Ploidy variation induces butterfly effect on chromatin topology in wheat.

Polyploidy is a prominent driver of plant diversification, accompanied with dramatic chromosomal rearrangement and epigenetic changes that affect gene expression. How chromatin interactions within and between subgenomes adapt to ploidy transition remains poorly understood. We generate open chromatin interaction maps for natural hexaploid wheat (AABBDD), extracted tetraploid wheat (AABB), diploid wheat progenitor Aegilops tauschii (DD) and resynthesized hexaploid wheat (RHW, AABBDD). Thousands of intra- and interchromosomal loops are de novo established or disappeared in AB subgenomes after separation of D subgenome, in which 37-95% of novel loops are lost again in RHW after merger of D genome. Interestingly, more than half of novel loops are formed by cascade reactions that are triggered by disruption of chromatin interaction between AB and D subgenomes. The interaction repressed genes in RHW relative to DD are expression suppressed, resulting in more balanced expression of the three homoeologs in RHW. The interaction levels of cascade anchors are decreased step-by-step. Leading single nucleotide polymorphisms of yield- and plant architecture-related quantitative trait locus are significantly enriched in cascade anchors. The expression of 116 genes interacted with these anchors are significantly correlated with the corresponding traits. Our findings reveal trans-regulation of intrachromosomal loops by interchromosomal interactions during genome merger and separation in polyploid species.

Dosage effect genes modulate grain development in synthesized Triticum durum-Haynaldia villosa allohexaploid.

Polyploidization in plants often leads to increased cell size and grain size, which may be affected by the increased genome dosage and transcription abundance. The synthesized Triticum durum (AABB)-Haynaldia villosa (VV) amphiploid (AABBVV) has significantly increased grain size, especially grain length, than the tetraploid and diploid parents. To investigate how polyploidization affects grain development at the transcriptional level, we perform transcriptome analysis using the immature seeds of T. durum, H. villosa, and the amphiploid. The dosage effect genes are contributed more by differentially expressed genes from genome V of H. villosa. The dosage effect genes overrepresent grain development-related genes. Interestingly, the vernalization gene TaVRN1 is among the positive dosage effect genes in the T. durum‒H. villosa and T. turgidum‒Ae. tauschii amphiploids. The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight. The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence, decreased cell size, grain size, and grain yield. These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development. The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improving wheat yield.

An RRM domain protein SOE suppresses transgene silencing in rice.

Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.

Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean.

Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.

Improving rice nitrogen-use efficiency by modulating a novel monouniquitination machinery for optimal root plasticity response to nitrogen.

Plant nitrogen (N)-use efficiency (NUE) is largely determined by the ability of root to take up external N sources, whose availability and distribution in turn trigger the modification of root system architecture (RSA) for N foraging. Therefore, improving N-responsive reshaping of RSA for optimal N absorption is a major target for developing crops with high NUE. In this study, we identified RNR10 (REGULATOR OF N-RESPONSIVE RSA ON CHROMOSOME 10) as the causal gene that underlies the significantly different root developmental plasticity in response to changes in N level exhibited by the indica (Xian) and japonica (Geng) subspecies of rice. RNR10 encodes an F-box protein that interacts with a negative regulator of auxin biosynthesis, DNR1 (DULL NITROGEN RESPONSE1). Interestingly, RNR10 monoubiquitinates DNR1 and inhibits its degradation, thus antagonizing auxin accumulation, which results in reduced root responsivity to N and nitrate (NO3-) uptake. Therefore, modulating the RNR10-DNR1-auxin module provides a novel strategy for coordinating a desirable RSA and enhanced N acquisition for future sustainable agriculture.

Intervention effect of Tuina pressing and kneading the Huantiao (GB30) acupoint on NF-κB p65 protein at spinal cord dorsal horn in sciatica rats / 中国骨伤

OBJECTIVE@#To observe the analgesic effect of Tuina by pressing and kneading the Huantiao (GB30) acupoint on rats with chronic constriction injury (CCI) and to explore the analgesic mechanism of Tuina on sciatica rats.@*METHODS@#Thirty-two SPF male SD rats weighing 180 to 220 g were randomly divided into fore groups:blank group (without any treatment), sham group (only exposed without sciatic nerve ligating), model group (sciatic nerve ligating) and Tuina group (manual intervention after lsciatic nerve ligating). The CCI model was prepared by ligating the right sciatic nerve of the rats, on the third day of modeling, the rats in the Tuina group were given pressing and kneading the Huantiao (GB30) point for 14 days, and the changes of paw withdrawal threshold(PWT), paw withdrawal latency(PWL) were measured before and on the 1st, 3rd, 7th, 10th, 14th and 17th days after modeling. The changes of sciatic functional index(SFI) were measured before and on the 1st and 17th day after modeling. The morphological changes of the sciatic nerve were observed by hematoxylin-eosin(HE) staining;and the differences in NF-κB protein expression in the right dorsal horn of the spinal cord of rats were detected.@*RESULTS@#Following modeling, there was no significant difference in PWT, PWL and SFI between the blank group and the sham group (P>0.05), but the PWT, PWL and SFI of the model group and the Tuina group decreased significantly (P<0.01). After manual intervention, the pain threshold of rats in Tuina group increased. On the 8th day of manual intervention (the 10th day after modeling), PWT in Tuina group increased significantly compared with that in model group (P<0.01). On the 5th day of manual intervention (the 7th day after modeling), the PWL of the massage group was significantly higher than that of the model group (P<0.01). The pain threshold of rats in Tuina group continued to rise with the continuous manipulation intervention. After 14 days of manipulative intervention, the sciatic nerve function index of rats in the Tuina group increased significantly(P<0.01). Compared with the blank group and sham group, the myelinated nerve fibers of sciatic nerve in the model group were disordered and the density of axons and myelin sheath was uneven. Compared with the model group, the nerve fibers of rats in the Tuina group were gradually continuous and the axons and myelin sheath were more uniform than those in the model group. Compared with the blank group and sham group, the expression of NF-κB protein in the right spinal dorsal horn of the model group was significantly increased(P<0.01). Compared with the model group, the expression of NF-κB protein in the right spinal dorsal horn of rats in Tuina group decreased significantly(P<0.01).@*CONCLUSION@#Pressing and kneading the Huantiao (GB30) point restores nerve fiber alignment;and improves the PWT、PWL and SFI in the CCI model by decreasing NF-κB p65 protein expression in the spinal dorsal horn. There fore, Tuina demmstrates an analgesic effect and improves the gait of rats with sciatica.

Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution.

BACKGROUND: Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat. The open chromatin enrichment and network Hi-C (OCEAN-C) is a powerful antibody-independent method to detect chromatin interactions between open chromatin regions throughout the genome. RESULTS: Here we generate open chromatin interaction maps for hexaploid wheat and its tetraploid and diploid relatives using OCEAN-C. The anchors of chromatin loops show high chromatin accessibility and are concomitant with several active histone modifications, with 67% of them interacting with multiple loci. Binding motifs of various transcription factors are significantly enriched in the hubs of open chromatin interactions (HOCIs). The genes linked by HOCIs represent higher expression level and lower coefficient expression variance than the genes linked by other loops, which suggests HOCIs may coordinate co-expression of linked genes. Thousands of interchromosomal loops are identified, while limited interchromosomal loops (0.4%) are identified between homoeologous genes in hexaploid wheat. Moreover, we find structure variations contribute to chromatin interaction divergence of homoeologs and chromatin topology changes between different wheat species. The genes with discrepant chromatin interactions show expression alteration in hexaploid wheat compared with its tetraploid and diploid relatives. CONCLUSIONS: Our results reveal open chromatin interactions in different wheat species, which provide new insights into the role of open chromatin interactions in gene expression during the evolution of polyploid wheat.

Correlative analysis of cervical curvature and atlantoaxial instability / 中国骨伤

OBJECTIVE@#To investigate the correlation between the changes of cervical curvature and atlantoaxial instability.@*METHODS@#The correlation between the changes of cervical curvature and atlantoaxial instability was retrospectively studied in 50 outpatients with abnormal cervical curvature (abnormal cervical curvature group) from January 2018 to December 2019. There were 24 males and 26 females in abnormal cervical curvature group, aged from 18 to 42 years old with an average of(30.62±5.83) years. And 53 patients with normal cervical curvature (normal cervical curvature group) during the same period were matched, including 23 males and 30 females, aged from 21 to 44 years with an average of(31.98±6.11) years. Cervical spine X-ray films of 103 patients were taken in lateral position and open mouth position. Cervical curvature and variance of bilateral lateral atlanto-dental space(VBLADS) were measured and recorded, Pearson correlation coefficient analysis was used to study the correlation between the changes of cervical curvature and atlantoaxial instability.@*RESULTS@#Atlantoaxial joint instability accounted for 39.6%(21/53) in normal cervical curvature group and 84.0%(42/50) in abnormal cervical curvature group. There was significant difference between two groups(P<0.01). VBLADS in abnormal cervical curvature group was (1.79±1.01) mm, which was significantly higher than that in normal cervical curvature group(0.55±0.75) mm(P<0.01). Pearson correlation coefficient analysis showed that the size of cervical curvature was negatively correlated with VBLADS.@*CONCLUSION@#Cervical curvature straightening and inverse arch are the cause of atlantoaxial instability, the smaller the cervical curvature, the more serious the atlantoaxial instability.

CD147 antibody specifically and effectively inhibits infection and cytokine storm of SARS-CoV-2 variants

SARS-CoV-2 and its variants are raging worldwide. Unfortunately, the global vaccination is not efficient enough to attain a vaccine-based herd-immunity and yet no special and effective drug is developed to contain the spread of the disease. Previously we have identified CD147 as a novel receptor for SARS-CoV-2 infection. Here, we demonstrated that CD147 antibody effectively inhibits infection and cytokine storm caused by SARS-CoV-2 variants. In CD147KO VeroE6 cells, infections of SARS-CoV-2, its variants (B.1.1.7, B.1.351) and pseudovirus mutants (B.1.1.7, B.1.351, B.1.525, B.1.526 (S477N), B.1.526 (E484K), P.1, P.2, B.1.617.1, B.1.617.2) were decreased. Meanwhile, CD147 antibody effectively blocked the entry of variants and pseudomutants in VeroE6 cells, and inhibited the expression of cytokines. A model of SARS-CoV-2-infected hCD147 transgenic mice was constructed, which recapitulated the features of exudative diffuse alveolar damage and dynamic immune responses of COVID-19. CD147 antibody could effectively clear the virus and alveolar exudation, resolving the pneumonia. We found the elevated level of cyclophilin A (CyPA) in plasma of severe/critical cases, and identified CyPA as the most important proinflammatory intermediate causing cytokine storm. Mechanistically, spike protein of SARS-CoV-2 bound to CD147 and initiated the JAK-STAT pathway, which induced expression of CyPA. CyPA reciprocally bound to CD147, triggered MAPK pathway and consequently mediated the expression of cytokine and chemokine. In conclusion, CD147 is a critical target for SARS-CoV-2 variants and CD147 antibody is a promising drug to control the new wave of COVID-19 epidemic.

Statins use and the prognosis of colorectal cancer: a meta-analysis.

BACKGROUND: Previous observational studies regarding the prognostic value of statin on colorectal cancer (CRC) patients showed various results. METHODS: Articles regarding the prognostic value of statin on CRC and published in English and before October 2020 were searched in the following databases: PubMed, Web of Science, EMBASE, Medline and Google Scholar. The multivariate hazard ratios (HRs) and their 95% confidence intervals (CI) were computed to explore associations between statins use and overall mortality or cancer-specific mortality of CRC. RESULTS: The study included 5 retrospective case-control studies (including 475 statins users and 1925 no-statin users) and 11 prospective cohort studies (including 40659 statins users and 344459 no-statin users). The present study showed that statins use might be significantly associated with lower overall mortality in CRC with a random effects model (HR = 0.81, 95% CI 0.76 to 0.86, I2 = 61.9%, p value for Q test <0.001). In addition, statins use might be significantly associated with lower cancer-specific mortality in CRC with a random effects model (HR = 0.78, 95% CI 0.72 to 0.85, I2 = 57.3%, p value for Q test = 0.007). CONCLUSIONS: In conclusion, the present study indicated that that statin use was a protective factor for CRC prognosis. However, the relationship between statins use and CRC prognosis requires repeated and large prospective studies to be verified.

The orphan nuclear receptor Nurr1 agonist amodiaquine mediates neuroprotective effects in 6-OHDA Parkinson's disease animal model by enhancing the phosphorylation of P38 mitogen-activated kinase but not PI3K/AKT signaling pathway.

Recent studies implicate the defects or altered expression of the orphan nuclear receptor Nurr1 gene in the substantia nigra in Parkinson's disease pathogenesis. In an attempt to corroborate the treatment-modifying disease that would replicate the effect of Nurr1, it has been found that amodiaquine and Nurr1 had the same chemical scaffolding, indicating a crucial structure-activity relationship. Interestingly, amodiaquine stimulate the transcriptional function of Nurr1 by physical interaction with its ligand-binding domain (LBD). However, the signaling route by which Nurr1 is activated by amodiaquine to cause the protective effect remains to be elucidated. We first demonstrated that amodiaquine treatment ameliorated behavioural deficits in 6-OHDA Parkinson's disease mouse model, and it promoted dopaminergic neurons protection signified by Tyrosine hydroxylase (TH) and dopamine transporter (DAT) mRNA; Tyrosine hydroxylase (TH) protein expression level and the immunoreactivity in the substantia nigra compacta. Subsequently, we used inhibitors to ascertain the effect of amodiaquine on Akt and P38 Mapk as crucial signaling pathways for neuroprotection. Wortmannin (Akt Inhibitor) induced a significant reduction of Akt mRNA; however, there was no statistical difference between the amodiaquine-treated group and the control group suggesting that amodiaquine may not be the active stimulant of Akt. Western blot analysis confirmed that the phosphorylated Akt decreased significantly in the amodiaquine group compared to the control group. In the same vein, we found that amodiaquine substantially increased the level of phosphorylated P38 Mapk. When P38 Mapk inhibited by SB203580 (P38-Mapk Inhibitor), the total P38 Mapk but not the phosphorylated P38 Mapk decreased significantly, while tyrosine hydroxylase significantly increased. These results collectively suggest that amodiaquine can augment tyrosine hydroxylase expression via phosphorylated P38 Mapk while negatively regulating the phosphorylated Akt in protein expression.

Synthesis and antibacterial activities of novel sulfonamide derivatives containing a fused-ring / 药学学报

To find antibacterial candidate compounds, eighteen novel sulfonamide derivatives containing a fused-ring were designed and synthesized on the basis of previous studies, with structures confirmed by 1H NMR, 13C NMR and MS. Antibacterial activities of the products were evaluated by the agar dilution method. The results show that these derivatives have different degrees of inhibitory activity on the tested bacteria, with the compounds IIi and IIr the most potent. The MIC of IIi for S. aureus, E. coli and MRSA was 8, 32 and 16 μg·mL-1, respectively, and the MIC of the IIr was 8, 64 and 32 μg·mL-1, respectively. The anti-MRSA activities of the two compounds is significant and is worthy of further structural optimization and study.

Surveillance and analysis of death causes of residents in a community of Shanghai from 2017 through 2019 / 上海预防医学

Objective:To determine the mortality， composition and trend of death causes of residents in Changxing community， Chongming District， Shanghai from 2017 through 2019， and provide scientific evidence for disease prevention and control strategies. Methods:Mortality data of household registered population in this community during January 1， 2017， and December 31， 2019， were collected. Causes of death were coded according to the ICD-10 and then analyzed by descriptive epidemiological method. Results:From 2017 through 2019， crude annual mortality of household registered residents in Changxing Community was 816.32/105， 825.01/105， and 770.16/105， respectively. The average annual mortality was 803.82/105. The leading death causes were cancer， circulatory disease， respiratory disease， and injury， poisoning and other external causes. Male mortality was higher than female mortality in all years. Conclusion:Main death causes of residents in Changxing Community are chronic non-communicable diseases， followed by external causes of injuries and poisoning. Our study provides scientific evidence for the improvement of health strategies by the local health administration， which warrants targeted health education measures to reduce the morbidity and mortality of chronic diseases and improve the health.

Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat.

BACKGROUND: Wheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization, processes which are often accompanied by genetic and epigenetic changes, including DNA methylation. However, the extent and effect of such changes during wheat evolution, particularly from tetraploid-to-hexaploid wheat, are currently elusive. RESULTS: Here we report genome-wide DNA methylation landscapes in extracted tetraploid wheat (ETW, AABB), natural hexaploid wheat (NHW, AABBDD), resynthesized hexaploid wheat (RHW, AABBDD), natural tetraploid wheat (NTW, AABB), and diploid (DD). In the endosperm, levels of DNA methylation, especially in CHG (H=A, T, or C) context, were dramatically decreased in the ETW relative to natural hexaploid wheat; hypo-differentially methylated regions (DMRs) (850,832) were 24-fold more than hyper-DMRs (35,111). Interestingly, those demethylated regions in ETW were remethylated in the resynthesized hexaploid wheat after the addition of the D genome. In ETW, hypo-DMRs correlated with gene expression, and TEs were demethylated and activated, which could be silenced in the hexaploid wheat. In NHW, groups of TEs were dispersed in genic regions of three subgenomes, which may regulate the expression of TE-associated genes. Further, hypo-DMRs in ETW were associated with reduced H3K9me2 levels and increased expression of histone variant genes, suggesting concerted epigenetic changes after separation from the hexaploid. CONCLUSION: Genome merger and separation provoke dynamic and reversible changes in chromatin and DNA methylation. These changes correlate with altered gene expression and TE activity, which may provide insights into polyploid genome and wheat evolution.

Effect of Chair Inclination Forward on Sit-to-Stand for Hemiplegics after Stroke / 中国康复理论与实践

Objective:To study the effect of chair inclination angles forward on sit-to-stand time and muscle activation of lower extremities in stroke patients with hemiplegia. Methods:From January to August, 2019, 15 stroke patients with hemiplegia finished five times sit-to-stand at seat slope 0°, 10° and 20° forward. The time, and surface electromyogram (sEMG) signals of rectus femoris, hamstrings, anterior tibialis and peroneus muscle were recorded. Results:The total EMG peak, root mean square and integrated electromyography (iEMG) of all the muscles decreased at seat slope 10° and 20° forward compared with those at 0° (F > 4.530, P < 0.05). The time decreased at seat slope 20° forward compared with that at 0° (P < 0.05). Conclusion:Seat inclination forward at some angles may improve the sit-to-stand performance in stroke patients with hemiplegia.

Effect of insulin-like growth factor 1 on phagocytosis and production of interleukin-10 in murine alveolar epithelial cells / 上海交通大学学报（医学版）

Objective • To investigate the effect of insulin-like growth factor 1 (IGF-1) on phagocytosis and production of interleukin-10 (IL-10) in the murine alveolar epithelial cell line MLE-12. Methods • After treatment with IGF-1 for 48 h, MLE-12 cells were incubated with fluorescent microspheres for 2 h in the presence or absence of wortmannin (phosphatidylinositol-3-kinase inhibitor). Flow cytometry was then used to assess cell phagocytosis of fluorescent microspheres. Enzyme linked immunosorbent assay (ELISA) was used to detect the content of IL-10 in MLE-12 cells culture supernatant stimulated by IGF-1 for 24 h. After pretreatment with IGF-1 for 2 h, MLE-12 cells were stimulated by lipopolysaccharides (LPS) for 24 h, and the expression of phosphorylated signal transduction and activator of transcription 3 (p-STAT3) in cytoplasm was detected by Western blotting.Results • With the increase of IGF-1 stimulation concentration, the ability of MLE-12 cells to phagocytose fluorescent microspheres increased, and the ability to phagocytose fluorescent microspheres reached the peak in the presence of IGF-1 at 50 ng/mL. However, the ability of IGF-1 to phagocytose fluorescent microspheres was completely blocked by wortmannin in MLE-12 cells. IGF-1 promoted IL-10 secretion and inhibited LPS-induced enhancement of STAT3 activation in MLE-12 cells. Conclusion • IGF-1 promotes phagocytosis of MLE-12 cells via the PI3K/protein kinase B (Akt) pathway and exhibits anti-inflammatory properties.

Chemical Constituents and Pharmacological Effect of Lonicerae Japonicae Flos / 中国实验方剂学杂志

Lonicerae Japonicae Flos is a commonly used traditional Chinese medicine with a long history. It has the functions of detoxification, heat dissipation and heat dissipation, with a high medicinal value. It is mainly distributed in Henan, Shandong, Guangdong and other places. Researches have shown that the chemical constituents of honeysuckle mainly include organic acids, flavonoids, iridoid glycosides, three terpenoid glycosides, three terpenoid glycosides and volatile oils. And the pharmacological effects of honeysuckle are mainly anti-inflammation and antipyretic, anti-tumor, anti-bacteria, anti-virus, anti-aging and anti-oxidation, lowering blood sugar, protecting liver, protecting lung, neuroprotective, enhancing immune function and anti-platelet aggregation. Because of its rich pharmacological effects and high medicinal value, it has been used in a variety of prescriptions, with wide clinical applications and its large social demands. In this paper, we have reviewed the literatures on the chemical constituents and pharmacological effects of honeysuckle in recent years, and learned that many scholars have studied it, isolated a variety of new chemical components from honeysuckle for the first time and studied the pharmacological effects of honeysuckle in detail. In this paper, we reviewed the research progress of chemical constituents and pharmacological effects of Lonicerae Japonicae Flos, providing references for more people to learn related knowledge of honeysuckle and a scientific basis for the development and utilization of Lonicerae Japonicae Flos.

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids.

Polyploidy occurs in some animals and all flowering plants, including important crops such as wheat. The consequences of polyploidy in crops remain elusive, partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids Sl Sl AA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more non-additively expressed genes in Sl Sl AA than in AADD. In AADD, non-additively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In Sl Sl AA, there was a tendency for expression dominance of Sl over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nucleotide small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in Sl Sl AA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons and gene expression coincide with unstable AADD genomes and stable Sl Sl AA genomes, which could help explain the evolutionary trajectories of wheat allotetraploids formed by different progenitors.

Rice Interploidy Crosses Disrupt Epigenetic Regulation, Gene Expression, and Seed Development.

Seed development in angiosperms requires a 2:1 maternal-to-paternal genome ratio (2m:1p) in the endosperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5' and 3' flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylation-related genes including OsMET1b and OsCMT3a were upregulated in the 2×4 cross (pollinating a diploid "mother" with a tetraploid "father") but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4×2 crosses. WUSCHEL homeobox2 (WOX2)-like (WOX2L), an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m:1p genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.