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Linked gene networks involved in nitrogen and carbon metabolism and levels of water-soluble carbohydrate accumulation in wheat stems 总被引:1,自引:0,他引:1
McIntyre CL Casu RE Rattey A Dreccer MF Kam JW van Herwaarden AF Shorter R Xue GP 《Functional & integrative genomics》2011,11(4):585-597
High levels of water-soluble carbohydrates (WSC) provide an important source of stored assimilate for grain filling in wheat.
To better understand the interaction between carbohydrate metabolism and other metabolic processes associated with the WSC
trait, a genome-wide expression analysis was performed using eight field-grown lines from the high and low phenotypic tails
of a wheat population segregating for WSC and the Affymetrix wheat genome array. The 259 differentially expressed probe sets
could be assigned to 26 functional category bins, as defined using MapMan software. There were major differences in the categories
to which the differentially expressed probe sets were assigned; for example, probe sets upregulated in high relative to low
WSC lines were assigned to category bins such as amino acid metabolism, protein degradation and transport and to be involved
in starch synthesis-related processes (carbohydrate metabolism bin), whereas downregulated probe sets were assigned to cell
wall-related bins, amino acid synthesis and stress and were involved in sucrose breakdown. Using the set of differentially
expressed genes as input, chemical–protein network analyses demonstrated a linkage between starch and N metabolism via pyridoxal
phosphate. Twelve C and N metabolism-related genes were selected for analysis of their expression response to varying N and
water treatments in the field in the four high and four low WSC progeny lines; the two nitrogen/amino acid metabolism genes
demonstrated a consistent negative association between their level of expression and level of WSC. Our results suggest that
the assimilation of nitrogen into amino acids is an important factor that influences the levels of WSC in the stems of field-grown
wheat. 相似文献
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Renata Stolf-Moreira Eliana G. M. Lemos L��cia Carareto-Alves Jackson Marcondes Selma S. Pereira Amanda A. P. Rolla Rodrigo M. Pereira Norman Neumaier Eliseu Binneck Ricardo V. Abdelnoor Maria C. N. de Oliveira Francismar C. Marcelino Jos�� R. B. Farias Alexandre L. Nepomuceno 《Plant Molecular Biology Reporter》2011,29(1):19-34
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Hofstetter JR Hitzemann RJ Belknap JK Walter NA McWeeney SK Mayeda AR 《Genes, Brain & Behavior》2008,7(2):214-223
We report here the confirmation of the quantitative trait locus for haloperidol-induced catalepsy on distal chromosome (Chr) 1. We determined that this quantitative trait locus was captured in the B6.D2- Mtv7a /Ty congenic mouse strain, whose introgressed genomic interval extends from approximately 169.1 to 191.3 Mb. We then constructed a group of overlapping interval-specific congenic strains to further break up the interval and remapped the locus between 177.5 and 183.4 Mb. We next queried single nucleotide polymorphism (SNP) data sets and identified three genes with nonsynonymous coding SNPs in the quantitative trait locus. We also queried two brain gene expression data sets and found five known genes in this 5.9-Mb interval that are differentially expressed in both whole brain and striatum. Three of the candidate quantitative trait genes were differentially expressed using quantitative real-time polymerase chain reaction analyses. Overall, the current study illustrates how multiple approaches, including congenic fine mapping, SNP analysis and microarray gene expression screens, can be integrated both to reduce the quantitative trait locus interval significantly and to detect promising candidate quantitative trait genes. 相似文献
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Street NR Skogström O Sjödin A Tucker J Rodríguez-Acosta M Nilsson P Jansson S Taylor G 《The Plant journal : for cell and molecular biology》2006,48(3):321-341
The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F(2)) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that 'genetical genomics' can be used to provide information on adaptation at the species level. The grandparents and F(2) population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response. 相似文献
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Fu BY Xiong JH Zhu LH Zhao XQ Xu HX Gao YM Li YS Xu JL Li ZK 《Molecular genetics and genomics : MGG》2007,278(6):599-609
Drought tolerance (DT) in rice is known to be controlled by many quantitative trait loci (QTLs) and involved differential
expression of large numbers of genes, but linking QTLs with their underlying genes remains the most challenging issue in plant
molecular biology. To shed some light on this issue, differential gene expression in response to PEG simulated drought in
3 unique genetic materials (a lowland rice, IR64 and its derived line, PD86 which has 11 introgressed DT QTLs, and a upland
rice IRAT109) was investigated using a PCR-based subtractive hybridization strategy. More than 300 unique subtracted cDNA
sequences, covering genes of diverse cellular activities and functions, were identified and confirmed by semi-quantitative
and quantitative RT-PCR. Detailed bioinformatics analyses of the data revealed two interesting results. First, the levels
and mechanisms of DT of the three rice lines were associated with the number and types of differentially expressed genes,
suggesting different DT mechanisms in rice are controlled by different sets of genes and different metabolic pathways, and
most differentially expressed genes under drought were able to contribute to DT. Second, there appeared a high correspondence
in genomic location between DT QTLs and clusters of differentially expressed genes in rice, suggesting some DT QTLs may represent
clusters of co-regulated and functionally related genes. Thus, differential gene expression analyses using genetically characterized
materials can provide additional insights into the molecular basis of QTLs and convergent evidence to shortlist the candidate
genes for target QTLs.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Bin-Ying Fu and Jian-Hua Xiong are contributed to this work equally. 相似文献
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The unicellular green alga Haematococcus pluvialis (Volvocales) is known for the ketocarotenoid astaxanthin (3, 3′-dihydroxy-β, β-carotene-4, 4′-dione) accumulation, which is induced under unfavorable culture conditions. In this work, we used cDNA microarray analysis to screen differentially expressed genes in H. pluvialis under astaxanthin-inductive culture conditions, such as combination of cell exposure to high irradiance and nutrient deprivation. Among the 965 genes in the cDNA array, there are 144 genes exhibiting differential expression (twofold changes) under these conditions. A significant decrease in the expression of photosynthesis-related genes was shown in astaxanthin-accumulating cells (red cells). Defense- or stress-related genes and signal transduction genes were also induced in the red cells. A comparison of microarray and real-time PCR analysis showed good correlation between the differentially expressed genes by the two methods. Our results indicate that the cDNA microarray approach, as employed in this work, can be relied upon and used to monitor gene expression profiles in H. pluvialis. In addition, the genes that were differentially expressed during astaxanthin induction are suitable candidates for further study and can be used as tools for dissecting the molecular mechanism of this unique pigment accumulation process in the green alga H. pluvialis.
Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. 相似文献
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Wang Z Ni Z Wu H Nie X Sun Q 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2006,113(7):1283-1294
In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. In this study, heterosis was estimated for eight root traits in 20 wheat hybrids derived from a NC Design II mating scheme. Positive mid-parent heterosis was detected in 96 of 160 hybrid–trait combinations, and positive high-parent heterosis was detected in 79 of 160 hybrid-trait combinations. Improved differential display was used to analyze alterations in gene expression between hybrids and their parents in roots at the jointing stage. More than 990 fragments were repeatedly displayed, among which 27.52% were differentially expressed between hybrids and their parents. Four differential expression patterns were observed. Thirty differentially expressed cDNA fragments and three genes with open reading frames were cloned, and their expression patterns were confirmed by reverse-northern blot and semi-quantitative RT-PCR analysis, respectively. We concluded that these differentially expressed genes, though mostly with unknown function, could play important roles for hybrids to demonstrate heterosis in root system traits.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .Z. Wang and Z. Ni contributed to this article equally. 相似文献
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