A novel long noncoding RNA CIL1 enhances cold stress tolerance in Arabidopsis.

With the intensification of global warming, extreme weather events have occurred more frequently, among which cold stress has become one of the major environmental factors that restrict global crop yield and production. Multiple long noncoding RNAs (lncRNAs) have been predicted or recognized in the plant response to cold stress, however, the molecular biological functions of most of these RNAs are still poorly understood. Here, we identified a novel lncRNA, COLD INDUCED lncRNA 1 (CIL1), as a positive regulator of the plant response to cold stress in Arabidopsis. CIL1 was significantly induced when the plant was exposed to cold stress. Moreover, knockdown mutants showed more sensitivity to cold stress than the wild type did, accompanied by an increased content of endogenous ROS (reactive oxygen species) and reduced osmoregulatory substances. Genome-wide transcriptome analysis indicated that 256 genes were downregulated and 34 genes were upregulated in cil1 mutants under cold stress, which were mainly involved in hormone signal transduction, ROS homeostasis and glucose metabolism. Our study implies that CIL1 has a positive effect on the plant response to cold stress by regulating the expression of multiple stress-related genes during the seedling stage.

QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study.

Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.

Fine-Tuning of the Grain Size by Alternative Splicing of GS3 in Rice.

Grain size is subtly regulated by multiple signaling pathways in rice. Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level. However, to our knowledge, the molecular mechanism underlying grain size regulation by alternative splicing is largely unknown. GS3, the first identified QTL for grain size in rice, is regulated at the transcriptional and post-translational level. In this study, we identified that GS3 is subject to alternative splicing. GS3.1 and GS3.2, two dominant isoforms, accounts for about 50% and 40% of total transcripts, respectively. GS3.1 encodes the full-length protein, while GS3.2 generated a truncated proteins only containing OSR domain due to a 14 bp intronic sequence retention. Genetic analysis revealed that GS3.1 overexpressors decreased grain size, but GS3.2 showed no significant effect on grain size. Furthermore, we demonstrated that GS3.2 disrupts GS3.1 signaling by competitive occupation of RGB1. Therefore, we draw a conclusion that the alternative splicing of GS3 decreases the amount of GS3.1 and GS3.2 disrupts the GS3.1 signaling to inhibit the negative effects of GS3.1 to fine-tune grain size. Moreover, the mechanism is conserved in cereals rather than in Cruciferae, which is associated with its effects on grain size. The results provide a novel, conserved and important mechanism underlying grain size regulation at the post-transcriptional level in cereals.

Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape (Brassica napus L.).

Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level, which increases the transcriptomic diversity. Oilseed rape (Brassica napus L.), one of the main oil crops worldwide, is prone to secondary dormancy. However, how alternative splicing landscape of oilseed rape seed changes in response to secondary dormancy is unknown. Here, we analyzed twelve RNA-seq libraries from varieties "Huaiyou-SSD-V1" and "Huaiyou-WSD-H2" which exhibited high (> 95%) and low (< 5%) secondary dormancy potential, respectively, and demonstrated that alternative splicing changes led to a significant increase with the diversity of the transcripts in response to secondary dormancy induction via polyethylene glycol 6000 (PEG6000) treatment. Among the four basic alternative splicing types, intron retention dominates, and exon skipping shows the rarest frequency. A total of 8% of expressed genes had two or more transcripts after PEG treatment. Further analysis revealed that global isoform expression percentage variations in alternative splicing in differently expressed genes (DEGs) is more than three times as much as those in non-DEGs, suggesting alternative splicing change is associated with the transcriptional activity change in response to secondary dormancy induction. Eventually, 342 differently spliced genes (DSGs) associated with secondary dormancy were identified, five of which were validated by RT-PCR. The number of the overlapped genes between DSGs and DEGs associated with secondary dormancy was much less than that of either DSGs or DEGs, suggesting that DSGs and DEGs may independently regulates secondary dormancy. Functional annotation analysis of DSGs revealed that spliceosome components are overrepresented among the DSGs, including small nuclear ribonucleoprotein particles (snRNPs), serine/arginine-rich (SR) proteins, and other splicing factors. Thus, it is proposed that the spliceosome components could be exploited to reduce secondary dormancy potential in oilseed rape. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01314-8.

Normal, novel or none: versatile regulation from alternative splicing.

Pre-mRNA splicing is a vital step in the posttranscriptional regulation of gene expression. Splicing is catalyzed by the spliceosome, a multidalton RNA-protein complex, through two successive transesterifications to yield mature mRNAs. In Arabidopsis, more than 61% of all transcripts from intron-containing genes are alternatively spliced, thereby resulting in transcriptome and subsequent proteome diversities for cellular processes. Moreover, it is estimated that more alternative splicing (AS) events induced by adverse stimuli occur to confer stress tolerance. Recently, increasing AS variants encoding normal or novel proteins, or degraded by nonsense-mediated decay (NMD) and their corresponding splicing factors or regulators acting at the posttranscriptional level have been functionally characterized. This review comprehensively summarizes and highlights the advances in our understanding of the biological functions and underlying mechanisms of AS events and their regulators in Arabidopsis and provides prospects for further research on AS in crops.

Three-Dimensional Superlithiophilic Interphase for Dendrite-Free Lithium Metal Anodes.

Lithium metal is among the most promising anode candidates of high-energy-density batteries. However, the formed dendrites result in low Coulombic efficiency and serious security issues. Designing lithiophilic sites is one of the effective strategies to control Li deposition. Herein, we propose a three-dimensional lithiophilic N-rich carbon nanofiber with the decoration of ZnO granules as a protective layer for a dendrite-free lithium metal anode. Theoretical evaluation indicates the synergistic effects of lithiophilic ZnO and N-containing functional groups enhance lithium adsorption and trigger uniform deposition. With the lithiophilic interlayer, the lithium deposition overpotential is only ∼20, 50, and 74 mV at 1, 3, and 6 mA cm-2, respectively, which are much lower than those without the functional interlayer (∼55, 130, and 238 mV). The average Coulombic efficiency of lithium stripping and plating is up to ∼97.4% (94.0% for that without the interlayer) at 0.5 mA cm-2. Meanwhile, the Li|LiFePO4 full cell with the superlithiophilic interlayer demonstrates a high capacity retention rate of 99.6% (91.0% for that without the interlayer) over 200 cycles at 1 C. The introduction of the lithiophilic interphase could provide a convenient strategy and guidance to design the configuration for the practical application of Li metal batteries.

A transcriptome analysis reveals a role for the indole GLS-linked auxin biosynthesis in secondary dormancy in rapeseed (Brassica napus L.).

BACKGROUND: Brassica napus L. has little or no primary dormancy, but exhibits great variation in secondary dormancy. Secondary dormancy potential in oilseed rape can lead to the emergence of volunteer plants that cause genetic contamination, reduced quality and biosafety issues. However, the mechanisms underlying secondary dormancy are poorly understood. In this study, cultivars Huaiyou-WSD-H2 (H) and Huaiyou-SSD-V1 (V), which exhibit low (approximately 5%) and high (approximately 95%) secondary dormancy rate, respectively, were identified. Four samples, before (Hb and Vb) and after (Ha and Va) secondary dormancy induction by polyethylene glycol (PEG), were collected to identify the candidate genes involved in secondary dormancy via comparative transcriptome profile analysis. RESULTS: A total of 998 differentially expressed genes (DEGs), which are mainly involved in secondary metabolism, transcriptional regulation, protein modification and signaling pathways, were then detected. Among these DEGs, the expression levels of those involved in the sulfur-rich indole glucosinolate (GLS)-linked auxin biosynthesis pathway were markedly upregulated in the dormant seeds (Va), which were validated by qRT-PCR and subsequently confirmed via detection of altered concentrations of indole-3-acetic acid (IAA), IAA conjugates and precursors. Furthermore, exogenous IAA applications to cultivar H enhanced secondary dormancy. CONCLUSION: This study first (to our knowledge) elucidated that indole GLS-linked auxin biosynthesis is enhanced during secondary dormancy induced by PEG, which provides valuable information concerning secondary dormancy and expands the current understanding of the role of auxin in rapeseed.

The relation of microsatellite instability to expression of hTERT in human gastric carcinoma.

OBJECTIVE: To investigate the role of microsatellite instability (MSI) in the pathogenesis of gastric carcinoma and its relationship with the expression of hTERT gene. METHODS: 75 cases of gastric carcinoma and paired normal control tissues were included in this study. MSI of BAT-25, BAT-26, D5S346, D17S250 and D2S1235 were detected by PCR, native polyacrylamide gel electrophoresis, and silver staining while the expression of hTERT was localized by immunohistochemistry at the same time. RESULTS: MSI positive rates of BAT-25, BAT-26, D5S346, D17S250 and D2S123 were 14.7%, 12.00%, 26.67%, 16% and 21.3%. MSI was obviously related with lymph node metastasis and pathologic stages respectively (P<0.05), but not with age, gender, histologic type, or infiltration depth (P>0.05). hTERT was not expressed in normal gastric mucosa, but in intestinal metaplasia, dysplasia, and gastric carcinoma. The positive rate of hTERT was 76% (57/75) in 75 cases of gastric carcinoma tissues. The expression of hTERT was obviously related to histological type (P<0.05), but not to age, gender, lymph node metastasis, depth of invasion, or staging, respectively (P>0.05). The positive rate was higher in poorly differentiated cases than in moderately and well differentiated cases (P<0.05). MSI accounted for 28.1% of 57 hTERT positive cases while MSI accounted for 72.2% in 18 hTERT negative cases. Spearman rank correlation analysis showed that MSI was negatively related to hTERT expression (r=0.387, P=0.001). CONCLUSION: MSI may play an important role in the pathogenesis and progression of gastric carcinoma by affecting the expression of TERT gene.

[The mixed major gene plus polygenes inheritance for female fertility in wheat (Triticum aestivum L.)].

Three sets of data for the P1, P2, F1, and F2 populations derived from three crosses between the normal fertility wheat (Triticum aestivum L.) cultivars with different ecotypes and the female sterile line (XND126) were used to investigate the inheritance of female fertility in wheat using mixed major gene plus polygenes inheritance model in 2005 and 2006. The results from the joint segregation analysis of the four generations showed that female fertility in wheat is controlled by two major genes plus polygenes, and the interaction between the two major genes is also detected.

[Locating maize male sterility gene induced by space flight using microsatellite markers].

Two F2 populations with different kinds of spike derived from maize male sterility materials RP(3)195 (A) x S37 (inbred line) ,which had been sib-bred for many generations,were used for sterility analysis and gene location. There were 138 and 247 plants in the two F2 populations respectively. Among the 326 pairs of microsatellite primers selected,56 were found polymorphic. Linkage analysis of F2 populations with the 56 pairs of primers showed that microsatellite markers bnlg197 and umc1012 were linked with the male sterility gene. The genetic distance between marker bnlgl97 and the male sterility gene in the two different F2 populations were 7 cM and 14.5 cM respectively. The genetic distance between marker umc1012 and the male sterility gene in the 138 plants was 28.5 cM. Thus the male sterility gene was located on chromosome 3L.