Genome-wide prediction in Brassica napus L.

(Canola/Rapeseed)
Dept Plant Breeding

JUSTUS-LIEBIG-

Habib

1 Jan ,

Rod

1 Snowdon ,

Richard

2 Nichols

1.Department of Plant Breeding, Heinrich-Buff-Ring 26-32,35392 Giessen, Germany; 2.The School of Biological and Chemical Sciences,Queen Mary, University of London,Mile End Road,London.E1 4NS,UK

h.jan@qmul.ac.uk

Project background
Next generation sequencing technologies generate enormous and cheap genomic data that can be used to predict the performance of plant lines. Genomic selection, is an approach using molecular markers from across the whole genome to estimate the breeding values of individuals, which can lead to rapid genetic gain (compared to phenotypic selection) due to early selection and high prediction accuracy. Here we assess the Linkage disequilibrium and signatures of selection due to domestication and selective introgression by plant breeders

History & selection signatures

Origins: As an allopolyploid B. napus has a three histories of domestication. A genome: half the genome originates from an oilseed brassica, B. rapa, which may have been domesticated over six thousand years ago in India. C genome: the other half is from a cabbage, B. oleracea. Hybridization & Polyploidisation is presumed Methods to be much more recent, perhaps on the silk route; swedes (a subspecies) are known by Roman times. Selective introgression: is likely to be more ancient on the A genome, through spontaneous crosses with B. rapa. The C genome has been targeted more recently by plant breeders using new technologies e.g. crossing with artificial allopolyploid hybrids

Possible interpretations
Long distance LD in C genome: caused by recent selective sweeps in 3 chromosomes. LD in A genome: ancient sweeps. Clustering in PCOs: breeding has separated lines with and without key QTLs (cf LD plots). Single origins of QTLs leads to clusters.

Principal Coordinate Analysis Entire genome

Objectives
Initial (this poster): evaluate the make-up of the lines moulded by domestication and breeding Ultimate: assessment of genomic prediction models using data from Brassica napus lines using GBLUP and Bayesian methods.
r2

Chr8 (A-genome)

Linkage Disequilibrium
0.9 0.8 0.7 0.6 0.5

LD in A-Genome

Chr9 (A-genome)

Materials
Elite breeding lines ( 2-MS female lines) (475 male lines) Phenotypic data from various German locations Parental SNP data (60K SNPs each line)

0.4 0.3 0.2 0.1 0

Chr1 (C-genome)
Distance_bp(KB)

1.2 1 0.8

LD in C-Genome

Chr4 (C-genome)

Methods
Plots of linkage disequilibrium among SNPs on each subgenome & chromosome PCOs of SNP data for the whole genome and for chromosomes with atypical LD

r2

0.6 0.4 0.2 0

Funding Sources:
INTERCROSSING (Marie Curie ITN) NPZ-Lembke Germany

Distance_bp(KB)