A Low-Phytate Soybean Line Disturbs Seed Development-Dependent mRNA Splicing in the Phytate synthesis gene inositol-1,3,4 trisphosphate 5/6-kinase (GmITPK3)

Low-phytate (LP) crops may improve the mineral bioavailability in monogastric animals, which will serve to decrease phosphate pollution. Recently, we reported a newly developed LP soybean line with normal emergence, growth, and yield when compared to the Natto-kotsubu (Natto) cultivar. The RNA-Seq was used to investigate the mechanism underlying reduction in phytic acid levels without impact to physiological characteristics in this LP line. an intron retention (IR) event was detected in inositol-1,3,4 trisphosphate 5/6-kinase 3 (GmITPK3) in LP leaves compared to the reference transcriptome and 34 % of the isoform belonged to an IR isoform. The PCR amplification results showed the LP line produced abundant IR transcripts (IRTs) compared to Natto cultivar and NP line. The predicted amino acid (AA) of IR may have no function compared to the non-intron retention transcript (nIRT). The abundance of each IRTs was changed during seeds development may maintain the phytic acid level in Natto cultivar, however, the abundant of IRTs produced in LP line may perturb the phosphorylation of InsP4 to InsP5 and/or create a negative feedback effect on InsP4 and InsP3 synthesis, leading to reduced phytic acid levels in the LP line during seed development. Hence, the GmITPK3 mutant might involve the decrease the level of phytic acid in seeds without harming the plants, thus representing a new strategy for LP crop development.