ORIGINAL ARTICLE Mapping of QTLs for oil content and fatty acid composition in Indian mustard [Brassica juncea (L.) Czern. and Coss.] Subhadra Singh & T. Mohapatra & Rakesh Singh & Z. Hussain Received: 2 July 2011 /Accepted: 2 March 2012 # Society for Plant Biochemistry and Biotechnology 2012 Abstract An AFLP linkage map of Brassica juncea (L.) Czern and Coss was constructed using 88 recombinant inbred lines (RILs) from a cross between an Indian cultivar ‘Varuna’ and an accession from Poland ‘BEC-144’. The map included 91 AFLP markers organized on 19 linkage groups covering a total map distance of 1679.1 cM. A total of 14 QTLs were detected for oil content (2 QTLs), erucic acid (2 QTLs), eicosenoic acid (2 QTLs), linolenic acid (3 QTLs), linoleic acid (3 QTLs) and palmitic acid (2 QTLs). A specific genomic region on LG2 was associated with contents of three fatty acids: erucic acid, eicosenoic acid and linoleic acid. Some of the markers showed absolute linkage with the QTLs associated with the levels of linolenic acid, linoleic acid and oil content. These markers may be used for improvement of fatty acid profile of B. juncea. Keywords Indian Mustard . AFLP . Fatty acid . Oil content . QTL mapping Abbreviations AFLP Amplified fragment length polymorphism LOD log likelihood odds ratio QTL quantitative trait loci RIL recombinant inbred lines Introduction Vegetable oils extracted from Brassica seeds are important plant commodities being a valuable source of energy. How- ever, their value and usefulness for food and industrial applications depend on their fatty acid composition. Indian mustard, Brassica juncea (2n 0 36, genome AABB) is grown traditionally as a mustard crop in many countries for the production of oil as it exhibits higher heat and drought tolerance, disease resistance and pod shatter resistance com- pared to B. napus (Woods et al. 1991; Burton et al. 1999). It is also an important source of two essential fatty acids: ω 6 (Linoleic acid: 9, 12–18: 2) and ω 3 (Linolenic acid: 9, 12, 15–18:3) which are necessary for growth and normal phys- iological function but cannot be completely synthesized in the human body. Mustard seeds contain 37 to 42% oil and six major fatty acids, i.e. palmitic acid (16:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), eicosenoic acid (20:1) and erucic acid (22:1) (Vangheesdaele and Four- nier 1980). Recently, there is increased interest in oil with higher levels of C18:1 and C18:2 fatty acid for human nutrition. Oils with high C 18:1 and C 18:3 levels possess a higher oxidative stability and produce less undesirable products during deep frying (Topfer et al. 1995). Therefore, increasing oil content and improving the fatty acid compo- sition in the seed oil are important breeding objectives in Brassica juncea. S. Singh Department of Genetics, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India T. Mohapatra National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India R. Singh (*) NRC on DNA Fingerprinting, National Bureau of Plant Genetic Resources, New Delhi 110012, India e-mail: singhnbpgr@yahoo.com Z. Hussain National Bureau of Plant Genetic Resources, New Delhi 110012, India J. Plant Biochem. Biotechnol. DOI 10.1007/s13562-012-0113-6