Genome-wide association analyses of loci for shatter resistance in Brassicas

Dehiscence of siliquae (shattering) is a major issue for rapeseed (canola, Brassica napus L.) growers because it causes significant yield loss. To date, genetic variation for shatter resistance in cultivated Brassicas has not been comprehensively characterised. We evaluated 192 accessions of Brassica napus, B. rapa, B. juncea and B. carinata, representing contemporary cultivars and elite lines from Australian and international programs, for shatter resistance using a pendulum test. Accessions were grown in outdoor pot and field experiments in 2010 in two locations. At physiological maturity, five pods from five plants per genotype were collected in plastic vials. The strength of individual pods was tested using a pendulum machine that struck the pod with a known force and recorded the energy absorbed by the pod before breaking – the rupture energy (RE). This work revealed significant variation for RE that could provide resistance to field shattering (a higher level of RE is required to achieve improved shatter resistance). All accessions were genotyped with 1513 markers based upon DArT, SSRs and two candidate genes that are reported to be involved in shatter resistance in Arabidopsis thaliana, a distant relative of Brassicas. Bayesian and principal coordinate analysis revealed the significant population structure within the germplasm. Molecular marker data was used to identify associations using a mixed model approach that accounts for population structure as a fixed effect and genetic relatedness as a random effect, as implemented in the TASSEL software program. Our results suggest that an association mapping strategy can be applied to identify and validate loci/alleles associated with shatter resistance.