Inheritance of seed phytate and phosphorus levels in common bean (Phaseolus vulgaris L.) and association with newly-mapped candidate genes

Common bean (Phaseolus vulgaris L.) is an important, high-quality staple food that provides large amounts of protein and mineral micronutrients to the diets of people in many countries. Phytates are a storage form of organic phosphorus which is used by the plant in various stages of growth and development but can have certain anti-nutrient properties due to chelation of minerals such as iron and zinc. At the same time, phytates provide certain health benefits and therefore are the subject of both mutagenesis and breeding programs for functional foods. The objective of this study was to evaluate the quantitative trait loci (QTL) associated with seed phytate and seed phosphorus concentration and content on a per-seed basis and to develop functional molecular markers for genes from the phytic acid synthesis pathway. We used a well-characterized mapping population, DOR364 x G19833, in three field experiments with three repetitions each and two levels of soil phosphorus fertilization, as well as a large set of previously and newly developed primer pairs for the genes myo-inositol (3)P-1 synthase, myo-inositol kinase and various inositol kinases. We identified an association of phytate concentration QTL with one of two paralogs of the myo-inositol (3)P-1 synthase gene family, located on linkage group b01 and expressed in common bean seed rather than in vegetative tissues. We also identified QTL for phytate concentration on linkage group b06 and phytate content on linkage groups b03, b04 and b10. We provide a synteny analysis based on common bean versus soybean genome comparisons of all the phytic acid pathway genes that were genetically mapped and indicate flanking markers that can be used for marker-assisted selection when the genes themselves are not polymorphic as PCR amplicons. We can conclude that natural variability in phytate levels is controlled by the seed-expressed myo-inositol (3)P-1 synthase gene (MIPS) as well as other loci in the common bean genome. This means that breeding of phytate levels in common bean must take into account allele variability at certain candidate genes, such as this seed MIPS gene, a recently cloned ABC trasnporter and additional QTL for the trait, which underlie the oligogenic inheritance for phytate concentration in common bean.