Genome-wide co-expression analysis in multiple tissues

Expression quantitative trait loci (eQTLs) represent genetic control points of gene expression, and can be categorized as cis- and trans-acting, reflecting local and distant regulation of gene expression respectively. Although there is evidence of co-regulation within clusters of trans-eQTLs, the extent of co-expression patterns and their relationship with the genotypes at eQTLs are not fully understood. We have mapped thousands of cis- and trans-eQTLs in four tissues (fat, kidney, adrenal and left ventricle) in a large panel of rat recombinant inbred (RI) strains. Here we investigate the genome-wide correlation structure in expression levels of eQTL transcripts and underlying genotypes to elucidate the nature of co-regulation within cis- and trans-eQTL datasets. Across the four tissues, we consistently found statistically significant correlations of cis-regulated gene expression to be rare (<0.9% of all pairs tested). Most (>80%) of the observed significant correlations of cis-regulated gene expression are explained by correlation of the underlying genotypes. In comparison, co-expression of trans-regulated gene expression is more common, with significant correlation ranging from 2.9%-14.9% of all pairs of trans-eQTL transcripts. We observed a total of 81 trans-eQTL clusters (hot-spots), defined as consisting of > or =10 eQTLs linked to a common region, with very high levels of correlation between trans-regulated transcripts (77.2-90.2%). Moreover, functional analysis of large trans-eQTL clusters (> or =30 eQTLs) revealed significant functional enrichment among genes comprising 80% of the large clusters. The results of this genome-wide co-expression study show the effects of the eQTL genotypes on the observed patterns of correlation, and suggest that functional relatedness between genes underlying trans-eQTLs is reflected in the degree of co-expression observed in trans-eQTL clusters. Our results demonstrate the power of an integrative, systematic approach to the analysis of a large gene expression dataset to uncover underlying structure, and inform future eQTL studies

Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat

The Spontaneously Hypertensive rat (SHR) is a widely used rodent model of hypertension and metabolic syndrome. Previously we identified thousands of cis-regulated expression quantitative trait loci (eQTLs) across multiple tissues using a panel of rat recombinant inbred (RI) strains derived from Brown Norway (BN) and SHR progenitors. These cis-eQTLs represent potential susceptibility loci underlying physiological and pathophysiological traits manifested in SHR. We have prioritised 60 cis-eQTLs, and confirmed differential expression between the parental strains by quantitative PCR (qPCR) in 43 (72%) of the eQTL transcripts. Quantitative trait transcript (QTT) analysis in the RI strains showed highly significant correlation between cis-eQTL transcript abundance and clinically relevant traits such as systolic blood pressure and blood glucose, with the physical location of a subset co-localising with "physiological" QTLs (pQTLs) for these same traits. These co-localising correlated cis-eQTLs (c3-eQTLs) are highly attractive as primary susceptibility loci for the co-localising pQTLs. Furthermore, sequence analysis of the c3-eQTL genes identified SNPs that are predicted to affect transcription factor binding affinity, splicing and protein function. These SNPs, which potentially alter transcript abundance and stability, represent strong candidate factors underlying not just eQTL expression phenotypes, but also the correlated metabolic and physiological traits. In conclusion, by integration of genomic sequence, eQTL and QTT datasets we have identified several genes that are strong positional candidates for pathophysiological traits observed in the SHR strain. These findings provide a basis for the functional testing and ultimate elucidation of the molecular basis of these metabolic and cardiovascular phenotypes

Acidification of soils by trees and forests.

The impact of isolated trees and natural forest vegetation on soil acidity is discussed. There is a considerable variation in impact between species on similar soils and between sites for any given species. The effect of coniferous plantations on soil acidity is reviewed and the causes of any increased acidity discussed. Crop species, initial soil conditions, silvicultural practices and the proportion of the tree removed at felling are all important factors influencing the long-term impact of plantations on soil acidity

Características físicas e carbono orgânico de solos sob diferentes tipos de uso da terra Soil physical characteristics and organic carbon content under different land uses

Na Bacia Hidrográfica Água Fria, em Barra do Choça (BA), o desenvolvimento da lavoura cafeeira e da pastagem tem sido feito mediante a supressão da vegetação nativa, inclusive em áreas de proteção ambiental. O objetivo deste trabalho foi avaliar os atributos físicos: granulometria, argila dispersa em água, grau de floculação, diâmetro médio ponderado e índice de estabilidade de agregados e C orgânico dos solos submetidos a diferentes tipos de uso da terra na referida bacia. Para as amostragens, foram selecionadas seis glebas: duas de café (cultivo mecanizado e não mecanizado), duas de pastagens e duas de matas nativas, empregadas como referência. Constatou-se que o uso da terra diminuiu a estabilidade de agregados, evidenciada pela redução no diâmetro médio ponderado, pelo aumento dos agregados de menor tamanho e pelos menores teores de C orgânico na seqüência mata-pastagem-cafezal.<br>In the watershed Água Fria, in Barra do Choça (BA), native vegetation and environmentally protected areas have been replaced by coffee and pasture cultivation. This study evaluated the physical characteristics, particle size distribution, water dispersible clay, flocculation, mean weight diameter and aggregate stability index and organic C concentration of soils under different land uses, in the area surroundings the above watershed. Soil samples were collected from six different fields: two coffee plantations (manual and mechanical cultivation), two pastures and two native forest areas were used as references. The different land uses reduced the aggregate stability, as indicated by the reduction of the mean weight diameter, increase of small-sized aggregates and lower organic C contents, in the order forest > pasture > coffee plantation