A natural gene drive system confers reproductive isolation in rice.

Hybrid sterility restricts the utilization of superior heterosis of indica-japonica inter-subspecific hybrids. In this study, we report the identification of RHS12, a major locus controlling male gamete sterility in indica-japonica hybrid rice. We show that RHS12 consists of two genes (iORF3/DUYAO and iORF4/JIEYAO) that confer preferential transmission of the RHS12-i type male gamete into the progeny, thereby forming a natural gene drive. DUYAO encodes a mitochondrion-targeted protein that interacts with OsCOX11 to trigger cytotoxicity and cell death, whereas JIEYAO encodes a protein that reroutes DUYAO to the autophagosome for degradation via direct physical interaction, thereby detoxifying DUYAO. Evolutionary trajectory analysis reveals that this system likely formed de novo in the AA genome Oryza clade and contributed to reproductive isolation (RI) between different lineages of rice. Our combined results provide mechanistic insights into the genetic basis of RI as well as insights for strategic designs of hybrid rice breeding.

COLD1 confers chilling tolerance in rice.

Rice is sensitive to cold and can be grown only in certain climate zones. Human selection of japonica rice has extended its growth zone to regions with lower temperature, while the molecular basis of this adaptation remains unknown. Here, we identify the quantitative trait locus COLD1 that confers chilling tolerance in japonica rice. Overexpression of COLD1(jap) significantly enhances chilling tolerance, whereas rice lines with deficiency or downregulation of COLD1(jap) are sensitive to cold. COLD1 encodes a regulator of G-protein signaling that localizes on plasma membrane and endoplasmic reticulum (ER). It interacts with the G-protein α subunit to activate the Ca(2+) channel for sensing low temperature and to accelerate G-protein GTPase activity. We further identify that a SNP in COLD1, SNP2, originated from Chinese Oryza rufipogon, is responsible for the ability of COLD(jap/ind) to confer chilling tolerance, supporting the importance of COLD1 in plant adaptation.

Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.

The concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomics study, especially for crop sciences. The rice pan-genome constructed from the second-generation sequencing (SGS) data is about 270 Mb larger than Nipponbare, the rice reference genome (NipRG), but it is still disadvantaged by incompleteness and loss of genomic contexts. The third-generation sequencing (TGS) with long reads can help to construct better pan-genomes. In this paper, we report a high-quality rice pan-genome construction method by introducing a series of new steps to deal with the long-read data, including unmapped sequence block filtering, redundancy removing, and sequence block elongating. Compared to NipRG, the long-read sequencing-based pan-genome constructed from 105 rice accessions, which contains 604 Mb novel sequences, is much more comprehensive than the one constructed from ∼3000 rice genomes sequenced with short reads. The repetitive sequences are the main components of novel sequences, which partially explain the differences between the pan-genomes based on TGS and SGS. Adding six wild rice accessions, there are about 879 Mb novel sequences and 19,000 novel genes in the rice pan-genome in total. In addition, we have created high-quality reference genomes for all representative rice populations, including five gapless reference genomes. This study has made significant progress in our understanding of the rice pan-genome, and this pan-genome construction method for long-read data can be applied to accelerate a broad range of genomics studies.

Lost genome segments associate with trait diversity during rice domestication.

BACKGROUND: DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. RESULTS: In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. CONCLUSIONS: We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Two pairs of 2-pyrone enantiomers and a benzophenone analogue from the endophytic fungus Penicillium egyptiacum.

Four new 2-pyrone derivatives, two pairs of enantiomers, (±)-egypyrone A [(±)-1] and (±)-egypyrone B [(±)-2], together with a new benzophenone analogue, orbiophenone B (3), were isolated from the endophytic fungus Penicillium egyptiacum. The enantiomeric mixtures (±)-1 and (±)-2 were separated through chiral HPLC, respectively. Their structures were elucidated by extensive analysis of spectroscopic data and the absolute configuration was determined by comparing the optical rotation of structurally similar molecule. Subsequently, the cytotoxic activities of (±)-1, (±)-2, and 3 against the U87 cell line were tested and no activity was observed at a concentration of 10 µM.

Unveiling a half-century mystery of molecular bases for three-line hybrid rice breeding system.

Hybrid rice derived from Wild Abortive (WA) cytoplasmic male sterility type three-line systems is widely used in production. The fertility restoration gene Rf4 can reduce WA352c transcript levels in a dose-dependent manner. A two-copy haplotype of Rf4 (H1) is identified as the most valuable haplotype for future hybrid rice breeding.

Unearthing old rice germplasm, illuminating a new way to improvement.

Rice germplasm collections contain vast reserves of genetic diversity but remain understudied. This Commentary highlights the effectiveness of mining genetic resources from germplasm as a means to overcome current yield constraints, using clustered-spikelet rice as an example.

A historical review of hybrid rice breeding.

The development of germplasm resources and advances in breeding methods have led to steady increases in yield and quality of rice (Oryza sativa L.). Three milestones in the recent history of rice breeding have contributed to these increases: dwarf rice breeding, hybrid rice breeding, and super rice breeding. On the 50th anniversary of the success of three-line hybrid rice, we highlight important scientific discoveries in rice breeding that were made by Chinese scientists and summarize the broader history of the field. We discuss the strategies that could be used in the future to optimize rice breeding further in the hope that China will continue to play a leading role in international rice breeding.

A centromere map based on super pan-genome highlights the structure and function of rice centromeres.

Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.

Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize.

KEY MESSAGE: Long intergenic non-coding RNA (lincRNA), cis-acting expression quantitative trait locus (cis-eQTL), maize, regulatory evolution. The law of genetic variation during domestication explains the evolutionary mechanism and provides a theoretical basis for improving existing varieties of maize. Previous studies focused on exploiting regulatory variations controlling the expression of protein-coding genes rather than of non-protein-coding genes. Here, we examined the genetic and evolutionary features of long non-coding RNAs from intergenic regions (long intergenic non-coding RNAs, lincRNAs) using population-scale transcriptome data and identified 1168 lincRNAs with cis-acting expression quantitative trait loci (cis-eQTLs). We found that lincRNAs are more likely to be regulated by cis-eQTLs, which exert stronger effects than the protein-coding genes. During maize domestication and improvement, upregulated alleles of lincRNAs, which originated from both standing variation and new mutation, accumulate more frequently and show larger effect sizes than the coding genes. A stronger signature of genetic differentiation was observed in their regulatory regions compared to those of randomly sampled lincRNAs. In addition, we found that cis-regulatory differentiation of lincRNAs is related to the sequence conservation of lincRNA transcripts. Non-conserved lincRNAs more tend to gain upregulated alleles and show a stronger relationship with selected traits than conserved lincRNAs between maize and its wild relatives. Our findings in maize improve the understanding of cis-regulatory variation in lincRNA genes during domestication and improvement and provide an effective approach for prioritizing candidates for further investigation.

Treatment of melanoma with dendritic cell vaccines and immune checkpoint inhibitors: A mathematical modeling study.

Dendritic cell (DC) vaccines and immune checkpoint inhibitors (ICIs) play critical roles in shaping the immune responses of tumor cells (TCs) and are widely used in cancer immunotherapies. Quantitatively evaluating the effectiveness of these therapies are essential for the optimization of treatment strategies. Here, based on the combined therapy of melanoma with DC vaccines and ICIs, we formulated a mathematical model to investigate the dynamic interactions between TCs and the immune system and understand the underlying mechanisms of immunotherapy. First, we obtained a threshold parameter for the growth of TCs, which is given by the ratio of spontaneous proliferation to immune inhibition. Next, we proved the existence and locally asymptotic stability of steady states of tumor-free, tumor-dominant, and tumor-immune coexistent equilibria, and identified the existence of Hopf bifurcation of the proposed model. Furthermore, global sensitivity analysis showed that the growth of TCs strongly correlates with the injection rate of DC vaccines, the activation rate of CTLs, and the killing rate of TCs. Finally, we tested the efficacy of multiple monotherapies and combined therapies with model simulations. Our results indicate that DC vaccines can decelerate the growth of TCs, and ICIs can inhibit the growth of TCs. Besides, both therapies can prolong the lifetime of patients, and the combined therapy of DC vaccines and ICIs can effectively eradicate TCs.

Toll-like receptor 10 expression in B cells is negatively correlated with the progression of primary Sjögren's disease.

Primary Sjögren's Disease (pSjD) is considered a B cell-mediated disease. Toll-like receptor 10 (TLR10) is highly expressed in human B cells, indicating that TLR10 probably plays a vital role in pSjD. We examined TLR10 expression in peripheral B subsets of pSjD patients and analyzed their association with disease activity. We observed that TLR10 expression in total, naïve, memory, and switched memory B cells was significantly increased in low-activity pSjD patients as compared with healthy controls and high-activity patients. TLR10 expression in the above mentioned B subsets (except naïve B) was negatively correlated with serum levels of anti-SSA antibody and BAFF, respectively. Moreover, a higher proportion of high-activity pSjD patients was observed in TLR10 low- than high-expressed patients. Our study concluded that TLR10 expression in CD19+ B and memory B was negatively correlated with pSjD disease activity, suggesting that TLR10 might take part in the progression of pSjD.

Severe immune-related adverse events of immune checkpoint inhibitors for advanced non-small cell lung cancer: a network meta-analysis of randomized clinical trials.

OBJECTIVE: A complete toxicity profile, toxicity profile, and safety ranking of immune checkpoint inhibitors (ICIs) for treatment of advanced non-small cell lung cancer (NSCLC) will be provided in this network meta-analysis. METHODS: We searched 14 randomized clinical trials (RCTs) including 9572 NSCLC patients by PubMed, EMBASE, Cochrane, and ClinicalTrials.gov. Randomized pairwise and network meta-analyses were used to compare the incidence of severe immune-related adverse events (irAEs) across different ICIs-based treatments using risk ratios (RRs) and 95% confidence intervals (CI). RESULTS: For severe dermatologic irAEs, the corresponding ranking of incidences of the nine groups from high to low was: nivolumab + ipilimumab + platinum (79.1%), pembrolizumab (75.2%), nivolumab + ipilimumab (72.9%), camrelizumab + platinum (64.9%), atezolizumab + platinum (47.4%), nivolumab (44.2%), durvalumab (40.5%), pembrolizumab + platinum (15.5%), platinum-based chemotherapy (10.3%). For severe colitis, the corresponding ranking of incidences of the seven groups from high to low was: nivolumab + ipilimumab + platinum (72.4%), nivolumab (63.1%), atezolizumab + platinum (56.9%), durvalumab (56.6%), pembrolizumab (54.9%), pembrolizumab + platinum (38.6%), platinum-based chemotherapy (7.4%). For severe endocrine irAEs, the corresponding ranking of incidences of the nine groups from high to low was: durvalumab (74.3%), atezolizumab + platinum (54.5%), nivolumab + ipilimumab (54.0%), camrelizumab + platinum (51.7%), nivolumab + ipilimumab + platinum (51.6%), pembrolizumab + platinum (49.8%), pembrolizumab (49.2%), nivolumab (46.3%), platinum-based chemotherapy (18.6%). For severe pneumonitis, the corresponding ranking of incidences of the nine groups from high to low was: nivolumab (84.3%), pembrolizumab (84.1%), durvalumab (66.1%), camrelizumab + platinum (61.4%), atezolizumab + platinum (50%), pembrolizumab + platinum (43.4%), platinum-based chemotherapy (16.2%), atezolizumab (6.2%). For severe hepatitis, the corresponding ranking of incidences of the eight groups from high to low was: pembrolizumab (68.8%), nivolumab + ipilimumab + platinum (65%), pembrolizumab + platinum (64.6%), durvalumab (57.9%), nivolumab (47.1%), atezolizumab + platinum (43.4%), camrelizumab + platinum (42%), platinum-based chemotherapy (11.2%). CONCLUSIONS: In addition to platinum-based chemotherapy, pembrolizumab + platinum for severe dermatologic irAEs and colitis, nivolumab for severe endocrine irAEs, atezolizumab for severe pneumonitis, camrelizumab + platinum for severe hepatitis may be associated with lower rates of irAEs than other immune-based regimens.

Plastidic pyruvate dehydrogenase complex E1 component subunit Alpha1 is involved in galactolipid biosynthesis required for amyloplast development in rice.

Starch accounts for over 80% of the total dry weight in cereal endosperm and determines the kernel texture and nutritional quality. Amyloplasts, terminally differentiated plastids, are responsible for starch biosynthesis and storage. We screened a series of rice mutants with floury endosperm to clarify the mechanism underlying amyloplast development and starch synthesis. We identified the floury endosperm19 (flo19) mutant which shows opaque of the interior endosperm. Abnormal compound starch grains (SGs) were present in the endosperm cells of the mutant. Molecular cloning revealed that the FLO19 allele encodes a plastid-localized pyruvate dehydrogenase complex E1 component subunit α1 (ptPDC-E1-α1) that is expressed in all rice tissues. In vivo enzyme assays demonstrated that the flo19 mutant showed decreased activity of the plastidic pyruvate dehydrogenase complex. In addition, the amounts of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) were much lower in the developing flo19 mutant endosperm, suggesting that FLO19 participates in fatty acid supply for galactolipid biosynthesis in amyloplasts. FLO19 overexpression significantly increased seed size and weight, but did not affect other important agronomic traits, such as panicle length, tiller number and seed setting rate. An analysis of single nucleotide polymorphism data from a panel of rice accessions identified that the pFLO19L haplotype was positively associated with grain length, implying a potential application in rice breeding. In summary, our study demonstrates that FLO19 is involved in galactolipid biosynthesis which is essential for amyloplast development and starch biosynthesis in rice.

Tumor growth towards lower extracellular matrix conductivity regions under Darcy's Law and steady morphology.

We study a classic Darcy's law model for tumor cell motion with inhomogeneous and isotropic conductivity. The tumor cells are assumed to be a constant density fluid flowing through porous extracellular matrix (ECM). The ECM is assumed to be rigid and motionless with constant porosity. One and two dimensional simulations show that the tumor mass grows from high to low conductivity regions when the tumor morphology is steady. In the one-dimensional case, we proved that when the tumor size is steady, the tumor grows towards lower conductivity regions. We conclude that this phenomenon is produced by the coupling of a special inward flow pattern in the steady tumor and Darcy's law which gives faster flow speed in higher conductivity regions.

Visual grading experiments and optimization in CBCT dental implantology imaging: preliminary application of integrated visual grading regression.

This study uses a general formulation of integrated visual grading regression (IVGR) and applies it to cone beam computed tomography (CBCT) scan data related to anatomical landmarks for dental implantology. The aim was to assess and predict a minimum acceptable dose for diagnostic imaging and reporting. A skull phantom was imaged with a CBCT unit at various diagnostic exposures. Key anatomical landmarks within the images were independently reviewed by three trained observers. Each provided an overall image quality score. Statistical analysis was carried out to examine the acceptability of the images taken, using an IVGR analysis that was formulized as a three-stage protocol including defining an integrated score, development of an ordinal regression, and investigation of the possibility for dose reduction through estimated parameters. For a unit increase in the logarithm of radiation dose, the odds ratio that the integrated score for an image assessed by observers being rated in a higher category was 3.940 (95% confidence interval: 1.016-15.280). When assessed by the observers, the minimum dose required to achieve a 75% probability for an image to be classified as at least acceptable was 1346.91 mGy·cm2 dose area product (DAP), a 31% reduction compared to the 1962 mGy·cm2 DAP default dosage of the CBCT unit. The kappa values of the intra and inter-observer reliability indicated moderate agreements, while a discrepancy among observers was also identified because each, as expected, perceived visibility differently. The results of this work demonstrate the IVGR's predictive value of dose saving in the effort to reduce dose to patients while maintaining reportable diagnostic image quality.

Identification of suitable reference genes for quantitative reverse transcription PCR in Luffa (Luffa cylindrica).

Reverse transcription real-time quantitative PCR is widely used to quantify gene expression. Reference genes are usually used as internal controls to measure the target gene expression level. To date, there is no consensus on the use of systematically validated reference genes in different tissues of Luffa. This study evaluated the expression stability of 11 candidate reference genes in different tissues using five algorithms (BestKeeper, comparative delta-Ct method, GeNorm, NormFinder, and RefFinder). Protein phosphatase 2A was the most stable gene, while alpha Tubulin was the least stable. The relative expression of ethylene-related genes in different tissues was also analyzed to reveal their role in sex determination. This study provides the basis for using suitable reference genes to evaluate targeted gene expression. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01182-8.

OsRE1 interacts with OsRIP1 to regulate rice heading date by finely modulating Ehd1 expression.

Heading date is a key agronomic trait affecting crop yield. In rice, Early heading date 1 (Ehd1) is an important B-type response regulator in determination of heading date. Although many regulatory factors of Ehd1 expression have been functionally characterized, the direct regulators of Ehd1 largely remain to be identified. Here, we identified a new regulator of Ehd1, OsRE1, that directly binds to the A-box motif in the Ehd1 promoter. Osre1 confers an early heading phenotype due to elevated expression levels of Ehd1. OsRE1 is a nucleus-localized bZIP transcription factor with a diurnal rhythmic expression pattern. Furthermore, we identified an OsRE1-interacting protein, OsRIP1, and demonstrated that OsRIP1 can repress the transcript expression of Ehd1 in an OsRE1-dependent manner. Our genetic data showed that OsRE1 and OsRIP1 may function upstream of Ehd1 in regulating heading date. Together, our results suggest that OsRE1 functions cooperatively with OsRIP1 to regulate heading date through finely modulating the expression of Ehd1. In addition, OsRE1 and OsRIP1 are two minor heading date regulators, which are more desirable for fine-tuning heading date to improve rice regional adaptability.

A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula).

KEY MESSAGE: A dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3ß-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.

A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica.

KEY MESSAGE: we identified a functional chromogen gene C from wild rice, providing a new insight of anthocyanin biosynthesis pathway in indica and japonica. Accumulation of anthocyanin is a desirable trait to be selected in rice domestication, but the molecular mechanism of anthocyanin biosynthesis in rice remains largely unknown. In this study, a novel allele of chromogen gene C, OrC1, from Oryza rufipongon was cloned and identified as a determinant regulator of anthocyanin biosynthesis. Although OrC1 functions in purple apiculus, leaf sheath and stigma in indica background, it only promotes purple apiculus in japonica. Transcriptome analysis revealed that OrC1 regulates flavonoid biosynthesis pathway and activates a few bHLH and WD40 genes of ternary MYB-bHLH-WD40 complex in indica. Differentially expressed genes and metabolites were found in the indica and japonica backgrounds, indicating that OrC1 activated the anthocyanin biosynthetic genes OsCHI, OsF3H and OsANS and produced six metabolites independently. Artificial selection and domestication of C1 gene in rice occurred on the coding region in the two subspecies independently. Our results reveal the regulatory system and domestication of C1, provide new insights into MYB transcript factor involved in anthocyanin biosynthesis, and show the potential of engineering anthocyanin biosynthesis in rice.