Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines

Abstract

BackgroundLow phytic acid (lpa) crops are potentially eco-friendly alternative to conventional normal phytic acid (PA) crops, improving mineral bioavailability in monogastric animals as well as decreasing phosphate pollution. The lpa crops developed to date carry mutations that are directly or indirectly associated with PA biosynthesis and accumulation during seed development. These lpa crops typically exhibit altered carbohydrate profiles, increased free phosphate, and lower seedling emergence, the latter of which reduces overall crop yield, hence limiting their large-scale cultivation. Improving lpa crop yield requires an understanding of the downstream effects of the lpa genotype on seed development. Towards that end, we present a comprehensive comparison of gene-expression profiles between lpa and normal PA soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. The lpa line used in this study carries single point mutations in a myo-inositol phosphate synthase gene along with two multidrug-resistance protein ABC transporter genes.ResultsRNA sequencing data of lpa and normal PA soybean lines from five seed-developmental stages (total of 30 libraries) were used for differential expression and functional enrichment analyses. A total of 4235 differentially expressed genes, including 512-transcription factor genes were identified. Eighteen biological processes such as apoptosis, glucan metabolism, cellular transport, photosynthesis and 9 transcription factor families including WRKY, CAMTA3 and SNF2 were enriched during seed development. Genes associated with apoptosis, glucan metabolism, and cellular transport showed enhanced expression in early stages of lpa seed development, while those associated with photosynthesis showed decreased expression in late developmental stages. The results suggest that lpa-causing mutations play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively.ConclusionsThis study provides a global perspective of transcriptomal changes during soybean seed development in an lpa mutant. The mutants are characterized by earlier expression of genes associated with cell wall biosynthesis and a decrease in photosynthetic genes in late stages. The biological processes and transcription factors identified in this study are signatures of lpa-causing mutations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2283-9) contains supplementary material, which is available to authorized users.

Global transcriptome and coexpression network analyses reveal cultivar‐specific molecular signatures associated with seed development and seed size/weight determination in chickpea

“…The genes encoding glucan synthases, cellulose synthases and xyloglucan endotransglucosylases/hydrolases exhibited higher transcriptional activity in JGK 3 cultivar during embryogenesis and/or mid‐maturation stages. These enzymes are the integral components of cell wall biosynthetic machinery and are involved in production of energy (Stork et al ., ; Mendu et al ., ; Redekar et al ., ). Further, the transcript abundance of genes involved in cell expansion (expansins), seed storage proteins (vicilins) and lipid transfer proteins was also significantly higher in the large‐seeded chickpea cultivar (Figure S9).…”

Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.)

“…To date, studies dedicated to the transcriptomic or proteomic profiling of developing seeds have been performed for several legume species, including the chickpea [26], soybean [27,28], barrel medic [29][30][31], common bean [13,32], and garden pea [33][34][35]. These large-scale assays allow global genetic programs involved in seed maturation to be dissected, and expression changes to be traced over time.…”

Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds

“…The expressions of genes involved in the metabolic activities in seeds are tightly regulated by the synergistic action of many transcription factors and other regulatory genes (Weber et al, 2005 ; Le et al, 2007 ). Two independent studies, one with barley low phytic acid ( lpa ) mutant, and another with soybean mips1/mrp-l/mrp-n (‘ 3mlpa ’) triple mutant have reported the effect of lpa mutations on the transcriptomic profiles of developing seeds (Bowen et al, 2007 ; Redekar et al, 2015 ). The differential expression of transcription factor genes such as WRKY and CAMTA (Calmodulin-binding Transcription Activator), was linked to phytic acid biosynthesis pathway, suggesting a complex regulatory mechanism (Redekar et al, 2015 ).…”