Rice Expression Atlas In Reproductive Development

Abstract

Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. A decrease in expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes which appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several cyclin-dependent kinases (CDKs), cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the most extensive and most comprehensive data set available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

“…We subsequently focused our analysis on microarraybased transcriptomic data from three prior studies that are most similar to our work (Ma et al, 2008;Fujita et al, 2010;Dong et al, 2013). We found that the rice transcriptome showed a reasonable number (338) of upregulated genes at meiotic anthers, a stage similar to F. vesca stage 9 anthers, yet we could not detect an enrichment of FBX genes among up-regulated genes in rice meiotic anthers (Supplemental Fig.…”

“…Developmental transcriptomic profiling of anther development was previously reported in Brassica rapa (Dong et al, 2013), rice (Fujita et al, 2010), and maize (Zea mays; Ma et al, 2008), all of which employed microarrays. We applied the same statistical standard using one-way ANOVA analysis in MultiExperiment Viewer (MeV; P value , 0.001) and detected only three up-regulated genes in the F2 stage of B. rapa whole flower bud collection, 87 up-regulated genes in the Q stage of maize anther collection, and 458 up-regulated probes in M2 and M3 stage rice anthers (see "Materials and Methods").…”

“…Transcriptomic studies have been conducted in pollen, sperm, and anthers in diverse plant species, including Arabidopsis, rice, B. rapa, maize, and cotton (Gossypium hirsutum; Honys and Twell, 2004;Ma et al, 2007Ma et al, , 2008Ma et al, , 2012Chen et al, 2010;Fujita et al, 2010;Deveshwar et al, 2011;Yang et al, 2011;Dong et al, 2013;Wuest et al, 2013). While some studies were focused on tapetum and male gametophytes, others compared anthers of male sterile mutants with anthers of the wild type.…”

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

“…Such a loading barrier would help maintain the separation of H3 nucleosome blocks from CENH3 nucleosome blocks. We analyzed the expression patterns of all rice chromosome 8 genes based on the microarraybased gene expression data that were compiled from 32 stages/ organs of rice reproductive development using a total of 95 microarray hybridizations (Fujita et al, 2010). Expression data were found for eight Cen8 genes.…”

Induction of Male-Sterility by Controlling of Gibberellin Biosynthesis in Rice (Oryza sativa)

“…Microarray analyses of the four stages (pre-meiotic, meiotic, single celled anther and trinucleate pollen) of anther development identified 1,000 genes specifically expressed in anther (Deveshwar et al 2011). In a similar study by Fujita et al (2010), the stages of rice reproductive development were dissected and gene expression levels were determined using microarray technology. The 2,593 probe sets were identified on developing anther, whereas only a few were detected in other reproductive stages like fertilization and embryonic stages.…”