Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence

Dario Cantu, Stephen P. Pearce, Assaf Distelfeld, Michael W. Christiansen, Cristobal Uauy, Eduard Akhunov, Tzion Fahima, Jorge Dubcovsky

Research output: Contribution to journalArticlepeer-review


Background: Increasing the nutrient concentration of wheat grains is important to ameliorate nutritional deficiencies in many parts of the world. Proteins and nutrients in the wheat grain are largely derived from the remobilization of degraded leaf molecules during monocarpic senescence. The down-regulation of the NAC transcription factor Grain Protein Content (GPC) in transgenic wheat plants delays senescence (>3 weeks) and reduces the concentration of protein, Zn and Fe in the grain (>30%), linking senescence and nutrient remobilization.Based on the early and rapid up-regulation of GPC in wheat flag leaves after anthesis, we hypothesized that this transcription factor is an early regulator of monocarpic senescence. To test this hypothesis, we used high-throughput mRNA-seq technologies to characterize the effect of the GPC down-regulation on the wheat flag-leaf transcriptome 12 days after anthesis. At this early stage of senescence GPC transcript levels are significantly lower in transgenic GPC-RNAi plants than in the wild type, but there are still no visible phenotypic differences between genotypes.Results: We generated 1.4 million 454 reads from early senescing flag leaves (average ~350 nt) and assembled 1.2 million into 30,497 contigs that were used as a reference to map 145 million Illumina reads from three wild type and four GPC-RNAi plants. Following normalization and statistical testing, we identified a set of 691 genes differentially regulated by GPC (431 ≥ 2-fold change). Transcript level ratios between transgenic and wild type plants showed a high correlation (R = 0.83) between qRT-PCR and Illumina results, providing independent validation of the mRNA-seq approach. A set of differentially expressed genes were analyzed across an early senescence time-course.Conclusions: Monocarpic senescence is an active process characterized by large-scale changes in gene expression which begins considerably before the appearance of visual symptoms of senescence. The mRNA-seq approach used here was able to detect small differences in transcript levels during the early stages of senescence. This resulted in an extensive list of GPC-regulated genes, which includes transporters, hormone regulated genes, and transcription factors. These GPC-regulated genes, particularly those up-regulated during senescence, provide valuable entry points to dissect the early stages of monocarpic senescence and nutrient remobilization in wheat.

Original languageEnglish
Article number492
JournalBMC Genomics
StatePublished - 7 Oct 2011

Bibliographical note

Funding Information:
We thank Dr. Alexander Kozik for his useful insights on Illumina data analysis, Dr. Charles Nicolet from the DNA Technologies Core Facility (Genome Center, UC Davis) and Alina Akhunova from the Integrated Genomics Facility (KSU) for technical assistance. We thank the Gene Expression Omnibus and the Transcriptome Shotgun Assembly at NCBI for the assistance provided in submitting sequencing reads and assemblies and to Dr. Ann Blechl for the GPC-RNAi transgenic lines. This project was supported by the National Research Initiative Competitive Grant no. 2008-35318-18654 from the USDA National Institute of Food and Agriculture and by the United States-Israel Binational Science Foundation (BSF) grant number 2007194.

ASJC Scopus subject areas

  • Genetics
  • Biotechnology


Dive into the research topics of 'Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence'. Together they form a unique fingerprint.

Cite this