Project description:Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality.
Project description:Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing interspecies interactions is dependent, at least initially, on the availability of model systems with well-annotated genomes and tractable genetics.
2013-12-20 | GSE53360 | GEO
Project description:EMG produced TPA metagenomics assembly of PRJNA986291 data set (CForBio.metagenome).
| PRJEB71756 | ENA
Project description:EMG produced TPA metagenomics assembly of PRJEB30246 data set (Metagenomic_analysis_nasopharyngeal_colonisation).
| PRJEB75197 | ENA
Project description:EMG produced TPA metagenomics assembly of PRJNA639280 data set (v).
Project description:This study produced a microarray-based screening for miRNAs responding to tetradecanoyl phorbol acetate (TPA) (for monocytic differentiation) treatment in various leukemia cell lines.
2013-12-01 | GSE33537 | GEO
Project description:EMG produced TPA metagenomics assembly of PRJNA650216 data set (PMC 728.11_cyano).
