Aberrant RNA splicing of the phytic acid synthesis gene inositol-1,3,4 trisphosphate 5/6-kinase in a low phytic acid soybean line

ABSTRACT Most phosphorus is stored as phytic acid in plant seed, although it is considered an anti-nutrient compound that reduces the bioavailability of minerals in monogastric animals. Low-phytic acid (LP) crops improve mineral bioavailability in monogastric animals, which can decrease environmental pollution due to phosphorus. Recently, we reported a newly developed LP soybean line by crossing the LP line CX1834 and Japanese normal phytic acid cultivar Natto-kotsubu (Natto), which showed superior traits in seedling emergence, growth, and yield compared with CX1834. The molecular mechanism underlying the LP trait in the LP line remains unclear. The LP line was used for a de novo RNA-Seq analysis, and we illustrated the aberrant RNA splicing of the phytic acid synthase gene inositol-1,3,4 trisphosphate 5/6-kinase 3 (GmITPK3) in the LP line. The expression level of phytic acid biosynthesis-related genes and inositol phosphate isomer concentrations were investigated. A de novo RNA-Seq analysis revealed that the intron retention (IR) transcript of GmITPK3 is highly expressed in the leaves of the LP line. Although expressed in both, the relative abundances of multiple IR transcripts were significantly higher in the LP line than that in the Natto cultivar. The IR transcripts of GmITPK3 encoding truncated proteins were missing an essential domain for their activity, while one possibly contained an abnormal ligand binding site. The relative abundance of IR transcripts was 1.9- to 5.4-times higher in the LP line than that in the Natto cultivar during seed development; accordingly, the production of phytic acid and its precursors in the developing seeds was lower in the LP line than that in the Natto cultivar. No mutation was detected at the exon–intron junction, where a splicing error occurs in GmITPK3 of the LP line, implying that a splicing error is attributed to unknown splicing factor genes involved in the splicing regulation of GmITPK3. Our results provide insights into the possible involvement of splicing errors in GmITPK3 for the trait of low phytic acid production in the LP line.