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Associative expression and systems analysis of complex traits in oilseed rape / canola - ASSYST (PRR-CROPP)

Reference	BB/G024952/1
Principal Investigator / Supervisor	Dr Judith Irwin
Co-Investigators / Co-Supervisors	Professor Ian Bancroft
Institution	John Innes Centre
Department	Crop Genetics
Funding type	Research
Value (£)	358,163
Status	Completed
Type	Research Grant
Start date	02/10/2009
End date	01/10/2013
Duration	48 months

Abstract

The PBI/NRC 454-NGS platform for SNP discovery will be evaluated and resulting markers, along with the public genome-wide SNPs from UGI and the public EST-SNPs from the AAFC/DLM project, will become available for the development of a public high throughput SNP genotyping platform. The platform will be used to provide the data for two new high-density SNP maps and for whole-genome association analysis. Global transcriptome data will be obtained from germinated seedlings of 93 DH lines from the mapping population 'Express' x 'V8' plus the two parental genotypes and the F1. Whole-seedling transcript libraries will be sequenced using the next-generation Illumina (Solexa) Genome Analyzer. The quantitative global transcript data will be used to identify polymorphic gene expression markers (GEMs) in the mapping population, and for eQTL analysis. Seedlings and developing seeds from B. napus lines will be utilised for hormone profiling and global transcriptome analysis. Alignment of metabolite QTL (mQTL), eQTL and QTLs controlling seed quality traits will identify target regions of the B. napus genome for further characterisation. We will adapt and apply computational biology techniques to identify relationships between the transcriptome and a range of developmental, metabolic and performance traits. We will use appropriate computational platforms for the more detailed analysis of a small number of specific pathways. A B. napus association mapping population of 450 genetically diverse genotypes will be compiled and phenotypic data obtained and used to identify genome regions contributing to variation in the regulation of genes involved in seedling development.

Summary

A pilot experiment will evaluate the capabilities of the PBI/NRC 454-NGS platform for SNP discovery. The resulting markers, along with the public genome-wide SNPs from UGI and the public EST-SNPs from the AAFC/DLM project, will become available for the development of a public high throughput SNP genotyping platform during 2008/09. The platform we develop will subsequently be used to screen two DH mapping populations and 450 members of a genotype diversity panel, providing the data for two new high-density SNP maps and for whole-genome association analysis. Global transcriptome data will be obtained from germinated seedlings of 93 DH lines from the mapping population 'Express' x 'V8' plus the two parental genotypes and the F1. Whole-seedling transcript libraries will be sequenced using the next-generation Illumina (Solexa) Genome Analyzer. The quantitative global transcript data will be used to identify polymorphic gene expression markers (GEMs) in the mapping population, and for eQTL analysis. Developing seed will be collected from a population of 250 DH spring type B. napus lines 18 days after flowering and immediately frozen. In addition, mature seed will be collected for analysing seed quality traits. The seedlings and developing seeds will be utilised for hormone profiling and global transcriptome analysis. Alignment of metabolite QTL (mQTL), eQTL and QTLs controlling seed quality traits will identify target regions of the B. napus genome for further characterisation. Quantitative plant hormone metabolite data from all plant populations being analysed in the project will be used for comparison of mQTL with developing seed and seedling trait QTL. Detailed, quantitative hormone profiles from the developing seed and seedling tissue samples will be obtained for 36 compounds. We will adapt and apply computational biology techniques to identify relationships between the transcriptome and a range of developmental, metabolic and performance traits. Thiswill exploit transcriptome datasets developed both prior to this project and during this project, and trait datasets which could include: Seedling biomass traits, quantitative developing seed and seedling hormone measurements, oil content and fatty acid composition, protein and fibre content, seed glucosinolate content, seed weight and seed yield along with mid-parent heterosis for all of the abovementioned traits. We will use appropriate computational platforms for the more detailed analysis of a small number of specific pathways. A B. napus association mapping population of 450 genetically diverse genotypes will be compiled by combining genetic diversity sets from previous studies. These include inbred lines from a core set of 150 rapeseed (B. napus ssp. napus) and 100 swede (B. napus ssp. pabularia) genebank accessions generated in a previous project (RESGEN) by UGI and other European partners, 54 older winter rapeseed varieties and breeding lines from a previous project in Germany (GABI-BRIDGE), 90 genetically diverse modern winter oilseed rape varieties and 180 fixed diversity founder lines. For analysis of the population structure a set of 100 genome-wide SSR markers distributed evenly over all chromosomes will be used. Seedling development of the entire association mapping population will be examined in a greenhouse experiment. The data generated in the greenhouse and field trials will be used for in depth analyses of the correlations between seedling vigour parameters, agronomic traits and seed quality characters, and for detection of marker-phenotype associations with all analysed traits. The B. napus SNP array will be used for high-throughput screening of the association mapping population. This data will be used to identify genome regions contributing to variation in the regulation of genes involved in seedling development.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	Crop Science, Plant Science, Systems Biology
Research Priority	X – Research Priority information not available
Research Initiative	European Research Area Network in Plant Genomics (ERA-PG) [2006-2009]
Funding Scheme	X – not Funded via a specific Funding Scheme

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