Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

<p>Abstract</p> <p>Background</p> <p>Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes.</p> <p>Results</p> <p>By the use of two distinct algorithms, implemented by <it>geNorm </it>and <it>NormFinder</it>, we have assessed the gene expression of nine candidate reference genes in cotton: <it>GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 </it>and <it>GhUBQ14</it>. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of <it>GhPP2A1 </it>and <it>GhUBQ14 </it>genes were the most stable across all samples and also when distinct plants organs are examined. <it>GhACT4 </it>and <it>GhUBQ14 </it>present more stable expression during flower development, <it>GhACT4 </it>and <it>GhFBX6 </it>in the floral verticils and <it>GhMZA </it>and <it>GhPTB </it>during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development.</p> <p>Conclusion</p> <p>We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of <it>GhUBQ14 </it>and <it>GhPP2A1 </it>housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs; <it>GhACT4 </it>and <it>GhUBQ14 </it>for flower development, <it>GhACT4 </it>and <it>GhFBX6 </it>for the floral organs and <it>GhMZA </it>and <it>GhPTB </it>for fruit development. We also provide the primer sequences whose performance in qPCR experiments is demonstrated. These genes will enable more accurate and reliable normalization of qPCR results for gene expression studies in this important crop, the major source of natural fiber and also an important source of edible oil. The use of bona fide reference genes allowed a detailed and accurate characterization of the temporal and spatial expression pattern of two MADS-box genes in cotton.</p

ANÁLISE SÓCIOECONÔMICA DOS AGROSILVICULTORES DO PROJETO DE REFLORESTAMENTO ECONÔMICO CONSORCIADO E ADENSADO (RECA), EM NOVA CALIFÓRNIA, RONDÔNIA

O assentamento agrícola de centenas de milhares de famílias na Amazônia gerou problemas ambientais e socioeconômicos significativos na região. Em 1984 foi implantado pelo Instituto nacional de Colonização e Reforma Agrária (INCRA) o Projeto de Assentamento Agrícola do Alto Madeira, em Vila Nova Califórnia-RO, divisa com o Estado do Acre. A partir de 1988, algumas lideranças rurais e produtores do assentamento resolvem priorizar o uso alternativo da terra com Sistemas Agroflorestais – SAFs, tendo como base o consórcio de culturas perenes regionais (cupuaçu, pupunha, castanha-do-brasil) e café, e formaram a Associação de Pequenos Agrosilvicultores do Projeto de Reflorestamento Econômico Consorciado e Adensado, que passou a ser conhecida como Projeto RECA. Este projeto teve como objetivos organizar os produtores e a produção primária e secundária, com o beneficiamento e comercialização dos produtos. O objetivo deste estudo foi analisar a situação produtiva e socioeconômica das propriedades e dos agrosilvicultores sócios do Projeto RECA. Foi efetuada a seleção de 50 unidade produtivas de produtores rurais, representando aproximadamente 1/3 das unidades produtivas para a mensuração de variáveis sócio econômicas e ambientais, através de amostragem intencional estratificada, em Dezembro 2004 e Janeiro de 2005. As 240 famílias associadas ao RECA são, na maioria (75%), migrantes da região centro-sul; com uma média de 13 anos no RECA; residem no lote a mais de 18 anos, que tem em média 82 hectares, sendo que em cada unidade de produção há 1,4 lotes, com 115 hectares, dos quais 55% encontra-se em floresta nativa, 29% em pastagem, 8% com SAFs, 6% em capoeiras e 2% em outros usos. Os produtos que geram maior renda são o cupuaçu, pupunha (semente, fruto e palmito), café e gado bovino, que somados respondem por 90% da renda bruta anual média, que é de R$20.800,00. O modelo de organização sócio-econômica do projeto RECA propiciou a melhoria das condições de vida dos produtores e da conservação ambiental, comprovando que as políticas direcionadas à agricultura familiar cooperativada, tanto nos processos produtivos relacionados ao uso da terra, como no beneficiamento e comercialização da produção através de agroindústrias, propiciou o acesso ao crédito e tecnologias, possibilitando melhorias no sistema de produção e aumento no valor agregado dos produtos, com retornos sociais e econômicos relevantes, verificados pela elevação da renda e qualidade de vida dos agricultores.------------------------------------------------------------- ---Agricultural settlement of hundreds of thousands of families in the Amazon caused significant environmental and socioeconomic problems in the region. In 1994 the National Institute for Settlement and Agrarian Reform (INCRA) established the Alto Madeira Agricultural Settlement Project in Vila California, State of Rondonia, on the border with the State of Acre. Beginning in 1988 some rural leaders and farmers of this settlement decided to focus on alternative land uses with agroforestry systems based on intercropping of native species (cupuaçu, peach palm and brazil nut) and coffee and established the Association of Small Farmers and Agrosilviculturalists of the Economic, Intercropped and Dense Reforestation Project which became known as Projeto Reca. This project had as objectives the organization of the farmers, the establishment of the agroforestry systems, the industrial processing and marketing the processed products to the local, regional and national markets. The objective of this study was to analyze the productive and socioeconomic situation of the properties and of the farmers of Projeto Reca. Between December 2004 and January 2005, 50 productive units representing 33$ 20.800,00. The model of socioeconomic organization of Projeto Reca resulted in significant improvement of farmers living conditions and promoted environmental conservation. This shows that policies for associations of small farmers aiming at promoting alternative land uses such as agroforestry systems, including adequate technologies, accessible credit lines, industrial processing and marketing strategies can be effective in adding value to products and improving efficiency and profitability of production systems, resulting in significant and sustainable economic and social benefits measured by higher income and better living conditions of farmers of Projeto Reca.Sistemas Agroflorestais, Amazônia, socioeconomia, RECA, Agroforestry Systems, Amazon, Socioeconomy, RECA, Farm Management,

Changes in soil organic carbon during 22 years of pastures, cropping or integrated crop/livestock systems in the Brazilian Cerrado.

Abstract: In Brazil?s central savanna region, government policy is to encourage the conversion of conventional plough tillage (PT) agriculture to no-till (NT) and raise the productivity of under-utilized pastures, including their conversion to integrated crop-livestock (ICL) systems, with the objective of increasing soil organic carbon (SOC) at the expense of atmospheric carbon dioxide. An experiment was established in 1991 by liming and fertilizing at two levels an area of native vegetation (NV). The treatments, replicated in randomized plots, included pastures, continuous cropping and ICL systems under PT or NT. The aim of this study was to quantify the SOC accumulation to 100 cm depth under these treatments over time. The high C:N ratios suggested that there was a high proportion of charcoal present in the soil. Increasing fertilizer inputs had no overall significant effect on SOC stocks. Stocks of SOC changed little under pastures. Analyses of ¹³C abundance showed that higher fertilizer inputs increased the decomposition rate of C derived from NV under pure grass pastures. Continuous cropping under NT preserved SOC and under PT there were significant losses. The highest SOC stocks were found under ILP treatments, but not all ILP treatments accumulated SOC even under NT. These results indicate that government initiatives to substitute PT with NT and to intensify beef cattle production will have only modest short-term gains in SOC accumulation

Insights into genetic and molecular elements for transgenic crop development.

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Ensaio nacional de aveias forrageiras, 1997: análise conjunta.

Planta forrageira, Aveia, Ensaio nacional; Forage; Oat; Essay.Resumo

Diversidade metabólica de microrganismos em rizosfera de linhagens e híbridos de milho contrastantes para fósforo - campo.

A avaliacao da diversidade microbiana e um bom indicador da qualidade dos solos e de diferencas existentes entre solos de rizosfera de plantas. O objetivo desse trabalho foi avaliar a diversidade metabolica de microrganismos totais da rizosfera, pelo sistema BIOLOG. O solos rizosferico de genotipos de milho, eficientes (E) e ineficientes (I) para fosforo, em alta e baixo P foram coletados na Embrapa Milho e Sorgo, Sete Lagoas, MG, Os hibridos avaliados foram: HT, HS1, HS2, eficientes e L22, ineficientes. Como amostras testemunhas: cerrado natural (mata), plantio direto e solo nao rizosferico dos hibridos e linhagens. As comunidades microbianas tivera, perfil distinto de utilizacao das fontes de carbono, conforme a analise de agrupamento e PCA. Amostras de rizosfera de hibridos e linhagens eficientes sob estresse de P tenderam a se agrupar, indicando que os microrganismos tiveram utilizacao semelhante de fontes de carbono, principalmente acidos carboxílicos. L3, L228 e HT HS2 foram perfil microbiano totalmente distinto quando sob alta dose de P. A diversidade microbiana em solos nao rizosfericos foi menor principalmente em alto P. O genotipos eficientes apresentaram, alta diversidade microbiana quando comparados com o cerrado natural