Sequence-based genetic markers for genes and gene families: Single-strand conformational polymorphisms for the fatty acid synthesis genes of Cuphea

Gene sequences are rapidly accumulating for many commercially and scientifically important plants, These resources create the basis for developing sequence-based markers for mapping and tracking known (candidate) genes, thereby increasing the utility of genetic maps. Members of most of the gene families underlying the synthesis of seed oil fatty acids have been cloned from the medium-chain oilseed Cuphea. Allele-specific-PCR (AS-PCR) and single-strand conformational polymorphism (SSCP) markers were developed for 22 fatty acid synthesis genes belonging to seven gene families of Cuphea using homologous and heterologous DNA sequences. Markers were developed for 4 fatty-acyl-acyl carrier protein thioesterase, 2 beta-ketoacyl-acyl carrier protein synthase I, 4 beta-ketoacylacyl carrier protein synthase II, 3 beta-ketoacyl-acyl carrier protein synthase III, 3 acyl carrier protein, 2 beta-ketoacyl-acyl carrier protein reductase, and 4 enoylacyl carrier protein reductase loci; Eighty-eight percent (14 of 16) of the SSCP loci were polymorphic, whereas only 9% (2 of 22) of the AS-PCR loci were polymorphic. These markers were mapped using a Cuphea viscosissima x C. lanceolata F-2 population and produced linkage groups of 10, 3, and 2 loci (3 loci segregated independently). The 10-locus linkage group had every gene but one necessary for the synthesis of 2- to 16-b carbon fatty acids from acetyl-CoA and malonyl-ACP (the missing gene family was not mapped). SSCP analysis has broad utility for DNA fingerprinting and mapping genes and gene families.