Transcriptome analysis during seed germination of elite Chinese bread wheat cultivar Jimai 20

Abstract

BackgroundWheat seed germination directly affects wheat yield and quality. Although transcriptome and proteome analyses during seed germination have been reported in some crop plant species, dynamic transcriptome characterization during wheat seed germination has not been conducted. We performed the first comprehensive dynamic transcriptome analysis during different seed germination stages of elite Chinese bread wheat cultivar Jimai 20 using the Affymetrix Wheat Genome Array.ResultsA total of 61,703 probe sets representing 51,411 transcripts were identified during the five seed germination stages of Jimai 20, of which 2,825 differential expression probe sets corresponding to 2,646 transcripts with different functions were declared by ANOVA and a randomized variance model. The seed germination process included a rapid initial uptake phase (0–12 hours after imbibition [HAI]), a plateau phase (12–24 HAI), and a further water uptake phase (24–48 HAI), corresponding to switches from the degradation of small-molecule sucrose to the metabolism of three major nutrients and to photosynthesis. Hierarchical cluster and MapMan analyses revealed changes in several significant metabolism pathways during seed germination as well as related functional groups. The signal pathway networks constructed with KEGG showed three important genes encoding the phosphofructokinase family protein, with fructose-1, 6-bisphosphatase, and UTP-glucose-1-phosphate uridylyltransferase located at the center, indicating their pivotal roles in the glycolytic pathway, gluconeogenesis, and glycogenesis, respectively. Several significant pathways were selected to establish a metabolic pathway network according to their degree value, which allowed us to find the pathways vital to seed germination. Furthermore, 51 genes involved in transport, signaling pathway, development, lipid metabolism, defense response, nitrogen metabolism, and transcription regulation were analyzed by gene co-expression network with a k-core algorithm to determine which play pivotal roles in germination. Twenty-three meaningful genes were found, and quantitative RT-PCR analysis validated the expression patterns of 12 significant genes.ConclusionsWheat seed germination comprises three distinct phases and includes complicated regulation networks involving a large number of genes. These genes belong to many functional groups, and their co-regulations guarantee regular germination. Our results provide new insight into metabolic changes during seed germination and interactions between some significant genes.

Transcriptomic changes during tuber dormancy release process revealed by RNA sequencing in potato

“…As a dynamic process, dormancy release impacted numerous physiological processes including carbohydrate metabolism, protein metabolism, lipid metabolism, transport process, phytohormone metabolism, stress response and redox regulation, cell organization, development, second metabolism and cell wall metabolism, these common metabolic processes involved in plant seeds dormancy release were confirmed in earlier publications (Pawłowski, 2007(Pawłowski, , 2010Sreenivasulu et al, 2008;He et al, 2011;Yu et al, 2014). Therefore, the differentially expressed genes identified by RNA-seq during tuber dormancy release could be discussed with other plant models.…”

Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

“…These arrays can be customized to contain probes that specifically differentiate transcripts from different subgenomes. The Affymetrix GeneChip Wheat Genome Array (Affymetrix, USA) is commercially available for verifying wheat gene expression, and has been used for independent studies such as low temperature tolerance gene models (LaudenciaChingcuanco et al, 2011), wheat and rust interactions (Coram et al, 2008), and transcriptome analysis during seed germination (Yu et al, 2014). However, rye chromatin 2RL has been shown to exhibit normal homoeologous relationships with the long arm of wheat chromosome 2B (2BL) (Naranjo and Fernandez-Rueda, 1991;Devos et al, 1995), suggesting that the rye genome is sufficiently similar to that of wheat to permit crosshybridization.…”

Sexual and asexual reproductive aspects of Leontochir ovallei, a rare and endangered geophyte of the Atacama Desert

“…The increase in germination due to exogenous aeration might indicate that L. ovallei seeds exhibit embryo dormancy as well as physical dormancy, which has been proposed to occur in the seeds of some species of the Alstroemeriaceae family [18]. Oxygen activates the oxidation of starch, lipids and proteins and stimulates the mobilization of several proteins that provide energy to sustain germination and embryo emergence and development [47][48][49]. L. ovallei appears to be a species whose seeds exhibit a high oxygen requirement.…”