Quantitative proteomic analyses of two soybean low phytic acid mutants to identify the genes associated with seed field emergence

Abstract

BackgroundSeed germination is essential to crop growth and development, and ultimately affects its harvest. It is difficult to breed soybeans low in phytic acid with a higher seed field emergence. Although additional management and selection could overcome the phytate reduction, the mechanisms of seed germination remain unknown.ResultsA comparative proteomic analysis was conducted between two low phytic acid (LPA) soybean mutants (TW-1-M and TW-1), both of which had a deletion of 2 bp in the GmMIPS1 gene. However, the TW-1 seeds showed a significantly lower field emergence compared to the TW-1-M. There were 282 differentially accumulated proteins (DAPs) identified between two mutants at the three stages. Among these DAPs, 80 were down-accumulated and 202 were up-accumulated. Bioinformatic analysis showed that the identified proteins were related to functional categories of oxidation reduction, response to stimulus and stress, dormancy and germination processes and catalytic activity. KEGG analysis showed that these DAPs were mainly involved in energy metabolism and anti-stress pathways. Based upon the conjoint analysis of DAPs with the differentially expressed genes (DEGs) previously published among three germination stages in two LPA mutants, 30 shared DAPs/DEGs were identified with different patterns, including plant seed protein, beta-amylase, protein disulfide-isomerase, disease resistance protein, pyrophosphate-fructose 6-phosphate 1-phosphotransferase, cysteine proteinase inhibitor, non-specific lipid-transfer protein, phosphoenolpyruvate carboxylase and acyl-coenzyme A oxidase.ConclusionsSeed germination is a very complex process in LPA soybean mutants. The TW-1-M and TW-1 showed many DAPs involved in seed germination. The differential accumulation of these proteins could result in the difference of seed field emergence between the two mutants. The high germination rate in the TW-1-M might be strongly attributed to reactive oxygen species-related and plant hormone-related genes. All these findings would help us further explore the germination mechanisms in LPA crops.

Network Inference of Transcriptional Regulation in Germinating Low Phytic Acid Soybean Seeds

“…In fact, 345 and 209 ABA-related genes were differentially expressed in the 1mlpa and 3mlpa lines, respectively. Not only was the ABA pathway affected in this study, but it was also affected in transcriptome and proteome studies of germinating lpa soybeans also carrying mips1 mutations (Yuan et al, 2017;Yu et al, 2019). This is significant as ABA is the sole hormone known to trigger and maintain seed dormancy and is a major inhibitor of seed germination (Cutler et al, 2010;Hubbard et al, 2010).…”

“…Though different components of the ABA signaling pathway were affected, it is notable that the pathway was disrupted in all three lpa lines and that it was also disrupted in the previous seed development study utilizing the same lines as well as in other germination studies on lpa soybeans (Redekar et al, 2017;Yuan et al, 2017;Yu et al, 2019). Hence, because ABA has a major influence on seed dormancy and germination, its perturbed function in lpa soybean seeds may significantly contribute to the poor seed germination associated with these mutations.…”

“…These studies revealed changes in gene transcripts and proteins involved in energy metabolism, phytohormone pathways, oxidation-reduction processes, and stress responses (Yuan et al, 2017;Yu et al, 2019).…”

“…Furthermore, selection within an lpa line might yield progeny with improved germination and field emergence ( Oltmans et al, 2005 ). For example, a soybean lpa mutation termed TW-1 had reduced field emergence and reduced viability following seed storage; however, these negative effects were reduced in a single-plant derived line isolated in TW-1 progeny termed TW-1-M ( Yuan et al, 2017 ; Yu et al, 2019 ). Limiting the wide-scale development of high performing lpa crops is a poor understanding of the molecular basis of seed phytic acid content in relation to seed vigor, i.e., the properties defining a seed’s potential performance during germination and emergence ( Hampton and TeKrony, 1995 ).…”

“…Previous studies with barley and soybean have investigated the effect of the lpa trait on developing seeds and found differences in energy metabolism and phytohormone signaling, as well as regulatory components that may be responsible for these variations ( Bowen et al, 2007 ; Redekar et al, 2015 , 2017 ). Transcriptomic and proteomic analyses of germinating seeds were used to understand the molecular basis of the improvement of field emergence and seed viability observed in the soybean mutant TW-1-M as compared with its parental line TW-1 ( Yuan et al, 2017 ; Yu et al, 2019 ). These studies revealed changes in gene transcripts and proteins involved in energy metabolism, phytohormone pathways, oxidation-reduction processes, and stress responses ( Yuan et al, 2017 ; Yu et al, 2019 ).…”