Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: Purpose: Comprehensive comparison of gene-expression profiles between 3mlpa (mutant with low phytic acid) and 3MWT (non-mutant with normal phyic acid) soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. Methods: mRNA sequencing reads (101SE) were generated in triplicate from five seed developmental stages of 3mlpa and 3MWT soybean line using Illumina HiSeq 2000. Results: 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. Conclusion: This study provides a global perspective of transcriptomal changes during soybean seed development in 3mlpa mutant. The results suggest that low phtic acid-causing mutations in 3mlpa play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively. RNA-Seq of five seed developing soybean seeds from mips1/mrp-l/mrp-n triple mutant line (with low phytic acid) and MIPS1/MRP-L/MRP-N non-mutant line (with normal phytic acid). The mRNA libraries from three biological replicates of each sample were sequenced as 101 SE using Illumina HiSeq 2000.

ORGANISM(S): Glycine max

SUBMITTER: M.A. Saghai Maroof

PROVIDER: E-GEOD-75575 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Redekar Neelam R NR Biyashev Ruslan M RM Jensen Roderick V RV Helm Richard F RF Grabau Elizabeth A EA Maroof M A Saghai MA

BMC genomics 20151218

<h4>Background</h4>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. 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 e ...[more]

PMID: 26678836

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Project description:Background: To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consisting of up to 27,000 soybean cDNAs. Results: It was discovered that genes related to cell growth and maintenance processes, as well as energy processes like photosynthesis, decreased in expression levels as the cotyledons approached the mature, dry stage. Genes involved with some storage proteins had their highest expression levels at the stage of largest fresh weight. However, genes encoding many transcription factors and DNA binding proteins showed higher expression levels in the desiccating and dry seeds than in most of the green stages. Conclusions: Data on 27,000 cDNAs have been obtained over five stages of soybean development, including the stages of major accumulation of agronomically-important products, using microarrays. Of particular interest are the genes found to peak in expression at the desiccating and dry seed stages, such as those annotated as transcription factors, which may indicate the preparation of pathways that will be needed later in the early stages of imbibition and germination. Five stages of development of soybean cotyledons were studied. The first three, with fresh weights of 25-50mg, 75-100mg, and 400-500mg, were green in color. The last two, yellow-colored cotyledons with a fresh weight of 200-300mg and dry whole seeds approximately 100-200mg in weight, were desiccating and yellow/brown in color. The green stage of 100-200mg fresh weight cotyledons was used as a reference for all other stages. Four replicates, including two dye swaps, were made of each of the first three (green) stages. Two replicates, including one dye swap, were made of each of the last two (yellow/dry) stages. The results from three different platforms (GPL229, GPL1012, and GPL1013) were combined.

Dataset Information

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

Publications

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

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