Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome

被引:170
作者
Rowe, Heather C. [1 ,2 ]
Hansen, Bjarne Gram [3 ]
Halkier, Barbara Ann [3 ]
Kliebenstein, Daniel J. [1 ,2 ]
机构
[1] Univ Calif Davis, Genet Grad Grp, Davis, CA 95616 USA
[2] Univ Calif Davis, Dept Plant Sci, Davis, CA 95616 USA
[3] Univ Copenhagen, Fac Life Sci, Dept Plant Biol, Plant Biochem Lab, DK-1871 Copenhagen, Denmark
关键词
D O I
10.1105/tpc.108.058131
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Genomic approaches have accelerated the study of the quantitative genetics that underlie phenotypic variation. These approaches associate genome-scale analyses such as transcript profiling with targeted phenotypes such as measurements of specific metabolites. Additionally, these approaches can help identify uncharacterized networks or pathways. However, little is known about the genomic architecture underlying data sets such as metabolomics or the potential of such data sets to reveal networks. To describe the genetic regulation of variation in the Arabidopsis thaliana metabolome and test our ability to integrate unknown metabolites into biochemical networks, we conducted a replicated metabolomic analysis on 210 lines of an Arabidopsis population that was previously used for targeted metabolite quantitative trait locus (QTL) and global expression QTL analysis. Metabolic traits were less heritable than the average transcript trait, suggesting that there are differences in the power to detect QTLs between transcript and metabolite traits. We used statistical analysis to identify a large number of metabolite QTLs with moderate phenotypic effects and found frequent epistatic interactions controlling a majority of the variation. The distribution of metabolite QTLs across the genome included 11 QTL clusters; 8 of these clusters were associated in an epistatic network that regulated plant central metabolism. We also generated two de novo biochemical network models from the available data, one of unknown function and the other associated with central plant metabolism.
引用
收藏
页码:1199 / 1216
页数:18
相关论文
共 78 条
[1]   Identification of quantitative trait loci for larval morphological traits in interspecific hybrids of Ochlerotatus triseriatus and Ochlerotatus hendersoni (Diptera: Culicidae) [J].
Anderson, Justin R. ;
Schneider, Jennifer R. ;
Grimstad, Paul R. ;
Severson, David W. .
GENETICA, 2006, 127 (1-3) :163-175
[2]  
[Anonymous], 1998, Genetics and Analysis of Quantitative Traits (Sinauer)
[3]   The metabolic world of Escherichia coli is not small [J].
Arita, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (06) :1543-1547
[4]  
BASTEN CJ, 1999, CARTOGRAPHER VERSION
[5]  
Beavis WD., 1994, P 49 ANN CORN SORGH, P250
[6]  
Beavis William D., 1998, P145
[7]   Positive selection driving diversification in plant secondary metabolism [J].
Benderoth, Markus ;
Textor, Susanne ;
Windsor, Aaron J. ;
Mitchell-Olds, Thomas ;
Gershenzon, Jonathan ;
Kroymann, Juergen .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (24) :9118-9123
[8]   The landscape of genetic complexity across 5,700 gene expression traits in yeast [J].
Brem, RB ;
Kruglyak, L .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (05) :1572-1577
[9]   Genetic dissection of transcriptional regulation in budding yeast [J].
Brem, RB ;
Yvert, G ;
Clinton, R ;
Kruglyak, L .
SCIENCE, 2002, 296 (5568) :752-755
[10]   Natural variation for carbohydrate content in Arabidopsis. Interaction with complex traits dissected by quantitative genetics [J].
Calenge, Fanny ;
Saliba-Colombani, Vera ;
Mahieu, Stephanie ;
Loudet, Olivier ;
Daniel-Vedele, Francoise ;
Krapp, Anne .
PLANT PHYSIOLOGY, 2006, 141 (04) :1630-1643