⁻¹ also improves the likelihood of achieving high yields. Very good financial returns can be achieved from high yielding shallot crops; however, farmers need better access to the services of agricultural field officers to conduct and interpret soil tests.Item Investigation into the relationship between ethylene and sulfur assimilation in Arabidopsis thaliana and onion (Allium cepa L.) : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science (with Honours) in Biochemistry at Massey University(Massey University, 2006) Sanggang, Fiona AnnThe phytohormone ethylene (C2H4) mediates the adaptive responses of plants to various nutrient deficiencies including iron (Fe)-deficiency, phosphorus (P)-deficiency and potassium (K)-deficiency. However, evidence for the involvement this hormone in the sulfur (S) deficiency response is limited to date. In this study, the effect of C2H4 treatment on the accumulation of the S-assimilation enzymes ATP sulfurylase (ATPS). adenosine-5 -phosphosulfate-reductase (APR), O-acetylserine-(thiol)-lyase (OASTL) and sulfite reductase (SiR) was examined in A. thaliana and onion (A. cepa). To complement this, the effect of short-term S-depletion on the expression of the 12-member gene family of the C2H4 biosynthetic enzyme, l-amino-cyclopropane-l-carboxylic acid (ACC) synthase (ACS) from A. thaliana, designated AtACS1-12, was also examined. Western analyses were used to show that plants of A. thaliana pre-treated with the C2H4-signalling inhibitor 1-MCP, had elevated levels of ATPS, APR and OASTL protein in leaf tissue at all time points examined, suggesting that C2H4 has an inhibitory effect on the accumulation of these enzymes. However, SiR appeared to be under dual regulation by C2H4: under S-sufficient conditions C2H4 appears to prevent the unnecessary accumulation of SiR and conversely promote the fast accumulation of SiR under S-depleted conditions. The changes in AtACS1-12 expression in the root and leaf tissues of S-sufficient and S-depleted plants of A. thaliana were examined by RT-PCR using gene-specific, exon-spanning primers. The expression patterns of AtACS2, AtACS6 and AtACS7 were comparable regardless of S availability and may therefore be housekeeping genes. In contrast, the expression of AtACS5 in leaf, and AtACS8 and AtACS9 in roots was repressed under S-depleted conditions, although the mechanism of this repression cannot be elucidated from this study. The protein products of these closely-related genes are believed to be phosphorylated and stabilised by a CDPK whose activity may be compromised by S-depletion. The inhibition of AtACS5, AtACS8 and AtACS9 expression, and the decrease in AtACS5, AtACS8 and AtACS9 accumulation, and hence less C2H4 production, may be part of the plant adaptive response to S-depletion, as the C2H4 -mediated repression of root growth is alleviated to allow the plant to better seek out the lacking nutrient. The expression of the MPK-stabilised genes AtACS2 and AtACS6 appeared to be similar regardless of S availability, although this may merely be a consequence of the scoring method used in this study, which cannot determine whether there was any difference in the level of expression of these genes. The expression of AtACS10 and AtACS12 was repressed in S-deficient plants. Although both AtACS10 and AtACS12 isozymes posses the hallmark seven conserved regions found in the ACSes of other plant species, they are also phylogenetically related to alanine and aspartate aminotransferases, and are known to encode aspartate (AtACS10) and aromatic amino acid transaminases (AtACS12). Therefore, the apparent downregulation of these genes suggests that the downregulation of amino acid metabolism may be part of the plant adaptive response to S-depletion. The downregulation of several AtACS genes, and therefore possibly also C2H4 biosynthesis, in S-deficient plants was accompanied by an accumulation of APR protein. The increase in APR protein that also occurred in 1-MCP-treated plants indicates that C2H4 may be involved in the plant response to S-depletion, because in both cases the upregulation of the S-assimilation pathway, as manifested by the accumulation of APR protein, occurred when C2H4 biosynthesis and signalling was repressed. However, the possible role of other phytohormoes in the plant response to S-depletion cannot be excluded, as there is evidence for crosstalk between the C2H4 signalling pathway and those of auxin, abscisic acid (ABA), cytokinins and jasmonic acid (JA). Furthermore, because C2H4 has been implicated in the response of various plants to Fe-deficiency, P-deficiency, and K-deficiency, in addition to S-deficiency, it may be a regulator of the plant adaptive response to nutrient stresses in general.Item Mathematical modelling of bulk stored onions in transport containers : a thesis presented in partial fulfilment of the requirements for the degree of Master of Horticultural Science in Agricultural Engineering at Massey University(Massey University, 1995) Clayton, MurrayExport onion bulbs are predominantly transported from New Zealand loose in sacks which are bulk loaded into intermodal transport containers. Product respiratory heat, water vapour, and volatiles are dispensed of by a fan unit installed in the end of the container, ventilating the stow by forcing ambient air from a false floor up through the crop and exhausting the air from a head space. The objective of this study was to mathematically model this system with respect to onion bulb temperature and weight loss, and internal container air temperature and relative humidity. These product and flowfield variables were predicted at different locations within the transport vessel. Bulb temperature and weight loss were simulated as dynamic variables using ordinary differential equations, and air temperature and relative humidity were simulated as quasi steady state variables using algebraic equations. A validation experiment was conducted to evaluate the simulation model by placing temperature and humidity sensors throughout the product and flowfield space measuring the respective properties. Onion and air temperatures were predicted with satisfactory accuracy in almost all measured locations of the container. Prediction of relative humidity varied considerably throughout the container, although excessive sensor errors were identified casting suspicion on some validation measurements. Simulated relative humidity could not therefore be fully verified. Bulb weight loss was predicted with variable levels of accuracy. Significant variability in the validation data was evident in the upper and lower regions of the container preventing complete model validation. Central regions of the container were simulated with satisfactory accuracy. A model sensitivity analysis revealed that container ventilation rate strongly influenced model performance with respect to temperature and relative humidity. The mass transfer coefficient, as expected, was most influential over product weight loss.Item Growth and nitrogen nutrition studies of onions (Allium cepa L.) : a thesis ... for the degree of Master of Horticultural Science in Horticultural Production at Massey University(Massey University, 1980) Ceesay, Momodou AlasanThe effect of nitrogen (N) fertilizer was studied in the field and in the greenhouse on the growth, development, maturation and storage life of onions (Allium cepa L.), cultivar "Pukekohe Long Keeper" (PLK). Samples were taken at specified harvest dates and morphological measurements, growth analysis and plant tissue analysis for nitrate-nitrogen (NO -N) and total nitrogen (total N) in the leaf blades, bulbs and roots of the onion plants were carried out. Also, high temperature storage for onions was investigated and compared with cool storage. Fresh and dry weight of the entire plant and the bulb dry weight increased with time to a maximum at the end of the growing period. Root dry weight, leaf dry weight, green leaf area and green leaf number increased with time then decreased as maturity approached. In general, whole plant fresh and dry weight and the plant parts, leaf and bulb, increased with increasing N fertilizer. Root dry weight was generally higher with the low N treatments than with the high N treatments. However, when N was too low, root growth was severely restricted. Low N rates tended to stimulate earlier bulb formation but delayed maturity. Very high N rates induced earlier maturity. Bulb weight and bulb diameter generally increased with increasing N fertilizer at the end of the growing season. Whole plant Relative Growth Rate (RGR) and bulb Relative Growth Rate (bulb RGR) were closely related. RGR and Leaf Area Ratio (LAR) decreased with time, however Net Assimilation Rate (NAR) was constant in the early growth stages but fluctuated in the later stages of growth. All the growth analysis parameters, RGR, NAR, LAR, Leaf Weight Ratio (LWR) and Specific Leaf Area (SLA), generally increased with increasing N fertilizer. The increase in RGR brought about by increases in N rate was mainly due to increases in LAR. The increase in LAR caused by increases in N levels was due mainly to increases in LWR. In general, NO -N and total N concentrations in the onion plant parts increased with increasing N fertilizer but declined as the plants advanced in age. Critical NO -N and total N concentrations for onions were determined from the relationship between relative growth and the NO -N and total N in the leaf blades, bulbs and roots. The NO -N concentration in the leaves and bulbs was found to be very low and appeared to be less reliable for determining the N status of the crop. The NO -N concentration in the roots was much higher, probably because nitrate is reduced in the roots in onions. However, analysing for total N, rather than NO -N, in the plant organs, in particular the leaf blades, is a much better method for monitoring the nitrogen status of an onion crop. The high N treatments generally removed more N than the low N treatments. A linear relationship was found between the bulb yield and the amount of N removed. For most soil conditions, 200 kg N/ha is considered an optimum level for onion production. There was little difference in storage life between bulbs stored under high temperature conditions and those under cool storage. Nitrogen fertilizer rates had no significant effect on bulb storability.Item Interaction between sulfur (S) and nitrogen (N) assimilation pathways in response to S and N supply in onion (Allium cepa L.) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Molecular Biology at Massey University, Palmerston North, New Zealand.(Massey University, 2014) Joshi, SrishtiThis thesis investigates the extent of interdependency between the sulfur (S) and nitrogen (N) assimilation pathways in the commercially important, S-accumulating, monocot species, onion CUDH2107 (Allium cepa L.), to elucidate some of the regulatory points of cross-talk between these two pathways. To test the interactions between the two pathways, a factorial S x N depletion experiment was set up. Plants were grown in short day conditions to maintain the pre-bulbing stage after which they were transferred to long day conditions to promote bulbing. At the end of the short day conditions, the plants were harvested as leaf, pseudo stem and root and at the end of the long day conditions, as leaf, bulb and roots, for each of the four treatments. The four treatments comprised of control treatment (designated C; comprising 14 mM N and 2 mM S), low S treatment (designated –S; comprising 14 mM N and 0.25 mM S), low N treatment (designated –N; comprising 3.5 mM N, 2 mM S) and coupled low S and N treatment (designated –S-N; comprising 0.25 mM S and 3.5 mM N). In terms of changes in biomass, both the root and the shoot biomass tended to be higher under the –S treatment at the bulbing stage, although these changes were only significant for the root biomass. Under the – N and the –S-N treatments, the shoot biomass was much lower when compared with the control plants at both the pre-bulbing and the bulbing stage, although no change in the root biomass was observed. The exception was at the bulbing stage under the –S-N treatment where the root biomass was significantly higher when compared with the control plants. At the transcriptional level in response to the -S treatment, the relative transcript abundance of commonly used S-starvation marker genes, AcHAST1;1LIKE1 and AcAPSR1 increased in both root and the leaf tissue and was more marked at bulbing. In contrast, transcript abundance of AcAPSK1, which marks a bifurcation in the S-assimilation pathway, decreased. At bulbing, a decrease in the relative transcript abundance of AcATPS1, AcSIR1 and AcOASTL3 in the leaf tissue and AcATPS1, AcAPSK1, AcOASTL2, AcNRT2;1LIKE1 and AcNiR1 in the root tissue was observed in response to the –S treatment. However, in response to N deprivation, under the –N as well as –S-N treatment, the transcript abundance of AcHAST1;1LIKE1 and AcAPSR1 was dramatically reduced in the roots with a significant induction in the leaf tissue at both the stages. In addition, relative transcript abundance of AcATPS1 , AcAPSK1 and AcSOX1 also increased whereas AcOASTL2, AcNR1 and AcNiR1 decreased under the –N and the –S-N treatments in the leaf tissue, at pre-bulbing. However, at bulbing, transcript levels of AcOASTL2 and AcNR1 also increased under both, the –N and the –S-N treatments. In the roots, at pre-bulbing, the relative transcript abundance of AcHAST1;1LIKE1, AcNRT2;1LIKE1 and all the down-stream reductive S and N assimilation genes investigated declined, while the transcript abundance of AcAPSK1 increased. A similar response was observed at the bulbing stage for most genes except AcSOX1 and AcOASTL3 which increased and AcOASTL1, AcOASTL2 and AcNRT2;1LIKE1 showed no change. Similar to the leaf under the –S-N treatment, the transcriptional profile of the genes investigated in the roots under the –S-N treatment also showed a dominant response to N depletion. In terms of protein accumulation and enzyme activity, AcSiR1 declined in the –S treatment but accumulated in the –N and the –S-N treatment in the leaf tissue at pre-bulbing whereas at bulbing, a decline in protein accumulation was observed under all three treatments. The AcSiR1 enzyme activity declined under the –S and the –N treatment but remained unchanged under the –S-N treatment in the leaf tissue at the pre-bulbing as well as the bulbing stage. In the roots, AcSiR1 accumulated under the –S treatment in both the stages whereas activity remained unchanged. No AcSiR1 protein could be detected under the –N treatment at both stages and in the –S-N treatment at pre-bulbing, whereas the activity increased under these treatments at both stages. Under the –S treatment in the leaf tissue, AcNiR1 accumulated slightly at both pre-bulbing and bulbing whereas the activity remained unchanged. Under the –N and the –S-N treatments, AcNiR1 declined in the leaves at pre-bulbing but accumulated at the bulbing stage. However, the activity remained unchanged at the pre-bulbing stage and was below the assay detection limit at bulbing. In the roots, the AcNiR1 accumulation response was similar to that in the leaf tissue under each treatment at both the stages, whereas the activity declined under all treatments at both stages except at the pre-bulbing stage under the –S treatment where it remained unchanged. The accumulation of a set of targeted metabolites was also compared over the four treatments. A decline in the S containing flavour precursors, including the lachrymatory factor, thiopropanal-S-oxide, was observed in all tissues in response to low S supply. However, glutathione only declined in the leaf at the bulbing stage. An effect of the –S treatment on the accumulation of N-containing metabolites was observed as an accumulation of the amino-acids in the pseudo-stem and the bulb. In contrast, a decline in the accumulation of the amino-acids and derivatives was observed in the leaf at bulbing. In response to the –N treatment, most of the N-containing metabolites declined systemically, including the N-pathway cysteine precursor, O-acetylserine and serine. Flavonol glucosides accumulated in a tissue-specific manner in the pseudostem at the pre-bulbing stage but declined in the bulb tissue. Generally, sugars accumulated systemically at both developmental stages whereas sugar phosphates accumulated only in the leaf and root tissue at the pre-bulbing stage. The lachrymatory factor thiopropanal-S-oxide, accumulated in the leaf at the pre-bulbing stage but declined at the bulbing stage in response to the –N treatment. The metabolite accumulation profile in the plants under the –S-N treatment was similar in all tissues to that of the –N treatment at both the stages. The results from the factorial experiment suggest a hierarchy of N nutrition over S nutrition in A. cepa, where the incorporation and accumulation of S metabolites as well as bulb formation is regulated by N availability. A putatively novel point of interaction between the S-assimilation and the N-assimilation pathways via sulfite reductase (AcSiR1) and nitrite reductase (AcNiR1) was also investigated. Recombinant AcSiR1 and AcNiR1 were each able to reduce both sulfite and nitrite, although with a higher specific activity for the physiological substrate in each case. Further, solid phase binding assay indicated a positive interaction between the two recombinant proteins, although this could not be confirmed by Isothermal titration calorimetry (ITC). In addition to this, in a short term S x N depletion experiment with Arabidopsis, AtSiR1 transcripts only declined in the –S-N treatment in the leaves whereas AtNiR1 transcripts declined in the –S, -N as well as –S-N treatment in wild type plants. In the roots, AtSiR1 transcripts decline in both the –N and the –S-N treatment in the roots whereas no significant change was observed in the AtNiR1 transcripts. In a sir1 T-DNA knock-down line of Arabidopsis, the AtSiR1 and the AtNiR1 transcripts did not change in response to any treatment in both leaf and the roots. Substrate redundancy between AcSiR1 and AcNiR1, in vitro, along with the other interaction studies suggest that although both AcSiR1 and AcNiR1 can reduce both substrates, the possibility of this being a direct point of cross-talk between the two pathways is not conclusively established.Item Regulation of sulfur assimilation in onion (Allium cepa L.) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Physiology at Massey University, Palmerston North, New Zealand(Massey University, 2008) Thomas, Ludivine A.Onion (Allium cepa L.) is an example of a species that accumulates very high levels of reduced sulfur (S)-containing compounds, particularly in the bulb as alk(en)yl-L-cysteine-sulfoxides (ACSOs) and it is these compounds, or their derivatives, that confers the distinct odour and pungent flavour. In common with higher plants, the S assimilation pathway in onion begins with the activation of uptaken sulfate (SO4 2-) to 5'-adenylylsulfate (APS), a reaction catalysed by ATP sulfurylase (ATPS; EC 2.7.7.4). Then, APS is reduced to sulfide (S2-) in a two-step process catalysed by the enzymes APS reductase (APSR; EC 1.8.4.9) and sulfite reductase (SiR; EC 1.8.7.1). To complete the reductive assimilation pathway, S2- is incorporated into the amino acid skeleton of O-acetylserine (OAS) to form cysteine, and this reaction is catalyzed by OAS (thiol)-lyase (OAS-TL; EC 4.2.99.8). While the regulation of the pathway is quite well defined in the plant model Arabidopsis, much less is known about its regulation in S accumulating species such as onion. The primary aim of this thesis, therefore, was to characterise the enzymes of the S assimilation pathway in onion, with a particular emphasis on ATPS. As part of this charaterisation two genotypes of onion were compared. These comprised a mild genotype, 'Texas Grano 438' (TG) with a lower level of S-containing compounds in the bulb tissues, and 'W202A' (W), a cultivar with a higher level of S containing compounds in the bulb tissues. As well, comparisons were made between seedlings (typically harvested at 7 weeks) and plants at a designated mature stage (at bulbing; typically after 4 months growth), and for plants grown in S-sufficient (S+) media or S-deficicnt (S-) media, as appropriate. In terms of plant growth, S-deprivation generally had a negative influence for both genotypes, with significant reductions in total biomass (measured as fresh weight) for TG at both the seedlings and mature stages. ATPS activity and accumulation were shown to be present in all tissues examined (leaf, root, bulb) as well as the chloroplasts, with highest activity measured in the roots, particularly in seedlings. ATPS activity and accumulation were also compared between the two genotypes (TG and W) with ATPS activity and accumulation higher in W, particularly at the seedling stage. In terms of the influence of S supply, in general higher ATPS activity was measured in chloroplast, leaf and root extracts from plants of both genotypes grown in the S- media, at the seedling stage. In roots of mature plants of both genotypes, a significant increase in activity was measured in response to S-deprivation, while in chloroplasts isolated from mature plants of both genotypes, highest activity was measure in those grown in the S+ media. Finally diurnal variations were observed in chloroplast, leaf and root extracts of both genotypes with a general trend of an increase in ATPS activity and accumulation a few hours after illumination and upon the onset of the dark period. Although a single gene coding for ATPS is presumed to be present in onion, the enzyme was characterized as two electrophoretic forms using 1D-PAGE during western analyses following fractionation of chloroplasts by anion exchange chromatography and also as an alignment of spots using 2D-PAGE. As protease inhibitors were routinely included in the extraction buffers, these forms suggest the occurrence of ATPS isoforms that may arise as a consequence of post-translational modifications. The regulation of ATPS by one mechanism of post-translational modification, phosphorylation, was therefore investigated using several techniques including the detection of a shift in molecular mass, a change in enzyme activity or pI (as determined by 2D-PAGE) and the capability to bind to 14-3-3 proteins using affinity chromatography. Following treatments of chloroplast extracts to promote either the phosphorylation (P+) or the dephosphorylation (P-) of proteins, no molecular mass change or change in activity was observed. However, after fractionation by 2D-PAGE, differences in the spot alignment of ATPS were visualized, suggesting that ATPS is a phosphoprotein. The enzyme was detected in pull-downs after affinity chromatography, suggesting that ATPS may also interact with 14-3-3 proteins (although this needs to be confirmed unequivocally). A model is advanced, therefore, in which upon phosphorylation, no variation in ATPS activity occurs but a change in the surface charged and possibly a change in conformation of the protein does occur to make the enzyme competent to interact with 14-3-3 proteins.