Breeding rapeseed for enhanced oil quality includes the development of vari
eties with low linolenic acid content. The breeder also aims to develop var
ieties with a high linoleic acid content because of its nutritional value.
Restriction fragment length polymorphism (RFLP) and random amplified polymo
rphic DNA (RAPD) markers have been developed for linolenic acid content, bu
t they are not best suited for a direct application in marker-assisted sele
ction. The RFLP technique is too complex and time-consuming and RAPD marker
s lack codominance, precluding the distinction of homozygous from heterozyg
ous individuals. In this report the conversion of a RAPD marker to a codomi
nant sequence characterized amplified region (SCAR) marker named L1L9 is de
scribed. One of the alleles consisting of an 899 bp fragment (allele A), is
associated with low linolenic acid content. The other allele consists of a
n 641 bp fragment (allele B) and is associated with high linolenic acid con
tent. This marker explains approximately 25% of the genetic variation for t
his trail. Linkage analysis in the mapping population indicates that the SC
AR marker probably tags an omega-3 desaturase gene in B. napus. Two RAPD ma
rkers were found to be associated with oleic/linoleic acid content. Markers
M14-350 and 106-650 explained approximately 10% and 7% of the genetic vari
ation for linoleic acid content, respectively. These two markers a ere foun
d linked at 12.3 cM in the segregating B. napus F-2 progeny used for mappin
g. All the markers reported in this paper should be useful in breeding prog
rammes for developing high linoleic and low linolenic acid rapeseed varieti
es.