Efeito da fermentação natural e do envelhecimento sobre a qualidade química e sensorial de cachaça orgânica Brasileira.

This study verified the effect of the spontaneous fermentation/natural ferment (NF) on the chemo-sensory quality of cachaça, comparing to the commercial ferment (CF). The effect of ageing (maturation) was also analysed in the beverage. Microbiological analysis (plating on selective media for total/wild yeast and bacteria counting) and physico-chemical analysis (pH, acidity and soluble solids) were performed in the samples of the must and the ferment collected during three cycles of fermentation in a semi-industrial scale. Samples of cachaça were stored in 5-L oak containers for 45 days, subsequently analyzing the physico-chemical characteristics (pH, acidity, alcohol content, copper and secondary compounds) and sensory acceptability (aroma, flavour, colour, body and global impression). The fermentation with NF showed higher number of wild yeasts; however there was no difference in the number of bacteria comparing to CF. An intense acidification occurred during the preparation of NF, which was also observed in the initial cycles of fermentation, but decreased afterwards. Greater alterations in cachaça composition were found to be more exclusively related to the maturation than to the type of ferment, except for the acidity. However, there was a significant loss of aroma, flavour and global impression after maturation but only in cachaça produced with the CF. The results revealed a strong interaction between ferment and maturation of the beverage, suggesting that substances produced by the microorganisms from different inocula during fermentation reacted differently with the wood components of the barrels influencing the sensory attributes.Este trabalho teve por objetivo avaliar o efeito da fermentação espontânea/fermento natural (NF) sobre a qualidade fisico-química e aceitabilidade da cachaça, comparando-se com o fermento comercial (CF). O efeito do envelhecimento (maturação) da bebida foi também avaliado. Análises microbiológicas (plaqueamento em meios seletivos para contagem de leveduras totais/selvagens e bactérias) e físico-químicas (pH, acidez e sólidos solúveis) foram conduzidas nas amostras do mosto e do fermento coletadas durante três ciclos fermentativos (escala semi-industrial). Amostras de cachaça foram armazenadas em barris de carvalho de 5 litros por 45 dias, seguindo-se a análise físico-química (pH, acidez, teor alcoolico, cobre e compostos secundários) e de aceitabilidade sensorial (aroma, sabor, cor, corpo e impressão global). A fermentação com NF mostrou maior número de leveduras selvagens; no entanto, não houve diferença significativa no número de bactérias quando comparada com CF. Uma intensa acidificação foi observada durante o preparo de NF, a qual foi verificada nos ciclos iniciais da fermentação, decrescendo a seguir. As alterações na composição da cachaça foram mais significativas em relação à maturação do que ao tipo de fermento, com exceção da acidez. No entanto, houve uma perda significativa de aroma, sabor e impressão global após a maturação na cachaça produzida com CF. Os resultados revelaram uma forte interação entre fermento e envelhecimento (maturação) da bebida, sugerindo que substâncias produzidas pelos microrganismos a partir de inóculos diferentes reagiram diferentemente com componentes da madeira dos barris, influenciando nos atributos sensoriais de aceitabilidade

Linkage disequilibrium and population structure in wild and cultivated populations of rubber tree (Hevea brasiliensis).

Abstract: Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr.de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation

Boosting predictive ability of tropical maize hybrids via genotype-by-environment interaction under multivariate GBLUP models.

Genomic selection has been implemented in several plant and animal breeding programs and it has proven to improve efficiency and maximize genetic gains. Phenotypic data of grain yield was measured in 147 maize (Zea mays L.) singlecross hybrids at 12 environments. Single-cross hybrids genotypes were inferred based on their parents (inbred lines) via single nucleotide polymorphism (SNP) markers obtained from genotyping-by-sequencing (GBS). Factor analytic multiplicative genomic best linear unbiased prediction (GBLUP) models, in the framework of multienvironment trials, were used to predict grain yield performance of unobserved tropical maize single-cross hybrids. Predictions were performed for two situations: untested hybrids (CV1), and hybrids evaluated in some environments but missing in others (CV2). Models that borrowed information across individuals through genomic relationships and within individuals across environments presented higher predictive accuracy than those models that ignored it. For these models, predictive accuracies were up to 0.4 until eight environments were considered as missing for the validation set, which represents 67% of missing data for a given hybrid. These results highlight the importance of including genotype-by-environment interactions and genomic relationship information for boosting predictions of tropical maize single-cross hybrids for grain yield

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

<div><p>As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled, including polyploid plant genomes. Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions. Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype. Here, we describe a first step in avoiding inappropriate collapse during assembly. In particular, we describe ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, we report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. We also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low. We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.</p></div

Ploidy estimation for an artificially combined wheat dataset.

<p>Reads from the large arms of chromosomes 5A, 5B and 5D were pooled, assembled and used for ploidy estimation. Only contigs with average coverage of 10X or above, and for which the individual ploidy in a given subgenome was estimated to be one were considered.</p><p>^aBased on BLAST alignments to the individual assemblies.</p><p>Ploidy estimation for an artificially combined wheat dataset.</p

Error probability surface depicting predictive influence of the average neighboring quality score.

<p>Note that Phred quality score 2 was not included.</p

Genotype distribution for switchgrass contigs with a ploidy estimate of four.

<p>Bars represent the frequency of each SNP genotype, for all identified variants in contigs estimated to have ploidy four.</p

Length simulation results.

<p>Color in each cell indicates the percentage of correct ploidy calls, out of 100 simulations of contigs sequenced at 50X coverage for each ploidy level.</p