Epigenetic modifications play important roles in plant and animal development. DNA methylation impacts the transposable element (TE) silencing, gene imprinting and expression regulation. Through a genome-wide analysis, DNA methylation peaks were characterized and mapped in maize embryo and endosperm genome, respectively. Distinct methylation level was observed across maize embryo and endosperm. The maize embryo genome contained more DNA methylation than endosperm. Totally, 985,478 CG islands (CGIs) were identified and most of them were unmethylated. More CGI shores were methylated than CGIs in maize suggested that DNA methylation level was not positively correlated with CpG density. The promoter sequence and transcriptional termination region (TTR) were more methylated than the gene body (intron and exon) region based on peak number and methylated depth. Result showed that 99% TEs were methylated in maize embryo, but a large portion of them (34.8%) were not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated region between embryo and endosperm are CGI shores. Our results indicated that DNA methylation is associated with both gene silencing and gene activation in maize. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 41.5% imprinting genes were similarly methylated and 58.5% imprinting genes were differentially methylated between embryo and endosperm. Methylation level was associated with allelic silencing of only a small number of imprinting genes. The expression of maize DEMETER-like (DME-like) gene and MBD101 gene (MBD4 homolog) were higher in endosperm than in embryo. These two genes may be associated with distinct methylation levels across maize embryo and endosperm. Through MeDIP-seq we systematically analyzed the methylomes of maize embryo and endosperm and results indicated that the global methylation status of embryo was more than that of the endosperm. Differences could be observed at the total number of methylation peaks, DMRs and specific methylated genes which were tightly associated with development of embryo and endosperm. Our results also revealed that many DNA methylation regions didn’t affect transcription of the corresponding genes.

Background: MicroRNAs are key regulators of plant growth and development with important roles in environmental adaptation. The microRNAs from the halophyte species Thellungiella salsuginea (salt cress), which exhibits extreme salt stress tolerance, remain to be investigated. The sequenced genome of T. salsuginea and the availability of high-throughput sequencing technology enabled us to discover the conserved and novel miRNAs in this plant species. It is interesting to identify the microRNAs from T. salsuginea genome wide and study their roles in salt stress response. Results: In this study, two T. salsuginea small RNA libraries were constructed and sequenced using Solexa technology. We identified 109 miRNAs that had previously been reported in other plant species. A total of 137 novel miRNA candidates were identified, among which the miR* sequence of 26 miRNAs was detected. In addition, 143 and 425 target mRNAs were predicted for the previously identified and Thellungiella-specific miRNAs, respectively. A quarter of these putative targets encode transcription factors. Furthermore, numerous signaling factor encoding genes, defense-related genes, and transporter encoding genes were amongst the identified targets, some of which were shown to be important for salt tolerance. Cleavage sites of seven target genes were validated by 5’ RACE, and some of the miRNAs were confirmed by qRT-PCR analysis. The expression levels of 26 known miRNAs in the roots and leaves of plants subjected to NaCl treatment were determined by Affymetrix microarray analysis. The expression of most tested miRNA families was up- or down-regulated upon NaCl treatment. Differential response patterns between the leaves and roots were observed for these miRNAs. Conclusions: Our results indicated that diverse set of miRNAs of T. salsuginea were responsive to salt stress and could play an important role in the salt stress response.

Background: After the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried in soil. It is interesting to study the mechanisms of gynophore development and pod formation in peanut. Results: In this study, transcriptome analysis of peanut gynophore was performed using Illumina HiSeq™ 2000 to understand the mechanisms of geocarpy. More than 13 million short sequences were assembled into 72527 unigenes with average size of 394 bp. A large number of genes that were not identified previously in peanut EST projects were identified in this study, including most genes involved in plant circadian rhythm, intra-cellular transportation, plant spliceosome, eukaryotes basal transcription factors, genes encoding ribosomal proteins, brassinosteriod biosynthesis, light-harvesting chlorophyll protein complex, phenylpropanoid biosynthesis and TCA cycle. RNA-seq based gene expression profiling results showed that before and after gynophore soil penetration, the transcriptional level of a large number of genes changed significantly. Genes encoding key enzymes for hormone metabolism, signaling, photosynthesis, light signaling, cell division and growth, carbon and nitrogen metabolism as well as genes involved in stress responses were high lighted. Conclusions: Transcriptome analysis of peanut gynophore generated a large number of unigenes which provide useful information for gene cloning and expression study. Digital gene expression study suggested that gynophores experience global changes and reprogram from light to dark grown condition to resume embryo and fruit development.

Salt stress could inhibit the growth and development of crops and negatively affect yield and quality. The objective of this study was to investigate the physiological responses of different asparagus cultivars to salt stress. Twenty days old seedlings ofasalt-tolerant Apollo andasalt-sensitive cultivar JL1 were subjected to 0 (CK) and120 mM NaCl stress for 20 d. Their changes in growth, ion contents, antioxidant enzyme activities and gene expression were analyzed. Salt stress significantly inhibited the growth of both cultivars, and JL1 showed a greater decrease than Apollo. The root development of Apollo was promoted by 120 mM NaCl treatment. The Na⁺ content in roots, stems, and leaves of both cultivars was increased under salt stress, while K⁺ content and K⁺/Na⁺ decreased. The salt-tolerant cultivar Apollo showed less extent of increase in Na⁺ and decrease in K⁺ content and kept a relatively high K⁺/Na⁺ ratio to compare with JL1. The contents of proline, soluble sugar and protein increased in Apollo, while thesesubstances changed differently in JL1 under salt stress. Activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were gradually increased under salt stress in Apollo, while the corresponding enzyme activities in JL1 were decreased at the late stage of salt stress. The expression of SOD, POD, and CAT genes of both cultivars changed in a similar way to the enzyme activities. Malondialdehyde (MDA) content was increased slightly in Apollo, while increased significantly in JL1. At the late stage of salt stress, Apollomaintained a relatively high K⁺/Na⁺, osmotic adjustment ability and antioxidant defense capability, and therefore exhibited higher tolerance to salt stress than that of JL1.

Peanut is one of the most important oil crops in the world, the growth and productivity of which are severely affected by salt stress. 24-epibrassinolide (EBL) plays an important role in stress resistances. However, the roles of exogenous EBL on the salt tolerance of peanut remain unclear. In this study, peanut seedlings treated with 150 mM NaCl and with or without EBL spray were performed to investigate the roles of EBL on salt resistance. Under 150 mM NaCl conditions, foliar application of 0.1 µM EBL increased the activity of catalase and thereby could eliminate reactive oxygen species (ROS). Similarly, EBL application promoted the accumulation of proline and soluble sugar, thus maintaining osmotic balance. Furthermore, foliar EBL spray enhanced the total chlorophyll content and high photosynthesis capacity. Transcriptome analysis showed that under NaCl stress, EBL treatment up-regulated expression levels of genes encoding peroxisomal nicotinamide adenine dinucleotide carrier (PMP34), probable sucrose-phosphate synthase 2 (SPS2) beta-fructofuranosidase (BFRUCT1) and Na⁺/H⁺ antiporters (NHX7 and NHX8), while down-regulated proline dehydrogenase 2 (PRODH). These findings provide valuable resources for salt resistance study in peanut and lay the foundation for using BR to enhance salt tolerance during peanut production.