BackgroundCommon bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs.ResultsUsing this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2 SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp.ConclusionsFor common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3805-4) contains supplementary material, which is available to authorized users.

Microorganisms are considered a genetic resource with great potential for achieving sustainable development of agricultural areas. The objective of this research was to determine the effect of microorganism application forms on the production of biomass, gas exchange, and nutrient content in upland rice. The experiment was conducted under greenhouse conditions in a completely randomized design in a factorial 7 × 3 + 1, with four replications. The treatments consisted of combining seven microorganisms with three application forms (microbiolized seed; microbiolized seed + soil drenched with a microorganism suspension at 7 and 15 days after sowing (DAS); and microbiolized seed + plant sprayed with a microorganism suspension at 7 and 15 DAS) and a control (water). Treatments with Serratia sp. (BRM32114), Bacillus sp. (BRM32110 and BRM32109), and Trichoderma asperellum pool provided, on average, the highest photosynthetic rate values and dry matter biomass of rice shoots. Plants treated with Burkolderia sp. (BRM32113), Serratia sp. (BRM32114), and Pseudomonas sp. (BRM32111 and BRM32112) led to the greatest nutrient uptake by rice shoots. Serratia sp. (BRM 32114) was the most effective for promoting an increase in the photosynthetic rate, and for the greatest accumulation of nutrients and dry matter at 84 DAS, in rice shoots, which differed from the control treatment. The use of microorganisms can bring numerous benefits of rice, such as improving physiological characteristics, nutrient uptake, biomass production, and grain yield.

O objetivo deste trabalho foi avaliar os efeitos de culturas de cobertura e dos sistemas plantio direto (PD) e convencional (PC) sobre indicadores biológicos do solo, cultivado com feijoeiro-comum, no inverno, sob irrigação. O experimento foi conduzido em Santo Antônio de Goiás, GO, em Latossolo Vermelho distrófico textura argilosa. Culturas de cobertura foram implantadas anualmente no verão, desde 2001, sendo utilizadas a braquiária, guandu, milheto, capim-mombaça, sorgo, estilosantes, braquiária consorciada com milho, e mata nativa, como tratamento referência. Em 2005, 60 dias após o corte das culturas de cobertura foi implantada a cultura do feijoeiro, cultivar BRS Valente, sob irrigação, com semeadura realizada em 16/6/2005 e colheita efetuada em 19/9/2005. Coletaram-se amostras de solo, na profundidade de 0-10 cm, em três épocas: novembro de 2004 (pré-plantio das culturas de coberturas), junho (pré-plantio do feijoeiro) e julho (florescimento do feijoeiro) de 2005. Avaliaram-se a respiração basal, o carbono e o nitrogênio da biomassa microbiana, a razão carbono da biomassa microbiana/carbono orgânico, a razão nitrogênio da biomassa microbiana/nitrogênio total e o quociente metabólico do solo. Esses atributos biológicos do solo são influenciados pelas culturas de cobertura, manejo do solo e épocas de amostragem.

Soybean oil contains around 60 % of polyunsaturated fatty acids, which are responsible for the low oxidative stability of soy-derived products. Soybean lines with low linolenic acid content can be obtained by genetic manipulation; however, a high proportion of the variation in fatty acids content is due to environmental factors. This work aimed to determine the effect of temperature on oil composition and on the activity of the enzymes CDP-choline:1,2-diacylglycerolcholine phosphotransferase (CPT) and acyl-CoA:lysophosphatidylcholine acyltransferase (LPCAT), responsible for maintenance of polyunsaturated fatty acids in the cytoplasmic acyl-CoA pool, that is used for oil synthesis in the seeds. CAC-1, a soybean variety with linolenic acid content of about 8 % and CC4, a BC3F4 CAC-1 derived line, with about 4 % linolenic acid, were used. The lines were cultivated under two temperature: 34/28ºC or 22/13ºC - day/night. The seeds were collected along seven development stages, according to their fresh weight. Fatty acid analysis was carried out by gas chromatography and CPT and LPCAT activities were determined by measuring the radioactivity incorporated in their products, phosphatidyl-[14C]choline and phosphatidylcholine-[14C]oleoyl, respectively. Linolenic acid contents were 3.89 and 6.92 % for line CC4 and 7.39 and 12.49 % for variety CAC-1, when submitted to high and low temperature conditions, respectively. Both enzymes were more active, in the development stages analyzed, in seeds produced under low temperature. Kinetics characterization of CPT and LPCAT were conducted previously.

ABSTRACT. Drought and rice blast disease caused by Magnaporthe oryzae are two of the most serious threats to global rice production. To explore the mechanisms underlying gene expression induced in rice by stresses, studies involving transcriptome analyses have been conducted over the past few years. Thus, it is crucial to have a reliable set of reference genes to normalize the expression levels of rice genes affected by different stresses. To identify potential reference genes for studies of the differential expression of target genes in rice under M. oryzae infection and drought conditions, the present study evaluated five housekeeping genes for the normalization of gene expression. The stability of the expression of these genes was assessed using the analytical software packages geNorm and NormFinder. For all samples analyzed, the stability rank was UBQ5 > GAPDH > eIF-4α > β-TUB > 18S rRNA. The data showed that the UBQ5, GAPDH, and eIF-4α genes are appropriate, high-performing reference genes and will be highly useful in future expression studies of fungal infections and drought in rice.

ABSTRACT. Gene expression related to drought response in the leaf tissues of two Brazilian upland cultivars, the drought-tolerant Douradão and the drought-sensitive Primavera, was analyzed. RNAseq identified 27,618 transcripts in the Douradão cultivar, with 24,090 (87.2%) homologous to the rice database, and 27,221 transcripts in the Primavera cultivar, with 23,663 (86.9%) homologous to the rice database. Gene-expression analysis between control and water-deficient treatments revealed 493 and 1154 differentially expressed genes in Douradão and Primavera cultivars, respectively. Genes exclusively expressed under drought were identified for Douradão, including two genes of particular interest coding for the protein peroxidase precursor, which is involved in three distinct metabolic pathways. Comparisons between the two drought-exposed cultivars revealed 2314 genes were R.D.D. Silveira et al. 8182©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (3): 8181-8200 (2015) differentially expressed (978 upregulated, 1336 downregulated in Douradão). Six genes distributed across 4 different transcription factor families (bHLH, MYB, NAC, and WRKY) were identified, all of which were upregulated in Douradão compared to Primavera during drought. Most of the genes identified in Douradão activate metabolic pathways responsible for production of secondary metabolites and genes coding for enzymatically active signaling receptors. Quantitative PCR validation showed that most gene expression was in agreement with computational prediction of these transcripts. The transcripts identified here will define molecular markers for identification of Cisacting elements to search for allelic variants of these genes through analysis of polymorphic SNPs in GenBank accessions of upland rice, aiming to develop cultivars with the best combination of these alleles, resulting in materials with high yield potential in the event of drought during the reproductive phase.

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RESUMO -Lipoxigenases (linoleato: oxigênio oxido-redutase -EC 1.13.11.12) são dioxigenases que catalisam a adição do oxigênio molecular ao sistema cis, cis, 1,4 -pentadieno dos ácidos graxos polinsaturados, formando hidroperóxidos dos ácidos graxos correspondentes. As lipoxigenases vegetais utilizam o ácido linolênico (C18:3) ou ácido linoléico (C18:2) como substrato e estão associadas a importantes processos fisiológicos, tais como: biossíntese de compostos regulatórios, crescimento e desenvolvimento, senescência, germinação de sementes, resposta a ferimento, proteína de reserva vegetativa e resistência a insetos e patógenos. Quando os tecidos da planta são danificados por patógenos ou mecanicamente, ocorre uma degradação seqüencial de lipídeos, cujo produto inicial são os hidroperóxidos resultante da ação das lipoxigenases. Entre os vários produtos formados, têm-se a traumatina, o ácido jasmônico, os aldeídos voláteis e os oxiácidos. Para avaliar a capacidade de as plantas de soja responderem, por meio da Via das Lipoxigenases, ao ataque do fungo causador da doença cancroda-haste -Diaphorte phaseolorum (Cke. e Ell) f. sp. meridionalis -foram realizadas a caracterização bioquímico-cinética do pool de lipoxigenases foliares de plantas de soja (Glycine max (L.) Merril ) e a quantificação dos produtos da Via das Lipoxigenases, utilizando-se um cultivar resistente (FT-Cristalina RCH) e um susceptível (FT-Cristalina) ao patógeno. As plantas dos dois cultivares, infectadas com o patógeno ou apenas injuriadas mecanicamente, apresentaram valores de atividade específica de lipoxigenases maiores que os respectivos controles, em diferentes valores de pH e temperatura, e o pool de lipoxigenases dos dois genótipos apresentou cinética de Michaelis-Menten na faixa de concentração de substrato analisada. Ocorreu aumento dos níveis de inibidores de proteases e aldeídos totais, os quais são produtos dessa via bioquímica. Pelos parâmetros bioquímico e cinético, há a sugestão de uma resposta das plantas de soja através das Via das Lipoxigenases .