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

BMC Genomics

Research Article

Cristobal Uauy¹  Tzion Fahima²  Eduard Akhunov³  Jorge Dubcovsky⁴  Stephen P Pearce⁴  Dario Cantu⁴  Michael W Christiansen⁵  Assaf Distelfeld⁶ 

[1] Department of Crop Genetics, John Innes Centre, Norwich, UK;Department of Evolutionary and Environmental Biology, University of Haifa, Israel;Department of Plant Pathology, Kansas State University, USA;Department of Plant Sciences, University of California, Davis, USA;Department of Plant Sciences, University of California, Davis, USA;Department of Genetics and Biotechnology, Aarhus University, Faculty of Agricultural Sciences, Slagelse, Denmark;Department of Plant Sciences, University of California, Davis, USA;Faculty of Life Sciences, Plant Sciences, Tel Aviv University, Israel;

关键词: Transcript Level;    Transcriptome Assembly;    Grain Protein Content;    Wild Type Sample;    Nutrient Remobilization;   

DOI  :  10.1186/1471-2164-12-492

 received in 2011-05-24, accepted in 2011-10-07,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundIncreasing 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.ResultsWe 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.ConclusionsMonocarpic 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.

【 授权许可】

Unknown   
© Cantu et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.