Abstract
The low phytic acid (lpa) trait in soybeans can be conferred by loss-of-function mutations in genes encoding myo-inositol phosphate synthase and two epistatically interacting genes encoding multidrug-resistance protein ATP-binding cassette (ABC) transporters. However, perturbations in phytic acid biosynthesis are associated with poor seed vigor. Since the benefits of the lpa trait, in terms of end-use quality and sustainability, far outweigh the negatives associated with poor seed performance, a fuller understanding of the molecular basis behind the negatives will assist crop breeders and engineers in producing variates with lpa and better germination rate. The gene regulatory network (GRN) for developing low and normal phytic acid soybean seeds was previously constructed, with genes modulating a variety of processes pertinent to phytic acid metabolism and seed viability being identified. In this study, a comparative time series analysis of low and normal phytic acid soybeans was carried out to investigate the transcriptional regulatory elements governing the transitional dynamics from dry seed to germinated seed. GRNs were reverse engineered from time series transcriptomic data of three distinct genotypic subsets composed of lpa soybean lines and their normal phytic acid sibling lines. Using a robust unsupervised network inference scheme, putative regulatory interactions were inferred for each subset of genotypes. These interactions were further validated by published regulatory interactions found in Arabidopsis thaliana and motif sequence analysis. Results indicate that lpa seeds have increased sensitivity to stress, which could be due to changes in phytic acid levels, disrupted inositol phosphate signaling, disrupted phosphate ion (Pi) homeostasis, and altered myo-inositol metabolism. Putative regulatory interactions were identified for the latter two processes. Changes in abscisic acid (ABA) signaling candidate transcription factors (TFs) putatively regulating genes in this process were identified as well. Analysis of the GRNs reveal altered regulation in processes that may be affecting the germination of lpa soybean seeds. Therefore, this work contributes to the ongoing effort to elucidate molecular mechanisms underlying altered seed viability, germination and field emergence of lpa crops, understanding of which is necessary in order to mitigate these problems.
Highlights
The development and commercialization of low phytic acid crops could represent one approach to enhanced management of phosphorus (P) in animal agriculture and to addressing mineral deficiency in humans
For each of the three subsets of genotypes (Table 1), the lpa and normal phytic acid lines were compared to identify genes that were differentially expressed at each stage
Using a set of four near isogenic lines, the number of differentially expressed genes (DEGs) in the MRP subset was limited to just 430. This number was obtained by designating genes as DEGs only if they were differentially expressed in each comparison of 2mlpa to the three normal phytic acid lines (2MWT, 2MWT-L, and 2MWT-N)
Summary
The development and commercialization of low phytic acid (lpa) crops could represent one approach to enhanced management of phosphorus (P) in animal agriculture and to addressing mineral deficiency in humans. Maize, rice, soybean, and wheat lines have been developed, and their seeds are shown to increase phosphorus availability in poultry and swine and reduce phosphorus pollution from the subsequent waste (Larson et al, 1998, 2000; Raboy et al, 2000; Wilcox et al, 2000; Hitz et al, 2002; Guttieri et al, 2004; Shi et al, 2007) Despite these advantages, lpa crops have not been commercialized, as they often exhibit poor seed and seedling vigor, low stress tolerance, and reduced germination and emergence rates (Meis et al, 2003; Oltmans et al, 2005; Bregitzer and Raboy, 2006; Raboy, 2007; Colombo et al, 2020). A fuller understanding of the molecular basis behind these negatives will assist crop breeders and engineers in successfully handling them
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