Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean.

Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.

Various potentially toxic element tolerances in different rice genotypes correlate with distinct physiological responses and alterations in DNA methylation.

Potentially toxic elements (PTEs) are harmful to plant growth and reduce crop productivity. In this work, we studied three rice genotypes (T-35, RZ-1, and RZ-2) to quantify the diverse PTE effects and tolerances by examining morphology, physiology, and DNA methylation patterns. Morphological results showed that T-35 exhibits the highest tolerance to all studied PTE stressors (Cu, Cd, Cr). Physiological responses under PTE stresses confirmed earlier findings, where T-35 showed a higher potassium (K+) content and more peroxidase (POD) accumulation in the roots than the other two rice genotypes. The differences in PTE tolerance levels observed among the three rice genotypes were also associated with variations in the heavy metal transportation (HMT) gene expression level. Moreover, methylation-sensitive blotting analysis of the selected genes showed that the DNA methylation changes occurring due to PTE treatments are mainly CHG hypomethylation in T-35 but hypermethylation in RZ-1 and RZ-2. Our results demonstrate a tight relationship among physiological response, expression levels of the HMT genes, and DNA methylation pattern under PTEs stresses. It is also indicated that plants use generic mechanisms to tolerate stresses; however, different genotypes employ different combinations of such tactics to confer tolerance, which results in diverse PTE stress tolerances. These findings shed light on the PTE stresses tolerance mechanism and help direct future breeding activities in rice.

Genome-wide locus-specific DNA methylation repatterning may facilitate rapid evolution of mercury resistance in rice.

BACKGROUND: Albeit a relatively stable epigenetic modification, DNA methylation in plants can be repatterned and play important roles in response to biotic and abiotic stresses. However, whether DNA methylation dynamics may contribute to cope with mercury (Hg) stress in plants remains to be fully investigated. OBJECTIVE: To probe the potential roles of DNA methylation dynamics in coping with Hg stress in rice. METHODS: Whole-genome bisulfite sequencing was used to profile the DNA methylation patterns of a rice Hg-resistant line (RHg) selected from a heterozygous mutant of the DNA methyltransferase 1 gene (OsMET1+/-), together with its Hg-sensitive wild-type plants of cv. Nipponbare (Nip) under both normal and Hg stress conditions. RESULTS: Genome-wide locus-specific differential methylation regions (DMRs) were detected between RHg and Nip under normal condition, the predominant DMR patterns were CG hypo-DMRs, CHG hypo-DMRs and CHH hyper-DMRs. In both lines, more hyper- than hypo-DMRs were detected at all three sequence contexts (CG, CHG and CHH) under Hg stress relative to normal condition. Comparison of DNA methylation changes in the two lines under Hg stress indicates that RHg had a more dynamic methylome than the control (Nip). Original DMRs in RHg trended to transform to opposite status (from hyper- to hypo- or vice versa) under Hg stress condition. Gene ontology analysis revealed that Hg-resistance-related DMGs were enriched in diverse biological processes. CONCLUSIONS: Our results suggest genome-wide locus-specific DNA methylation repatterning can facilitate rapid acquisition of Hg resistance in rice.

SET DOMAIN GROUP 721 protein functions in saline-alkaline stress tolerance in the model rice variety Kitaake.

To isolate the genetic locus responsible for saline-alkaline stress tolerance, we developed a high-throughput activation tagging-based T-DNA insertion mutagenesis method using the model rice (Oryza sativa L.) variety Kitaake. One of the activation-tagged insertion lines, activation tagging 7 (AC7), showed increased tolerance to saline-alkaline stress. This phenotype resulted from the overexpression of a gene that encodes a SET DOMAIN GROUP 721 protein with H3K4 methyltransferase activity. Transgenic plants overexpressing OsSDG721 showed saline-alkaline stress-tolerant phenotypes, along with increased leaf angle, advanced heading and ripening dates. By contrast, ossdg721 loss-of-function mutants showed increased sensitivity to saline-alkaline stress characterized by decreased survival rates and reduction in plant height, grain size, grain weight and leaf angle. RNA sequencing (RNA-seq) analysis of wild-type Kitaake and ossdg721 mutants indicated that OsSDG721 positively regulates the expression level of HIGH-AFFINITY POTASSIUM (K+ ) TRANSPORTER1;5 (OsHKT1;5), which encodes a Na+ -selective transporter that maintains K+ /Na+ homeostasis under salt stress. Furthermore, we showed that OsSDG721 binds to and deposits the H3K4me3 mark in the promoter and coding region of OsHKT1;5, thereby upregulating OsHKT1;5 expression under saline-alkaline stress. Overall, by generating Kitaake activation-tagging pools, we established that the H3K4 methyltransferase OsSDG721 enhances saline-alkaline stress tolerance in rice.

JMJ17-WRKY40 and HY5-ABI5 modules regulate the expression of ABA-responsive genes in Arabidopsis.

Abscisic acid (ABA) plays a crucial role in the adaptation of young seedlings to environmental stresses. However, the role of epigenetic components and core transcriptional machineries in the effect of ABA on seed germination and seedling growth remain unclear. Here, we show that a histone 3 lysine 4 (H3K4) demethylase, JMJ17, regulates the expression of ABA-responsive genes during seed germination and seedling growth. Using comparative interactomics, WRKY40, a central transcriptional repressor in ABA signaling, was shown to interact with JMJ17. WRKY40 facilitates the recruitment of JMJ17 to the ABI5 chromatin, which removes gene activation marks (H3K4me3) from the ABI5 chromatin, thereby repressing its expression. Additionally, WRKY40 represses the transcriptional activation activity of HY5, which can activate ABI5 expression by directly binding to its promoter. An increase in ABA concentrations decreases the affinity of WRKY40 for the ABI5 promoter. Thus, WRKY40 and JMJ17 are released from the ABI5 chromatin, activating HY5. The accumulated ABI5 protein further shows heteromeric interaction with HY5, and thus synergistically activates its own expression. Our findings reveal a novel transcriptional switch, composed of JMJ17-WRKY40 and HY5-ABI5 modules, which regulates the ABA response during seed germination and seedling development in Arabidopsis.

Chromatin Remodeling Protein ZmCHB101 Regulates Nitrate-Responsive Gene Expression in Maize.

Nitrate is the main source of nitrogen for plants and an essential component of fertilizers. Rapid transcriptional activation of genes encoding the high-affinity nitrate transport system (HATS) is an important strategy that plants use to cope with nitrogen deficiency. However, the specific transcriptional machineries involved in this process and the detailed transcriptional regulatory mechanism of the core HATS remain poorly understood. ZmCHB101 is the core subunit of the SWI/SNF-type ATP-dependent chromatin remodeling complex in maize. RNA-interference transgenic plants (ZmCHB101-RNAi) display abaxially curling leaves and impaired tassel and cob development. Here, we demonstrate that ZmCHB101 plays a pivotal regulatory role in nitrate-responsive gene expression. ZmCHB101-RNAi lines showed accelerated root growth and increased biomass under low nitrate conditions. An RNA sequencing analysis revealed that ZmCHB101 regulates the expression of genes involved in nitrate transport, including ZmNRT2.1 and ZmNRT2.2. The NIN-like protein (NLP) of maize, ZmNLP3.1, recognized the consensus nitrate-responsive cis-elements (NREs) in the promoter regions of ZmNRT2.1 and ZmNRT2.2, and activated the transcription of these genes in response to nitrate. Intriguingly, well-positioned nucleosomes were detected at NREs in the ZmNRT2.1 and ZmNRT2.2 gene promoters, and nucleosome densities were lower in ZmCHB101-RNAi lines than in wild-type plants, both in the absence and presence of nitrate. The ZmCHB101 protein bound to NREs and was involved in the maintenance of nucleosome occupancies at these sites, which may impact the binding of ZmNLP3.1 to NREs in the absence of nitrate. However, in the presence of nitrate, the binding affinity of ZmCHB101 for NREs decreased dramatically, leading to reduced nucleosome density at NREs and consequently increased ZmNLP3.1 binding. Our results provide novel insights into the role of chromatin remodeling proteins in the regulation of nitrate-responsive gene expression in plants.

Transgenerational memory of gene expression changes induced by heavy metal stress in rice (Oryza sativa L.).

BACKGROUND: Heavy metal toxicity has become a major threat to sustainable crop production worldwide. Thus, considerable interest has been placed on deciphering the mechanisms that allow plants to combat heavy metal stress. Strategies to deal with heavy metals are largely focused on detoxification, transport and/or sequestration. The P1B subfamily of the Heavy Metal-transporting P-type ATPases (HMAs) was shown to play a crucial role in the uptake and translocation of heavy metals in plants. Here, we report the locus-specific expression changes in the rice HMA genes together with several low-copy cellular genes and transposable elements upon the heavy metal treatment and monitored the transgenerational inheritance of the altered expression states. We reveal that plants cope with heavy metal stress by making heritable changes in gene expression and further determined gene-specific responses to heavy metal stress. RESULTS: We found most HMA genes were upregulated in response to heavy metal stress, and furthermore found evidence of transgenerational memory via changes in gene regulation even after the removal of heavy metals. To explore whether DNA methylation was also altered in response to the heavy metal stress, we selected a Tos17 retrotransposon for bisulfite sequencing and studied its methylation state across three generations. We found the DNA methylation state of Tos17 was altered in response to the heavy metal stress and showed transgenerational inheritance. CONCLUSIONS: Collectively, the present study elucidates heritable changes in gene expression and DNA methylation in rice upon exposure to heavy metal stress and discusses implications of this knowledge in breeding for heavy metal tolerant crops.