ABSTRACT. Quantitative real-time polymerase chain reaction (RTqPCR) is a powerful tool used to measure gene expression. However, because of its high sensitivity, the method is strongly influenced by the quality and concentration of the template cDNA and by the amplification efficiency. Relative quantification is an effective strategy for correcting random and systematic errors by using the expression level of reference gene(s) to normalize the expression level of the genes of interest. To identify soybean reference genes for use in studies of flooding stress, we compared 5 candidate reference genes (CRGs) with the NormFinder and GeNorm programs to select the best internal control. The expression Gene expression in flooding-stressed soybeans stability of the CRGs was evaluated in root tissues from soybean plants subjected to hypoxic conditions. Elongation factor 1-beta and actin-11 were identified as the most appropriate genes for RT-qPCR normalization by both the NormFinder and GeNorm analyses. The expression profiles of the genes for alcohol dehydrogenase 1, sucrose synthase 4, and ascorbate peroxidase 2 were analyzed by comparing different normalizing combinations (including no normalization) of the selected reference genes. Here, we have identified potential genes for use as references for RT-qPCR normalization in experiments with soybean roots growing in O 2 -depleted environments, such as flooding-stressed plants.
Resumo -O objetivo deste trabalho foi avaliar a eficiência de coeficientes de similaridade em genótipos de feijão por meio de marcadores RAPD. A eficiência dos coeficientes de similaridade de Jaccard, Sorensen-Dice, Russel e Rao, Ochiai, Coincidência Simples, Rogers e Tanimoto, Hamann, Kulczynski 2, Yule e Phi no agrupamento de 35 cultivares locais e comerciais de feijão foi analisada com base em 104 marcadores RAPD. Os coeficientes foram comparados por dendrogramas, pela eficiência da projeção no espaço bidimensional e por grupos formados pelo método de otimização de Tocher. Os diferentes coeficientes de similaridade apresentaram variação quanto à eficiência de projeção no espaço bidimensional e quanto ao número de grupos formados pelo método de otimização de Tocher. Os coeficientes de Russel e Rao e de Yule são os mais discordantes, e os coeficientes de Sorensen-Dice, Ochiai e Kulczynski 2 são mais eficientes que os demais. O coeficiente de Russel e Rao não tem a capacidade de agrupar as cultivares em seus respectivos centros de domesticação.Termos para indexação: Phaseolus vulgaris, divergência genética, análise de agrupamento. Efficiency of similarity coefficients based on RAPD markers in common bean genotypesAbstract -The objective of this work was to evaluate the efficiency of similarity coefficients of bean genotypes based on RAPD markers. The efficiency of Jaccard, Sorensen-Dice, Russel and Rao, Ochiai, Simple Maching, Rogers and Tanimoto, Hamann, Kulczynski 2, Yule and Phi coefficients in the clustering and ordination of 35 common bean genotypes was evaluated through 104 RAPD markers. The coefficients were compared by the evaluation of dendrograms, projection efficiency in bidimensional space and groups formed using Tocher's optimization method. The different similarity coefficients altered the projection efficiency in a two-dimensional space and formed different number of groups by Tocher's optimization procedure. Among these coefficients, Russel and Rao and Yule's are the most discordants, and the Sorensen-Dice, Ochiai and Kulczynski 2 present the higher efficiency. Russel and Rao coefficient is not able for separating bean cultivars according to domestication centers.Index terms: Phaseolus vulgaris, genetic divergence, cluster analysis.(1) Aceito para publicação em 6 de novembro de 2002. IntroduçãoCultivares melhoradas oriundas de programas de melhoramento, denominadas cultivares comerciais para fins deste estudo, e cultivares locais, tradicionalmente cultivadas por pequenos agricultores, constituem o pool gênico primário, disponível para hibridização em programas de melhoramento (Harlan & De Wet, 1971). O conhecimento da diversidade genética entre as cultivares comerciais e entre estas e as locais é extremamente útil aos melhoristas por permitir melhor organização dos recursos genéticos e melhor aproveitamento da diversidade genética disponível.Diferentes métodos filogenéticos têm sido empregados no estudo da divergência genética e caracterização da diversidade entre e dentro de espécies vegetais. ...
ABSTRACT. Sweet sorghum has considerable potential for ethanol and energy production. The crop is adaptable and can be grown under a wide range of cultivation conditions in marginal areas; however, studies of phenotypic stability are lacking under tropical conditions. Various methods can be used to assess the stability of the crop. Some of these methods generate the same basic information, whereas others provide additional information on genotype x environment (G x E) interactions and/or a description of the genotypes and environments. In this study, we evaluated the complementarity of two methods, GGEBiplot and Toler, with the aim of achieving more detailed information on G x E interactions and their implications for selection of sweet sorghum genotypes. We used data from 25 sorghum genotypes grown in different environments and evaluated the following traits: flowering (FLOW), green mass yield (GMY), total soluble solids (TSS), and tons of Brix per hectare (TBH). Significant G x E interactions were found for all traits. The most stable genotypes identified with the GGEBiplot method were CMSXS643 for FLOW, CMSXS644 and CMSXS647 for GMY, CMSXS646 and CMSXS637 for TSS, and BRS511 and CMSXSS647 for TBH. Especially for TBH, the genotype BRS511 was classified as doubly desirable by the Toler method; however, unlike the result of the GGEBiplot method, the genotype CMSXS647 was also found to be doubly undesirable. The two analytical methods were complementary and enabled a more reliable identification of adapted and stable genotypes.
Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits. In this study, we analyzed conserved and divergent root transcriptional responses between flood-tolerant Embrapa 45 and flood-sensitive BR 4 soybean cultivars under hypoxic stress conditions with RNA-seq. To understand how soybean genes evolve and respond to hypoxia, stable and differentially expressed genes were characterized structurally and compositionally comparing its mechanistic relationship. Between cultivars, Embrapa 45 showed less up- and more down-regulated genes, and stronger induction of phosphoglucomutase (Glyma05g34790), unknown protein related to N-terminal protein myristoylation (Glyma06g03430), protein suppressor of phyA-105 (Glyma06g37080), and fibrillin (Glyma10g32620). RNA-seq and qRT-PCR analysis of non-symbiotic hemoglobin (Glyma11g12980) indicated divergence in gene structure between cultivars. Transcriptional changes for genes in amino acids and derivative metabolic process suggest involvement of amino acids metabolism in tRNA modifications, translation accuracy/efficiency, and endoplasmic reticulum stress in both cultivars under hypoxia. Gene groups differed in promoter TATA box, ABREs (ABA-responsive elements), and CRT/DREs (C-repeat/dehydration-responsive elements) frequency. Gene groups also differed in structure, composition, and codon usage, indicating biological significances. Additional data suggests that cis-acting ABRE elements can mediate gene expression independent of ABA in soybean roots under hypoxia.
Resumo -O objetivo deste trabalho foi caracterizar a diversidade genética dentro e entre cultivares locais e comerciais de feijão, por meio de marcadores RAPD, e avaliar a capacidade destes em agrupar genótipos de feijão de acordo com o centro de domesticação e coloração de semente. Foram avaliadas 35 cultivares, 13 comerciais e 22 locais, de diversas regiões do Rio Grande do Sul. As distâncias gené-ticas foram obtidas pelo complemento do coeficiente de similaridade de Sorensen-Dice e a representação simplificada destas distâncias realizada mediante um dendrograma. Marcadores RAPD foram eficientes ao agrupar cultivares de acordo com o centro de domesticação, mas não foram capazes de separar as cultivares de acordo com a coloração da semente. Cultivares locais e comerciais, mesoamericanas, foram agrupadas separadamente. Cultivares comerciais, em cultivo no Rio Grande do Sul apresentam alto grau de similaridade.Termos para indexação: Phaseolus vulgaris, variação genética, análise de agrupamento. Genetic diversity in cultivars and landraces of common bean based on RAPD markers analysisAbstract -The objective of this work was to characterize the genetic diversity within and among cultivars and landraces of common bean from RAPD markers analysis, and to evaluate the capacity of this markers in clustering common bean genotypes according to domestication centers and seed color. Thirty five common bean genotypes including 13 commercial cultivars and 22 landraces, from State of Rio Grande do Sul, Brazil, were evaluated. Genetic distances were calculated using Sorensen-Dice's similarity coefficient, displayed in a dendrogram. RAPD markers were efficient in separating cultivars and landraces according to domestication centers, but not according to seed color. Mesoamerican commercial cultivars and landraces have been clustered in different groups. A high degree of similarity was observed among cultivars in use in Rio Grande do Sul.
RESUMO-O sorgo granífero tem apresentado significativa expansão em área e em produtividade no Brasil nos últimos anos, em razão do aumento da demanda de grãos para alimentação animal. O melhoramento de plantas tem contribuído para o aumento de produtividade, com a oferta de novos híbridos adaptados às diversas áreas de produção. O presente trabalho teve o objetivo de selecionar aqueles mais produtivos e estáveis em cultivo de verão em três localidades. Os experimentos foram instalados em Sete Lagoas, MG, Nova Porteirinha, MG e Pelotas, RS. O delineamento experimental foi em blocos casualizados, com três repetições. Os híbridos comerciais BRS 310 e BRS 330 foram usados como testemunhas. Houve diferenças significativas entre os híbridos para as quatro características avaliadas, mostrando haver variabilidade entre os híbridos. A interação genótipos x ambientes foi significativa para índice de colheita de panículas e produtividade de grãos. A produtividade média das testemunhas nos três ambientes foi de 4,5 t ha-1 , sendo que 11 híbridos foram estatisticamente superiores às mesmas. Os híbridos 1099030 e 1099048 apresentaram desempenho superior aos demais híbridos, com produtividade acima de 6,0 t ha-1 , e ciclo de maturação mais precoce do que a testemunha mais produtiva: BRS 330. Palavras-chave: Sorghum bicolor; seleção de híbridos; produtividade; interação genótipos x ambientes.
Saccharine sorghum has been analyzed as a supplementary prime matter for ethanol production, especially during the sugarcane off-season period. However, it has proven to be highly susceptible to insect attacks during the cultivation cycle. The fall armyworm should be emphasized due to its voracity and high damage capacity enhanced by feeding-caused decrease in photosynthetic area. Current analysis studies the biology and determines the nutritional indexes of Spodoptera frugiperda in saccharine sorghum. Cultivars of saccharine sorghum BRS 506, BRS 509 and BRS 511were evaluated. Duration and survival of the egg, caterpillar, pre-pupal and pupal phases were determined, coupled to weight of pupae and caterpillar, life span, fecundity and pre-egg laying period. Although S. frugiperda completed its life cycle on cultivars BRS 506 and BRS 511, egg-laying and egg feasibility rates were low, whereas insects did not lay eggs on cultivar BRS 509. There was no significant difference in feeding intake by S. frugiperda among these three sorghum cultivars. Results suggest that saccharine sorghum is not a suitable host for S. frugiperda. Biological data reveal that the three saccharine sorghum cultivars are recommended for the grain production system since the number of specimens of the next generation is low or null.
RESUMO-O trabalho teve o objetivo de estimar a temperatura base (Tb) para estudos de exigência térmica para quatro variedades de sorgo sacarino oriundos do programa de melhoramento da Fepagro (Fepagro 19) e da Embrapa (BRS 506, BRS 509 e BRS 511). Foram realizadas três épocas de semeadura (outubro, novembro e dezembro) em dois anos agrícolas (2011/2012 e 2012/2013) em Santa Maria, RS. Os métodos utilizados para o cálculo da Tb foram o do menor desvio padrão em graus dia, menor desvio padrão em dias, coeficiente de variação em graus dia e coeficiente de regressão, seguindo a metodologia desenvolvida por Yang et al. (1995). A determinação da temperatura base inferior de cada genótipo auxilia na caracterização da exigência térmica específica dos genótipos de sorgo sacarino, favorecendo o planejamento da época de semeadura mais adequada, evitando uma possível estacionalidade de produção. Os valores de Tb para os genótipos estudados variam entre 8,2 °C e 14,8 °C, dependendo do método de estimativa da Tb.
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