Genetical metabolomics of flavonoid biosynthesis in Populus: a case study

Genetical metabolomics [metabolite profiling combined with quantitative trait locus (QTL) analysis] has been proposed as a new tool to identify loci that control metabolite abundances. This concept was evaluated in a case study with the model tree Populus. Using HPLC, the peak abundances were analyzed of 15 closely related flavonoids present in apical tissues of two full-sib poplar families, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24, and correlation and QTL analysis were used to detect flux control points in flavonoid biosynthesis. Four robust metabolite quantitative trait loci (mQTL), associated with rate-limiting steps in flavonoid biosynthesis, were mapped. Each mQTL was involved in the flux control to one or two flavonoids. Based on the identities of the affected metabolites and the flavonoid pathway structure, a tentative function was assigned to three of these mQTL, and the corresponding candidate genes were mapped. The data indicate that the combination of metabolite profiling with QTL analysis is a valuable tool to identify control points in a complex metabolic pathway of closely related compounds.     

遗传基因组学(Genetical genomics)的研究进展

遗传基因组学(geneticalgenomics)是将微阵列技术和数量性状座位(QTL)分析结合起来,全基因组水平上定位基因表达的QTL(eQTL).它为研究复杂性状的分子机理和调控网络提供全新的手段.遗传基因组这个概念和研究策略在2001年由Janson和Nap首先提出,到目前为止,遗传基因组学已应用于酵母、老鼠、人以及玉米等植物.研究结果表明:基因表达水平的差异是可遗传的复杂性状;eQTL可以分为顺式作用eQTL和反式作用eQTL,顺式作用eQTL就是某个基因的eQTL定位到该基因所在的基因组区域,表明可能是该基因本身的差别引起mRNA水平的差别,反式作用就是eQTL定位到其他基因组区域,表明其他基因的差别控制该基因mRNA水平的差异.将eQTL结果、基因功能注解以及多种统计分析方法相结合,不仅能更准确地鉴别控制复杂性状及其相关基因表达的候选基因,而且能构建相应的基因调控网络.     

Tight junctions: closing in on the seal

The claudins have recently been identified as a large family of transmembrane proteins located at tight junctions between epithelial cells; they create the paracellular diffusion barrier and, surprisingly, may also confer channel-like selectivity for passage of solutes through the tissue barrier.     

Genetical genomics in livestock: potentials and pitfalls

Genetical genomics combines gene mapping and gene expression approaches to identify loci controlling gene expression (eQTLs) that may underlie functional trait variation. The combination of genomic tools has great potential to facilitate dissection of complex traits, but studies need careful design and interpretation. Here we explore both the potential and the pitfalls of this approach with illustrations from actual studies. There are now an appreciable number of studies in model species and even humans demonstrating the feasibility of genetical genomics. However, most studies are too limited in size and design to unlock the full potential of the approach. Limited statistical power of studies exacerbates the problem of detection of false-positive eQTL and some reported results should be interpreted with caution. As one approach to more successful implementation of genetical genomics, we propose to combine expression studies with fine mapping of functional trait loci. This synergistic approach facilitates the implementation of genetical genomics for species without inbred resources but is equally applicable to model species. These properties make it particularly suitable for livestock populations where many QTL are already in the public domain and potentially very large pedigreed populations can be accessed.     

Genetical studies on oenothera. IV

Ohne Zusammenfassung     

Genetical study on the formation of anthocyanins and flavonols in turnip varieties. Genetical studies on anthocyanins in brassicaceae II

Genetic studies were made on the root color of turnip varieties. In the cross between the red (raphanusin, pelargonidin glucoside) and the white varieties, F₁ hybrids were all purple (rubrobrassicin, cyanidin glucoside), and F₂ progenies were segregated into three groups: purple (rubrobrassicin), red (raphanusin), and white in the ratio of 9:3:4, respectively. This indicates the presence of two pairs of conditional alleles, as previously found in the case of radish. As to the flavonols in turnip varieties, isorhamnetin and kaempferol were found in the plants forming rubrobrassicin in roots, and only kaempferol in the plants producing raphanusin in roots; whereas isorhamnetin was found together with a trace of kaempferol in the plants with white root.     

A metabolomics approach to characterize phenotypes of metabolic transition from late pregnancy to early lactation in dairy cows

Introduction

Dairy cows experience metabolic stress during the transition from late pregnancy to early lactation, due to the complex adaptation processes affecting energy homeostasis in support of milk production, collectively referred to as homeorhesis. According to the individual efficiency of this adaptation, some cows develop severe metabolic diseases while others are able to maintain metabolic health.

Objectives

This study aimed to characterize patterns and changes of metabolic phenotype during the transition period, and to identify how far different metabolic pathways are affected by or contributing to the complex system of homeorhesis.

Methods

Blood samples were collected from 26 German Holstein cows, repeatedly during the transition period: 42 and 10 days before calving and 3, 21 and 100 days after calving. Blood serum samples were subjected to a liquid chromatography–mass spectrometry based targeted metabolomics analysis using the AbsoluteIDQ p180 Kit of Biocrates Life Science AG (Innsbruck, Austria). Processed metabolomics data were evaluated by multivariate data analysis techniques such as principal component analysis (PCA) and partial least squares-discriminant analysis and by heatmap visualization.

Results

The PCA revealed a clear separation according to sampling days, indicating a notable shift of the metabolic phenotype during the transition period. The heatmap showed that acylcarnitines provided a consistent clustering within sampling days, while the concentration of glycerophospholipids and sphingolipids were remarkably decreased 10 days before and 3 days after calving than earlier and later in the transition period.

Conclusion

Analyzing longitudinal changes of the blood metabolome and identifying new biomarkers by this approach can help understanding the multifaceted metabolic adaptation of transition dairy cows.

     

Identifying static and kinetic lipid phenotypes by high resolution UPLC-MS: unraveling diet-induced changes in lipid homeostasis by coupling metabolomics and fluxomics

A novel method to differentiate diet-induced alterations in plasma lipid phenotypes "static (concentration of lipids) and kinetic (endogenous production, e.g., denovo lipogenesis)" was employed. C57Bl6 mice were randomized into 2 groups and fed either a high-carbohydrate, low-fat (HC) or a carbohydrate-free, high-fat diet (HF) diet for 13 days; D(2)O was administered via intraperitoneal injection and then adding D(2)O to the drinking water for 96 h. Principal component analysis (PCA) revealed differences in the plasma lipid content, for example, triglycerides (TG) 50:2, 50:3, and 52:2 were up-regulated in mice fed the HC diet, whereas TG 52:4, 52:1, 54:5, 54:3, 54:4, and 54:2 were higher in animals fed the HF diet. However, although the fractional contribution of synthesis was ~10-fold lower in HF vs HC fed mice, changes in TG concentration were not entirely mediated by altered de novo lipogenesis. In addition, the ability to couple isotope labeling measurements with PCA analyses revealed cases where there were no differences in the concentration of a compound but its source was substantially altered. In summary, this strategy determined (i) the presence/absence of differences in concentration and (ii) the contribution of different pathways and synthesis that could affect lipid biology in a mouse model respectively.     

Genetical studies in the genusSorghum

Summary The mode of inheritance of one seedling character and nine mature plant characters has been worked out in detail in the different interspecific crosses in the genusSorghum. The majority of the factor pairs exhibited simple inheritance. However, clear evidence for breakdown of dominance in different genetic backgrounds and data for the presence of modifier gene complexes has also been obtained. The implication of these results to the genetic evolution of the variousSorghums species, is critically discussed. Further, the bearing of loci found duplicate with respect to various qualitative characters, has also been considered in relation to the polyploid origin ofArundinacea Sorghums. The genetics of the two new variants have been studied and the taxonomic importance of such anomalies is brought out.

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Zusammenfassung Die Vererbungsweise von Merkmalen innerhalb der GattungSorghum wurde an verschiedenen interspezifischen Kreuzungen eingehend untersucht (1 Samenmerkmal, 9 Merkmale der reifen Pflanze). Die Mehrzahl der Faktorenpaare zeigte einfachen Erbgang. Es ergaben sich jedoch auch klare Beweise für Dominanzverschiebungen in verschiedenem genetischem Milieu und Hinweise auf das Vorliegen von Modifikationsgenen. Die Folgerungen aus diesen Ergebnissen für die genetische Evolution der verschiedenenSorghum-Arten wurden kritisch diskutiert und die Bedeutung der für verschiedene qualitative Merkmale gefundenen polymeren Gene in Beziehung zum polyploiden Ursprung derArundinacea-Sippe vonSorghum behandelt. Die Genetik zweier neuer Varianten ist untersucht und die taxonomische Bedeutung derartiger Anomalien dargelegt worden.

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These studies were largely undertaken at the Division of Botany, I.A.R.I., New Delhi where the authors were previously located. They are, therefore, grateful to the Director, I.A.R.I., Dean of P.G. School and Head of the Division of Botany for their keen interest and facilities. One of us (M.A.T.) is also grateful to the Government of Maharashtra (Department of Agriculture), Dr.M. B. Ghatge, Director of Agriculture, Maharashtra State and Dr.B. S. Kadam for encouragement during the course of this investigation.