SCAR and RAPD markers associated with 18-carbon fatty acids in rapeseed, Brassica napus

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.