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.