Background: The productivity of the medicinally significant perennial herb Rehmannia glutinosa is severely affected after the first year of cropping. While there is some information available describing the physiological and environmental causes of this yield decline, there is as yet no data regarding the changes in gene expression which occur when the species is continuously cropped. Results: Using a massively parallel (Solexa) DNA sequencing platform, it was possible to identify and quantify the abundance of a large number of R. glutinosa miRNAs. We contrasted the miRNA content of first year crop plants with that of second year crop ones, and were able to show that of 89 conserved (belonging to 25 families) and six novel miRNAs (six families), 29 of the former and three of the latter were differentially expressed. The three novel miRNAs were predicted to target seven genes, and the 29 conserved ones 308 genes. The potential targets of 32 of these differentially expressed miRNAs involved in the main transcription regulation, plant development and signal transduction. A functional analysis of the differentially expressed miRNAs suggested that several of the proposed targets could be directly or indirectly responsible for the development of the tuberous root. Conclusion: We have compared differential miRNAs expression in the first year crop (FP) R. glutinosa plants and second year crop (SP) ones. The outcome identifies some potential leads for understanding the molecular basis of the processes underlying the difficulty of maintaining the productivity of continuously cropped R. glutinosa.

During asexual reproduction the embryogenic callus can differentiate into a new plantlet, offering great potential for fostering in vitro culture efficiency in plants. The immature embryos (IMEs) of wheat (Triticum aestivum L.) are more easily able to generate embryogenic callus than mature embryos (MEs). To understand the molecular process of embryogenic callus formation in wheat, de novo transcriptome sequencing was used to generate transcriptome sequences from calli derived from IMEs and MEs after 3d, 6d, or 15d of culture (DC). In total, 155 million high quality paired-end reads were obtained from the 6 cDNA libraries. Our de novo assembly generated 142,221 unigenes, of which 59,976 (42.17%) were annotated with a significant Blastx against nr, Pfam, Swissprot, KOG, KEGG, GO and COG/KOG databases. Comparative transcriptome analysis indicated that a total of 5194 differentially expressed genes (DEGs) were identified in the comparisons of IME vs. ME at the three stages, including 3181, 2085 and 1468 DEGs at 3, 6 and 15 DC, respectively. Of them, 283 overlapped in all the three comparisons. Furthermore, 4731 DEGs were identified in the comparisons between stages in IMEs and MEs. Functional analysis revealed that 271transcription factor (TF) genes (10 overlapped in all 3 comparisons of IME vs. ME) and 346 somatic embryogenesis related genes (SSEGs; 35 overlapped in all 3 comparisons of IME vs. ME) were differentially expressed in at least one comparison of IME vs. ME. In addition, of the 283 overlapped DEGs in the 3 comparisons of IME vs. ME, excluding the SSEGs and TFs, 39 possessed a higher rate of involvement in biological processes relating to response to stimuli, in multi-organism processes, reproductive processes and reproduction. Furthermore, 7 were simultaneously differentially expressed in the 2 comparisons between the stages in IMEs, but not MEs, suggesting that they may be related to embryogenic callus formation. The expression levels of genes, which were validated by qRT-PCR, showed a high correlation with the RNA-seq value. This study provides new insights into the role of the transcriptome in embryogenic callus formation in wheat, and will serve as a valuable resource for further studies addressing embryogenic callus formation in plants.

Seed vigor encompasses the germination capacity, ability to form seedlings, and potential for production of seeds, and during storage, the deterioration of seed vigor is an inevitable biological process. However, changes in the microflora of the seed surface and seed vigor under different storage conditions have rarely been studied. In this study, the changes in fungal species on the surface and embryo and their effects of the hybrid maize cultivar Zhengdan958 seeds under different storage conditions were studied. The seed vigor was evaluated according to standard germination, MDA content, respiration rate, ATP content and the integrity of the ATP synthase subunits of seed embryos, with the aim of providing a basis for revealing the molecular mechanism of seed deterioration. The results revealed that at 33% relative humidity (RH), the dominant microflora constituent on the seed surface was Fusarium sp. In the seed embryo, the dominant microflora constituent was Aspergillus fumigatus. At 91% RH, the dominant microflora constituent on the seed surface was Aspergillus Jensen. In the seed embryo, the dominant microflora constituent was Penicillium sp. With the increased RH in the storage environment, the seed germination rate decreased by 86.67%. The respiration rate decreased by 0.04 mg·g^-1·h^-1 after 24 h imbibition. The seed embryo was hardly stained via TTC. The MDA content increased by 0.99 nmol·g^-1, and the ATP content decreased by 0.33 μmol·g^-1 after 24 h imbibition. The mRNA integrity of ATP synthase α, β, γ and δ subunits, except for ε subunit, in the seed embryo decreased to different degrees. These findings suggest that a change in the microflora is one of the most important factors causing a decrease in or total loss of seed vigor.

In this study, hybrid maize (Zea mays L.) cultivar ‘Zhengdan 958' seeds were used as materials to reveal the mechanism of seed aging. After artificial aging treatment (45℃, 100% relative humidity), the seed vigor, O2- production, ATP content, and ATP synthase activity of seed embryo were investigated, and the integrity of ATP synthase subunit mRNAs in seed embryo and different organs (scutellum, radicle, and plumule) was analyzed by the reverse transcription blocking and double-primer amplification method. The results showed that the germination rate and radicle growth rate of maize seeds decreased, the viability of embryo decreased and the respiration intensity of seeds decreased after artificial aging treatment. The O2- production rate in embryo reached the peak on the 3rd day of aging treatment, and then decreased, the O2- production rate and content in radicle and plumule increased significantly. The ATP content and ATP synthase activity in embryo decreased. The mRNA integrity of ATP synthase ε-subunit and γ-subunit increased first and then decreased. The mRNA integrity of δ-subunit did not change significantly. The mRNA integrity of α-subunit and β-subunit decreased continuously in artificial aging treatment. The damage degree of mRNA integrity of ATP synthase subunits in radicle and plumule was much greater than that in scutellum. These results revealed that the production and accumulation of ROS in radicle and plumule could lead to different degrees of damage to ATP synthase subunit mRNAs and the activity of ATP synthase and the content of ATP in embryo decreased, which resulted in the lack of energy supply during germination, and this maybe one of the major factors causing maize seed aging.