Genetic Basis of the Low-Phytate Trait in the Soybean Line CX1834

The low-phytate (LP) trait in plant seeds offers important nutritional and environmental benefits for food and feed uses. Mutants with reduced phytate content are commonly produced by chemical mutagenesis, as is the case for soybean [Glycine max (L.) Merr.] line CX1834. Quantitative trait loci (QTL) for LP in CX1834 have previously been reported, however the genetic basis for this trait has not been identified. In this study, we examined several possible chromosomal map locations for the LP mutation in CX1834. After eliminating the myo-inositol phosphate synthase (MIPS) gene family as the location of the LP mutations based on mapping studies, we focused on candidate genes in regions of known low-phytate QTL on linkage groups (LGs) L and N. Using the soybean whole-genome sequence, we identified genes encoding two putative multidrug resistance-associated proteins (MRPs). The sequence of a segment of the CX1834 MRP gene on LG N was compared with sequences from 16 other soybean lines with normal phytate content. A single nucleotide mutation from A to T, resulting in substitution of a stop codon for an Arg residue, was detected in the MRP gene on LG N of the low phytate line, but not in the normal counterparts. Further comparative sequence analysis of normal and LP progeny from a cross of CX1834 with V99-3337 (normal phytate) also indicated the A to T substitution in LP individuals, suggesting a mutation in an MRP gene as the possible cause of the low-phytate phenotype.