Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines. (December 2015)

• Record Type: Journal Article
• Authors: Redekar, Neelam; Biyashev, Ruslan; Jensen, Roderick; Helm, Richard; Grabau, Elizabeth; Maroof, M.
• Is Part Of: BMC genomics. Volume 16:Number 1(2015)
• Page Start: 1
• Page End: 16
• Publication Date: 2015-12
• Subjects: Phytic acid -- myo-inositol phosphate synthase -- Multidrug-resistance protein ABC transporter -- Seed development -- Transcriptomics -- Differential gene expression -- Functional enrichment -- Apoptosis -- Photosynthesis; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-015-2283-9
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Low 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. Thelpa crops developed to date carry mutations that are directly or indirectly associated with PA biosynthesis and accumulation during seed development. Theselpa 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. Improvinglpa crop yield requires an understanding of the downstream effects of thelpa genotype on seed development. Towards that end, we present a comprehensive comparison of gene-expression profiles betweenlpa and normal PA soybean lines (Glycine max ) at five stages of seed development using RNA-Seq approaches. Thelpa line used in this study carries single point mutations in amyo -inositol phosphate synthase gene along with two multidrug-resistance protein ABC transporter genes. Results RNA sequencing data oflpa 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 oflpa seed development, while those associated with photosynthesis showed decreased expression in late developmental stages. The results suggest thatlpa -causing mutations play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively. Conclusions This study provides a global perspective of transcriptomal changes during soybean seed development in anlpa 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 oflpa -causing mutations.