BBSRC Renewable Industrial Products from Rapeseed - UK-BRC

BBSRC Renewable Industrial Products
from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
•  Project overview
•  Associative Transcriptomics
•  Functional genotypes to be produced
•  Traits to be addressed
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
RIPR OVERVIEW
5 year sLoLa (1/1/14 – 31/12/18)
Oilseed rape:
Co-products (economic sustainability)
Nutrient use efficiency (environmental sustainability)
BBSRC-funded (BB/L002124/1) with industry in-kind support
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
BBSRC Renewable Industrial Products
from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
•  Project overview
•  Associative Transcriptomics
•  Functional genotypes to be produced
•  Traits to be addressed
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
GENETIC VARIATION
•  Genetic variation controls productivity and quality of crops
•  Both gene sequence variation and gene expression variation are important
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
USE “FUNCTIONAL GENOTYPES” FOR MAPPING
CDS or unigene reference sequence
mRNA
3,000,000,000 bases of
sequence per plant
(~ one complete human genome)
Score both SNPs and transcript abundance
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
ASSOCIATION GENETICS
Linkage Disequilibrium analysis
Gene sequence variation from functional genotypes
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
ASSOCIATION GENETICS
Linkage Disequilibrium analysis
+ Gene expression
“polymorphisms” (GEPs)
Regression
Gene expression variation from functional genotypes
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
IDENTIFICATION OF CANDIDATE GENES
•  Association analyses provide molecular markers to support breeding
•  Associative Transcriptomics often identifies causative gene variants
SNP
C2
SNP
GEP
A9
GEP
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
BBSRC Renewable Industrial Products
from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
•  Project overview
•  Associative Transcriptomics
•  Functional genotypes to be produced
•  Traits to be addressed
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
618 REPLICATED GENOTYPES GROWN IN NOTTINGHAM 2013/4
389 B. napus ASSYST
54 B. rapa Wageningen
21 B. rapa commercial seeds
110 B. oleracea Warwick
27 B. oleracea commercial seeds
17 Brassicaceae commercial seeds
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
RNA PREPARED IN YORK 2014
Completed and
passed QC as of
9/5/14:
584
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
mRNAseq DATA PRODUCED BY TGAC 2014
Completed and
passed QC as of
9/5/14:
~130
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
FUNCTIONAL GENOTYPES GENERATED BY YORK
Genotypes produced
as of 9/5/14 :
B. napus
B. rapa
B. oleracea
0
0
0
Leaf tissue from
diversity panel
Hypothetically ordered unigenes / CDS
Illumina
mRNAseq
(100-base
SE reads)
BWA-based
scoring pipeline
Transcript
abundance
quantification
SNP
scoring
Functional genotypes
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
DATA MANAGEMENT BY TGAC
November 2014
Develop visualization approaches for large
datasets
January 2015
Develop syntenic genome displays for
Brassica – Arabidopsis
February 2015
Make unigene/CDS reference sequences
available via Ensembl database
April 2015
Make SNPs and GEPs available via Ensembl
database
June 2015
Make phenotypic data available via TGAC
CropstoreDB
August 2015
Make marker-trait associations available via
Ensembl database
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
HOMOEOLOGOUS RECOMINATION IN CULTIVARS
Segregating
deletions and
homoeologous
exchanges
inferred from
regions of
skewed gene
expression
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
INFERRED GENE ORDER IN NASCENT B. napus
Feed-in ERA-CAPS project “Evo-Genapus” (York, Giessen, Rennes)
•  Started 1/4/14
Overall aim:
•  Characterise relationships between genome structural changes and trait
variation in B. napus
Early resource:
•  Reconstruction of gene order in nascent B. napus (A, C pan-genomes)
Progress:
•  99,664 CDS gene models from B oleracea (TO1000) and B. rapa (Chiifu v2)
mapped to respective genomes in v4 Pseudomolecules
•  Constructing v5 Pseudomolecules from TO1000 and Chiifu v2 assemblies
•  Will interpolate B. napus-specific/looped-out/additional diploid CDS
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
INFERRED GENE ORDER IN NASCENT B. napus
Gene order in diploid-based (v4) pseudomolecules very highly conserved in
B. napus Darmor bzh genome sequence
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
BBSRC Renewable Industrial Products
from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
•  Project overview
•  Associative Transcriptomics
•  Functional genotypes to be produced
•  Traits to be addressed
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
TARGET TRAITS
2013-14
Polytunnel growth for
high throughput
phenotyping
(Nottingham)
2014-17
Field trials for nutrient use
efficiency
(ADAS, Nottingham)
Tocopherols
(York)
Phytosterols
(RRes)
Waxes
(RRes)
Functional polysaccharides
(IFR)
Nutrient homeostasis
(Nottingham, York, Cologne)
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
DATA ANALYSIS
2013-14
Polytunnel growth for
high throughput
phenotyping
(Nottingham)
2014-17
Field trials for nutrient use
efficiency
(ADAS, Nottingham)
Tocopherols
(York)
Phytosterols
(RRes)
Waxes
(RRes)
Functional polysaccharides
(IFR)
Nutrient homeostasis
(Nottingham, York, Cologne)
2015
B. napus Associative Transcriptomics (York)
2015
Functional genotypes
(York, TGAC)
2015-18
Hypothesis testing for control of traits and predictive capabilities of markers (All)
Fertiliser model development
Economic & environmental modelling
(ADAS, JHI, Cargill)
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
PROJECT OUTPUTS
2013-14
Polytunnel growth for
high throughput
phenotyping
(Nottingham)
2014-17
Field trials for nutrient use
efficiency
(ADAS, Nottingham)
Tocopherols
(York)
Phytosterols
(RRes)
Waxes
(RRes)
Functional polysaccharides
(IFR)
Nutrient homeostasis
(Nottingham, York, Cologne)
2015
B. napus Associative Transcriptomics (York)
2015
Functional genotypes
(York, TGAC)
2015-18
Hypothesis testing for control of traits and predictive capabilities of markers (All)
Fertiliser model development
Economic & environmental modelling
(ADAS, JHI, Cargill)
Outputs:
•  Data models established for rapeseed transcriptomics and traits
•  Functional genotype determined for ~600 Brassica accessions
•  Genetic bases of key traits better understood
•  Predictive markers identified and validated for key traits
•  Improved germplasm available for pre-breeding
•  Models for economic and environmental sustainability of rapeseed
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014
RIPR OVERVIEW
5 year sLoLa (1/1/14 – 31/12/18)
Oilseed rape:
Co-products (economic sustainability)
Nutrient use efficiency (environmental sustainability)
BBSRC-funded (BB/L002124/1) with industry in-kind support
BBSRC Renewable Industrial Products from Rapeseed (RIPR) Programme
Ian Bancroft
15th May 2014