Nitrogen (N), an essential plant macronutrient, is among the most limiting factors of crop yield. To sustain modern agriculture, N is often amended in soil in the form of chemical N fertilizer, a major anthropogenic contributor to nutrient pollution that affects climate, biodiversity and human health. To achieve agricultural sustainability, a comprehensive understanding of the regulation of N response in plants is required, in order to engineer crops with higher N use efficiency. Recently, epigenetic mechanisms, such as histone modifications, have gained increasing importance as a new layer of regulation of biological processes. However, our understanding of how epigenetic processes regulate N uptake and assimilation is still in its infancy. To fill this knowledge gap, we first performed a meta-analysis that combined functional genomics and network inference approaches to identify a set of N-responsive epigenetic regulators and predict their effects in regulating epigenome and transcriptome during plant N response. Our analysis suggested that histone modifications could serve as a regulatory mechanism underlying the global transcriptomic reprogramming during plant N response. To test this hypothesis, I applied chromatin immunoprecipitation-sequencing (ChIP-Seq) to monitor the genome-wide changes of four histone marks (H3K27ac, H3K4me3, H3K36me3 and H3K27me3) in response to N supply in tomato plants, followed by RNA-Seq to profile the transcriptomic changes. To investigate the organ specificity of histone modifications, I assayed shoots and roots separately. My results suggest that up to two-thirds of differentially expressed genes (DEGs) are modified in at least one of the four histone marks, supporting an integral role of histone modification in regulating N response. I observed a synergistic modification of active histone marks (H3K27ac, H3K4me3 and H3K36me3) at gene loci functionally relevant to N uptake and assimilation. Surprisingly, I uncovered a non-canonical role of H3K27me3, which is conventionally associated with repressed genes, in modulating active gene expression. Interestingly, such regulatory role of H3K27me3 is specifically associated with highly expressed genes or low expressed genes, depending on the organ context. Overall, I revealed the multi-faceted role of histone marks in mediating the plant N response, which will guide breeding and engineering of better crops with higher N use efficiency

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2016-08-17T18:27:17Z No. of bitstreams: 1 2000 - Pedro Nilson Alves Berto.pdf: 654186 bytes, checksum: ef66a21a2e6b0ca326c348f84fb13d3e (MD5) / Made available in DSpace on 2016-08-17T18:27:17Z (GMT). No. of bitstreams: 1 2000 - Pedro Nilson Alves Berto.pdf: 654186 bytes, checksum: ef66a21a2e6b0ca326c348f84fb13d3e (MD5) Previous issue date: 2000-12-12 / CHAPTER I: In a Inceptisol soil, at Santa Cruz Sugar Mill, Campos dos Goytacazes/RJ, an experiment was conducted with the purpose to evaluate, during the cycle of second ratoon answers to the application of sugarcane agroindustry wastes, in consitions of harverst management with and without previous burning, using the growth quantitative analysis and utilizing the RB72454 sugarcane variety. The experimental field was planted in April 1992. The plant cane cut ocurred in July 1993. The first ratoon was harvested in August 1994, when the test was reinstalled to evaluation in the second ratoon, which harvest was in September 1995. The tested treatment were: 1 = CC = raw cane; 2 ? CC + TF = raw cane + 30 t.ha-1 of filter cake; 3 ? CC + TF + B = raw cane + 20 tons of filter cake ha-1 + 10 t.ha-1 of bagasse; 4 ? CQ = burned cane; 5 ? CQ + TF = burned cane + 30 t.ha-1 of filter cake; 6 ? CQ + TF + B = burned cane + 20 t.ha-1 of filter cake + 10 t.ha-1 of bagasse. The physiological rates discussed and interpreted were: a) Number of stalks by linear meter; b) Stalk height (m); c) Total biomass (g.m-2 soil); d) Leaf area index (m2 leaf. m-2 soil); e) Growth tax of the cultural (g.m-2 leaf. day-1); f) Liquid assimilation tax (g.m-2 leaf.day-1); g) Leaf nitrogen concentration; h) Stalk nitrogen concentration. The results allowed the following conclusions: 1) The application of the sugar agroindustry wastes (filter cake and bagasse) in areas harvest with or without burning, didn?t increased the stalks number and canes height. 2) The fact of not have significant differences to the stalks number rates by linear meters and canes height, reflected directly in a not statistical difference among the evaluated treatments, beeing relative a industrial stalks final productivity in t.ha. 3) The value of total biomass, obtained in the various treatments, was very low, mainly in function of hydric deficit ocurred in the period of the development of the experiment. 4) O I.A.F. (leaf area index), showed little significant changes in the first samples (second, fourth and sixth months), with higher values to burning treatments, in function of a higher stalks number by meter found in this parcels. 5) The straw index calculated (20, 6 t.ha-1) affected the ratoon budding, lowing the stalks population. 6) The leaf area index stayed lower than that considered ideal to the development of a productive sugarcane plantation, correlating with the law productivity obtained, beeing a good physiological parameter to the estimation of a sugarcane?s production. 7) The growth tax of the culture showed the highest values between 120 e 240 days after cut, similar to all treatments during the vegetative development cycle and coincided to the highest foliar area index. 8) The liquid assimilation tax was affected by the hydric stress in the period of the maximum growth of the culture. 9) The nitrogen leafs concentration, as the nitrogen stalks concentration didn?t show differences among the treatments. The fact that the soil studied was a Inceptisol soil, with great natural fertility and that ocurred a great hydric stress during the culture cycle, may have equalized the answers. -------------------------------------------------------------------- CHAPTER II: In a Inceptisol soil of Santa Cruz sugar mill; located at Campos dos Goytacazes,RJ, an experiment was conducted to evaluate the influence, in the chemical and biological properties of the soil, during the sugar cane second ratoon, of the sugar industry wastes (filter cake and bagasse) applied into experimental parcels harvested with and without previous burning of the cane. The experimental field was planted in April 1992. The harvest of the cane ocurred in July 1993. The first 1994, ratoon was harvested in August when the experiment was reinstalled for evaluation in the second ratoon, which harvest was done in September 1995. The tested treatments were: 1= CC= raw cane; 2- CC+TF= raw cane + 30 t.ha -1 of filter cake; 3-CC+TF+B= raw cane + 20 tons of filter cake ha-1 + 10 t. ha-1 of bagasse; 4-CQ= burned cane; 5- CQ +TF= burned cane + 30 t ha-1 of filter cake; 6-CQ + TF + B= burned cane + 20 t.ha-1 of filter cake + 10 T.ha-1 of bagasse. The parameters discussed and interpreted were: a) manufacturable stalks productivity in t.ha-1; b) Sugar production in t Pol ha -1; c) microbial soil biomass-carbon in mgCg -1 of soil; d) agroindustrial wastes effect among treatments on the productivity of second and the third curts of the in t.sugarcane ha-1; e) treatments effects on soil chemical properties; f)straw index determination. The results allowed the following conclusions: 1- The application of the sugar agroindustry wastes (filter cake and bagasse), in the sugar cane fields harvested with or without burning, didn`t result in increasing of productivity, in t.ha-1 or in t.ha-1. 2- Raw cane treatments, that received industrial wastes, showed expressive higher values of BMS-C, in comparison with burned cane treatments, mainly in raw cane treatment with filter cake. 3- The Inceptisol soil, may have facilitaded the similarity of the production results (t cane ha-1), due to the its high natural fertility. 4- Straw index, equivalent to 20,6 t. straw ha, may have affected the ratoon budding of the raw cane treatments. 5- generally speaking, the soil chemical properties studied haven`t been modified when the treatments are compared. / CAP?TULO I: Em solo Cambissolo eutr?fico, da usina Santa Cruz, RJ, foi conduzido experimento objetivando avaliar, durante ciclo de segunda soca (terceiro corte da cultura da cana-de-a??car), respostas ? aplica??o de res?duos da agroind?stria a?ucareira, em condi??es de manejo de colheita com e sem pr?via queima, utilizando-se da an?lise quantitativa de crescimento e empregando-se a variedade RB72454. O campo experimental foi plantado no m?s de abril de 1992. O corte da cana-planta ocorreu em julho de 1993. A primeira soca foi colhida em agosto de 1994, ocasi?o em que se reinstalou o ensaio para avalia??o na Segunda soca ou terceiro corte, cuja colheita aconteceu em setembro de 1995. Os tratamentos efetuados foram: 1 ? CC = cana-crua; 2 ? CC + TF = cana crua + 30 toneladas. ha-1 de torta de filtro; 3 ? CC + TF + B = cana-crua + 20 toneladas de torta de filtro . ha-1 + 10 toneladas . ha-1 de baga?o; 4 ? CQ = cana queimada; 5 ? CQ + TF = cana queimada + 30 toneladas . ha-1 de torta de filtro; 6 ? CQ + TF + B = cana queimada + 20 toneladas . ha-1 de torta de filtro + 10 toneladas . ha-1 de baga?o. Os par?metros fisiol?gicos discutidos e interpretados foram: a) n?mero de colmos por metro linear; b) altura do colmo (m); c) fitomassa total (g.m-2 solo); d) ?ndice de ?rea foliar (m2 folha . m-2 solo); c) taxa de crescimento da cultura (g. m- 2 solo.dia-1); f) taxa de assimila??o l?quida (g.m-2 folha.dia-1); g) concentra??o de nitrog?nio nas folhas; h) concentra??o de nitrog?nio no colmo. Os resultados obtidos permitiram as seguintes conclus?es: 1. A aplica??o dos res?duos da agroind?stria a?ucareira (torta de filtro e baga?o), nas ?reas colhidas com e sem queima, n?o resultou em aumento no n?mero de colmos por metro linear e nem na altura das canas. 2. O fato de n?o haver diferen?as significativas para os par?metros n?mero de colmos por metro linear e de altura das canas, refletiu-se diretamente na n?o diferen?a estat?stica entre os tratamentos avaliados, no que se refere ? produtividade final dos colmos industrializ?veis em t.ha-1. 3. O valor da fitomassa total, obtida nos diversos tratamentos, apresentou-se muito baixo, em fun??o principalmente do d?ficit h?drico ocorrido no per?odo de condu??o do experimento. 4. O I.A.F. (?ndice de ?rea foliar), apresentou varia??es significativas nas primeiras amostragens (segundo, quarto e sexto meses), com valores maiores para os tratamentos com queima, em fun??o de maior n?mero de colmos por metro encontrado nestas parcelas. 5. O ?ndice de palhi?o calculado (20,6 t.ha-1) afetou a brota??o de soqueiras dos tratamentos com cana crua, prejudicando a popula??o de colmos. 6. O ?ndice de ?rea foliar ficou abaixo do considerado ideal para a forma??o de lavoura produtiva, correlacionando-se com a baixa produtividade obtida, mostrando-se como um bom par?metro fisiol?gico para estimativa da produ??o canavieira. 7. A taxa de crescimento da cultura apresentou valores m?ximo entre 120 e 240 dias ap?s o corte, foi semelhante para todos tratamentos ao longo do ciclo de desenvolvimento vegetativo e coincidiu com os per?odos de ?ndice de ?rea foliar m?ximos. 8. A taxa de assimila??o l?quida foi afetada pelo estresse h?drico no per?odo de m?ximo crescimento da cultura. 9. A concentra??o de nitrog?nio nas folhas, assim como a concentra??o de nitrog?nio nos colmos, n?o apresentou diferen?as entre tratamentos. O fato de o solo estudado ser um Cambissolo eutr?fico, com alta fertilidade natural e de ter ocorrido forte stress h?drico durante o ciclo da cultura, pode ter nivelado as respostas. -------------------------------------------------------------------- CAP?TULO II: Num Cambissolo eutr?fico da usina Santa Cruz, localizada no munic?pio de Campos dos Goytacazes, RJ, foi conduzido experimento objetivando avaliar, durante ciclo de segunda soca (terceiro corte) da cultura da cana-de-a??car, o efeito de res?duos da fabrica??o do a??car, (torta de filtro e baga?o), aplicados em parcelas experimentais posteriormente colhidas com cana crua e com cana sem queima, nas suas propriedades qu?micas e biol?gicas. O campo experimental foi plantado no m?s de abril de 1992. O corte da cana-planta ocorreu em julho de 1993. A primeira soca foi colhida em agosto de 1994, ocasi?o em que se reinstalou o ensaio para avalia??o na segunda soca ou terceiro corte, cuja colheita aconteceu em setembro de 1995. Os tratamentos efetuados foram: 1 ? CC = cana crua; 2 ? CC + TF = cana crua + 30 toneladas.ha-1 de torta de filtro; 3 ? CC + TF + B = cana crua + 20 toneladas de torta de filtro.ha-1 + 10 toneladas.ha-1 de baga?o; 4 ? CQ = cana queimada; 5 ? CQ + TF = cana queimada + 30 toneladas .ha-1 de torta de filtro; 6 ? CQ + TF + B = cana queimada + 20 toneladas.ha-1 de torta de filtro + 10 toneladas.ha-1 de baga?o. Os par?metros discutidos e analisados foram: a) produtividade de colmos industrializ?veis em t.ha-1; b) produ??o de a??car em t POL.ha-1; c) biomassa microbiana do solo-carbono em mgC.g-1 de solo; d) efeito dos res?duos agroindustriais entre tratamentos, nas produtividades dos segundo e terceiro cortes, em t cana.ha-1; e) efeito dos tratamentos sobre as propriedades qu?micas do solo; f) determina??o do ?ndice do ?palhi?o?. Os resultados obtidos permitiram as seguintes conclus?es: 1 ? A aplica??o dos res?duos da agroind?stria a?ucareira (torta de filtro e baga?o), nos canaviais colhidos com e sem queima, n?o resultou em aumentos de produtividade, quer seja em t cana.ha-1 ou em t pol.ha-1. 2 ? Os tratamentos com cana crua que receberam res?duos industriais, apresentaram valores significativamente maiores de BMS-C, em compara??o ao tratamento cana queimada. Houve uma maior propor??o de carbono imobilizado na biomassa microbiana do solo, principalmente no tratamento cana crua com torta de filtro adicionada. 3 ? O tipo de solo estudado, Cambissolo Eutr?fico, pode ter facilitado a semelhan?a dos resultados de produ??o (t cana.ha-1), em fun??o de sua alta fertilidade natural. 4 ? O ?ndice de Palhi?o, equivalente a 20,6 t.ha-1 de palha, pode ter afetado a brota??o de soqueiras dos tratamentos com cana crua. 5 ? De modo geral, as propriedades qu?micas do solo estudadas n?o foram alteradas quando se compararam os tratamentos.

Integrated aquaponic food production systems are capable of producing more food on less land using less water than conventional food systems, and marine systems offer the potential of conserving freshwater resources. However, critical factors such as suitable species combinations, environmental conditions (salinity and pH), and nutrient management (animal to plant ratio, C/N ratio, and dietary crude protein) have not been fully understood for marine systems. There were four objectives in this project. The first objective was to evaluate the growth performance of potential comparable combination (whiteleg shrimp with three halophytic plants) for the development of marine aquaponics with BFT under different salinities. The second objective was to evaluate stocking densities and the C/N ratio on growth and production of whiteleg shrimp and three halophytes. The third objective was evaluation of varying concentrations of dietary crude protein in practical diets fed to shrimp raised in biofloc aquaponic saltwater systems. The fourth objective was to evaluate effects of pH levels and additional C on the growth and production of whiteleg shrimp and five plant species in marine aquaponics. Four conclusions were determined: 1) Regarding marine aquaponics, whiteleg shrimp and the three halophytes (Atriplex hortensis, Salsola komarovii, and Plantago coronopus) are suitable combinations for future development. According to the research results, shrimp performed better in a salinity of 15 and 20 ppt; yet, plants performed better in a salinity of 10 and 15 ppt. Therefore, a salinity of 15 ppt is suggested as the optimal saline condition for shrimp and the three halophytes in an indoor marine aquaponics system. In addition, inoculating probiotics do have the efficiency of stabilizing water quality, cultivating microbial community, and enhancing the health of shrimp and plants in the operation of aquaponics. 2) The stocking density ratio and C/N ratio exerted significant impacts on the performance of shrimp and plants in marine aquaponics. Shrimp performed better with the stocking density of 2:1 and 3:1, with no impact from the C/N ratio. Conversely, plants performed better with the stocking density of 3:1 and 5:1 with the C/N ratio at 15. Therefore, a stocking density ratio of 3:1 with a C/N ratio at 15 is suggested as the optimal condition for shrimp and the three halophytes in an indoor marine aquaponic food production system. Inoculating the water with biofloc and applying probiotics regularly can enhance the management of water quality and the health of shrimp and plants in aquaponics. 3) Among the findings of the study, shrimp growth was not affected by the protein content of the feed, suggesting that it is possible to use feeds with lower protein concentration when culturing shrimp in biofloc-based marine aquaponics. However, plants grew better in the treatments with higher protein content feed in the early and middle stages of production. Hence, for maximum production, providing a higher protein concentration feed (35 %) in the early stages of system start-up, and switching to a lower protein concentration feed (30 %) in the later stages of cultivation might be feasible. 4) The current study found no significant effects of pH or additional C on shrimp performance. In contrast, plants grew better in lower pH treatments, while additional C supplements improved the performance of plants grown in higher pH treatments and had similar results to the lower pH treatments. We suggest that RO water is not suitable source of water for shrimp-based marine aquaponics if ionic composition is not managed. The addition of C, however, led to improved growth and yields of most plants. Hence, adding C can be a promising approach in marine aquaponics to enhance the resistance to the abiotic stress of plants and improve their growth.<div> <br>The present study on marine aquaponics has produced important findings that will fill some knowledge gaps, provide management guidelines for production, and facilitate its development. <br></div>