Associative expression and systems analysis of complex traits in oilseed rape / canola (ASSYST)
Final Report Abstract
The ERANET ASSYST project generated a large, genetically and geographically diverse collection of Brassica napus inbred lines as a public resource for genetic association studies in this important crop species. This population was subjected to extensive phenotypic analyses in multi-location field trials and growth-chamber experiments and has been distributed to scientists and breeders on all contintents as a public resource for oilseed rape/canola genetics and improvement. We also generated extensive gene expression data from seeds and seedlings of segregating B. napus doubled-haploid populations using microarray and digital gene expression platforms and pertormed a comprehensive analysis of seed and seedling growth hormone profiles in these populations by HPLC-MS/MS. A subset of the ASSYST diversity set was subjected to whole-transcriptome analysis via mRNA deep sequencing. The project established robust and novel "Associative Transcriptomics" methodology for discovery of genetic associations to complex traits using sequencing-based transcriptome analyses (mRNAseq) in genetically diverse populations. In addition, transcriptome data from segregating biparental mapping populations was integrated with quantitative metabolite, hormone and phenotype data using a systems-genetics approach that combined an analysis of gene co-expression networks with expression QTL (eQTL) approaches. Weighted gene co-expression network analysis (WGCNA) was investigated for its potential to find key regulatory genes involved in relevant pathways and traits in S. napus. This multidimensional approach revealed important regulatory expression networks controlling biosynthesis of important nutritional and antinutritional seed compounds, for example. A high-density B. napus 6000-SNP array was designed and used to screen the diversity collection and biparental populations for high-density genetic mapping and association studies, respectively. Experience gained form the SNP analyses was applied to the design of a highly successful Brassica 60k SNP array. High-density SNP maps of the segregating populations facilitate a more precise identification ol potential regulatory candidate genes underlying important cis-eQTL. The expression of genes (i) for which eQTL hotspots are observed in the linkage mapping populations, and (ii) which are identified as candidates by systems genetics approaches based on global gene expression and hormone profiles were examined in the ASSYST diversity set by quantitative real-time PCR for associative expression mapping. The success of the ASSYST project has laid the foundation for a number of important new international consortia, with involvement of academic and industrial partners, working to improve. Implement and understand genetic diversity for important agronomic traits in oilseed rape and canola.
Publications
- (2010) Towards unambiguous transcript mapping in the allotetraploid Brassica napus. Genome 53: 929-938
Parkin I, Clarke W, Sidebottom C, Zhang W, Robinson S, Links MG, Karcz S, Higgins E, Fobert P, Sharpe A
- (2011) Genome dissection in the polyploid crop oilseed rape by transcriptome sequencing. Nature Biotechnology 29: 762-766
Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng J, Wang X, Liu S, Trick M
- (2011) Patterns of molecular variation in a species-wide germplasm set of Brassica napus. Theor Appl Genet
Bus A, Körber N, Snowdon RJ, Stich B
(See online at https://doi.org/10.1007/s00122-011-1676-7) - (2012) Associative Transcriptomics of traits in the polyploid crop species Brassica napus. Nature Biotechnology 30:798-802
A.L. Harper, M. Trick, J. Higgins, F. Fraser, L. Clissold, R. Wells, C. Hattori, P. Werner and I. Bancroft
- (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics 13: 281
Bus A, Hecht J, Hüttel B, Reinhardt R, Stich B
(See online at https://doi.org/10.1186/1471-2164-13-281) - (2012) Potential to improve oilseed rape and canola breeding in the genomics era. Plant Breeding 131: 351-360
Snowdon RJ, Ifliguez Luy F
(See online at https://doi.org/10.1111/j.1439-0523.2012.01976.x) - (2012) Seedling development in a Brassica napus diversity set and its relationship to agronomic performance. Theor Appl Genet 125: 1275-1287
Körber N, Wittkop B, Bus A, Friedt W, Snowdon RJ, Stich B
(See online at https://doi.org/10.1007/s00122-012-1912-9) - (2012) Use of mRNA-Seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. BMC Genomics 13:247
J. Higgins, A. Magusin, M. Trick, F. Fraser and I. Bancroft
- (2013) Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet 126: 1-11
Edwards D, Batley J, Snowdon RJ
(See online at https://doi.org/10.1007/s00122-012-1964-x) - (2013) Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L. PlosONE
Clarke WE, Federico ML, Gajardo HA, Gerhardt DJ, Higgins E, Sharpe AG, Snowdon RJ, Parkin lAP, Iniguez-Luy FL
(See online at https://doi.org/10.1371/journal.pone.0081992)
