Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonicarice

Abstract

BackgroundPlant growth depends on synergistic interactions between internal and external signals, and yield potential of crops is a manifestation of how these complex factors interact, particularly at critical stages of development. As an initial step towards developing a systems-level understanding of the biological processes underlying the expression of overall agronomic potential in cereal crops, a high-resolution transcriptome analysis of rice was conducted throughout life cycle of rice grown under natural field conditions.ResultsA wide range of gene expression profiles based on 48 organs and tissues at various developmental stages identified 731 organ/tissue specific genes as well as 215 growth stage-specific expressed genes universally in leaf blade, leaf sheath, and root. Continuous transcriptome profiling of leaf from transplanting until harvesting further elucidated the growth-stage specificity of gene expression and uncovered two major drastic changes in the leaf transcriptional program. The first major change occurred before the panicle differentiation, accompanied by the expression of RFT1, a putative florigen gene in long day conditions, and the downregulation of the precursors of two microRNAs. This transcriptome change was also associated with physiological alterations including phosphate-homeostasis state as evident from the behavior of several key regulators such as miR399. The second major transcriptome change occurred just after flowering, and based on analysis of sterile mutant lines, we further revealed that the formation of strong sink, i.e., a developing grain, is not the major cause but is rather a promoter of this change.ConclusionsOur study provides not only the genetic basis for functional genomics in rice but also new insight into understanding the critical physiological processes involved in flowering and seed development, that could lead to novel strategies for optimizing crop productivity.

Tissue-specific expression, developmentally and spatially regulated alternative splicing, and protein subcellular localization of OsLpa1 in rice

“…It is yet to be revealed whether the high expression is related to biosynthesis of PA or other unknown molecules in these tissues. It is well-known that PA is accumulated in both aleurone layers and embryos (Raboy, 2009), andSato et al (2011) also showed that LOC_Os02g57400 had the highest expression level in rice Nipponbare embryos (7-42 DAF). However, the promoter::GUS transgenic plant assay showed a high level of OsLpa1 expression in the aleurone layers and to a lesser extent in the embryo (Figs.…”

The analysis of magnesium transport system from external solution to xylem in rice root

“…There are nine MRS2/MGT genes in rice (Gebert et al 2009). To date, the possibility that some of them were expressed preferentially in the roots has been derived from microarray experiments (Sato et al 2011a(Sato et al , 2011b. Characterization of MRS2/MGT and its functions in rice may be worthy of further examination.…”

Caracterização do relógio biológico e seu impacto no metabolismo da cana-de-açúcar

“…Embora haja trabalhos realizados em laboratório com condições bastante próximas às naturais (Filichkin et al, 2011), os estudos realizados com Arabidopsis (Richards et al, 2012) e arroz (Izawa et al, 2011;Sato et al, 2011;Nagano et al, 2012) (Izawa et al, 2011).…”

“…Experimentos conduzidos em campo com arroz focados na análise do relógio biológico mostraram que o relógio biológico não 41 só é ativo, mas atua, de fato, conjuntamente com as variações ambientais (Izawa et al, 2011;Sato et al, 2011;Nagano et al, 2012). O padrão de expressão dos transcritos de arroz associados às vias reguladas pelo relógio biológico é bastante influenciado por componentes ambientais, como temperatura e luz solar (Nagano et al, 2012).…”

“…De fato, experimentos em arroz conduzidos em campo mostram que o relógio biológico é responsivo a estas mudanças ambientais e responde a elas através de variações no conjunto dos genes cuja expressão rítmica é regulada por ele (Izawa et al, 2011;Nagano et al, 2012). Análises globais de transcriptomas de plantas cultivadas em campo sugerem que a expressão gênica responde às variações ambientais em escalas diárias e sazonais (Sato et al, 2011;Richards et al, 2012 …”