Integrated transcriptomic and metabolomic analysis provides insight into the pollen development of CMS-D1 rice.

BACKGROUND: Cytoplasmic male sterility (CMS) has greatly improved the utilization of heterosis in crops due to the absence of functional male gametophyte. The newly developed sporophytic D1 type CMS (CMS-D1) rice exhibits unique characteristics compared to the well-known sporophytic CMS-WA line, making it a valuable resource for rice breeding. RESULTS: In this research, a novel CMS-D1 line named Xingye A (XYA) was established, characterized by small, transparent, and shriveled anthers. Histological and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assays conducted on anthers from XYA and its maintainer line XYB revealed that male sterility in XYA is a result of delayed degradation of tapetal cells and abnormal programmed cell death (PCD) of microspores. Transcriptome analysis of young panicles revealed that differentially expressed genes (DEGs) in XYA, compared to XYB, were significantly enriched in processes related to chromatin structure and nucleosomes during the microspore mother cell (MMC) stage. Conversely, processes associated with sporopollenin biosynthesis, pollen exine formation, chitinase activity, and pollen wall assembly were enriched during the meiosis stage. Metabolome analysis identified 176 specific differentially accumulated metabolites (DAMs) during the meiosis stage, enriched in pathways such as α-linoleic acid metabolism, flavone and flavonol biosynthesis, and linolenic acid metabolism. Integration of transcriptomic and metabolomic data underscored the jasmonic acid (JA) biosynthesis pathway was significant enriched in XYA during the meiosis stage compared to XYB. Furthermore, levels of JA, MeJA, OPC4, OPDA, and JA-Ile were all higher in XYA than in XYB at the meiosis stage. CONCLUSIONS: These findings emphasize the involvement of the JA biosynthetic pathway in pollen development in the CMS-D1 line, providing a foundation for further exploration of the molecular mechanisms involved in CMS-D1 sterility.

DNAL7, a new allele of NAL11, has major pleiotropic effects on rice architecture.

MAIN CONCLUSION: dnal7, a novel allelic variant of the OsHSP40, affects rice plant architecture and grain yield by coordinating auxins, cytokinins, and gibberellic acids. Plant height and leaf morphology are the most important traits of the ideal plant architecture (IPA), and discovering related genes is critical for breeding high-yield rice. Here, a dwarf and narrow leaf 7 (dnal7) mutant was identified from a γ-ray treated mutant population, which exhibits pleiotropic effects, including dwarfing, narrow leaves, small seeds, and low grain yield per plant compared to the wild type (WT). Histological analysis showed that the number of veins and the distance between adjacent small veins (SVs) were significantly reduced compared to the WT, indicating that DNAL7 controls leaf size by regulating the formation of veins. Map-based cloning and transgenic complementation revealed that DNAL7 is allelic to NAL11, which encodes OsHSP40, and the deletion of 2 codons in dnal7 destroyed the His-Pro-Asp (HPD) motif of OsHSP40. In addition, expression of DNAL7 in both WT and dnal7 gradually increased with the increase of temperature in the range of 27-31 °C. Heat stress significantly affected the seedling height and leaf width of the dnal7 mutant. A comparative transcriptome analysis of WT and dnal7 revealed that DNAL7 influenced multiple metabolic pathways, including plant hormone signal transduction, carbon metabolism, and biosynthesis of amino acids. Furthermore, the contents of the cytokinins in leaf blades were much higher in dnal7 than in the WT, whereas the contents of auxins were lower in dnal7. The contents of bioactive gibberellic acids (GAs) including GA1, GA3, and GA4 in shoots were decreased in dnal7. Thus, DNAL7 regulates rice plant architecture by coordinating the balance of auxins, cytokinins, and GAs. These results indicate that OsHSP40 is a pleiotropic gene, which plays an important role in improving rice yield and plant architecture.

Effect of noninvasive embryo viability testing versus conventional IVF on the live birth rate in IVF/ICSI patients: a study protocol for a double-blind, multicenter, randomized controlled trial.

BACKGROUND: Preimplantation genetic testing for aneuploidy (PGT-A) was demonstrated to be superior to conventional IVF in reducing the incidence of miscarriage and abnormal offspring after the first embryo transfer (ET). PGT-A requires several embryo trophectoderm cells, but its negative impacts on embryo development and long-term influence on the health conditions of conceived children have always been a concern. As an alternative, noninvasive PGT-A (niPGT-A) approaches using spent blastocyst culture medium (SBCM) achieved comparable accuracy with PGT-A in several pilot studies. The main objective of this study is to determine whether noninvasive embryo viability testing (niEVT) results in better clinical outcomes than conventional IVF after the first embryo transfer. Furthermore, we further investigated whether niEVT results in higher the live birth rate between women with advanced maternal age (AMA, > 35 years old) and young women or among patients for whom different fertilization protocols are adopted. METHODS: This study will be a double-blind, multicenter, randomized controlled trial (RCT) studying patients of different ages (20-43 years) undergoing different fertilization protocols (in vitro fertilization [IVF] or intracytoplasmic sperm injection [ICSI]). We will enroll 1140 patients at eight reproductive medical centers over 24 months. Eligible patients should have at least two good-quality blastocysts (better than grade 4 CB). The primary outcome will be the live birth rate of the first embryo transfer (ET). Secondary outcomes will include the clinical pregnancy rate, ongoing pregnancy rate, miscarriage rate, cumulative live birth rate, ectopic pregnancy rate, and time to pregnancy. DISCUSSION: In this study, patients who undergo noninvasive embryo viability testing (niEVT) will be compared to women treated by conventional IVF. We will determine the effects on the pregnancy rate, miscarriage rate, and live birth rate and adverse events. We will also investigate whether there is any difference in clinical outcomes among patients with different ages and fertilization protocols (IVF/ICSI). This trial will provide clinical evidence of the effect of noninvasive embryo viability testing on the clinical outcomes of the first embryo transfer. TRIAL REGISTRATION: Chinese Clinical Trial Registry (ChiCTR) Identifier: ChiCTR2100051408. 9 September 2021.

Orthodontic treatment improves magnetic resonance imaging features and quality of life in adult patients with temporomandibular disorders.

OBJECTIVE: This research intends to clarify the magnetic resonance imaging (MRI) features as well as changes in symptoms and quality of life (QoL) in adult patients with temporomandibular disorders (TMDs) before and after orthodontic treatment. METHODS: Clinical data of 57 TMD patients before and after orthodontic treatment were collected and analyzed retrospectively. The anterior and posterior regions of the temporomandibular joint (TMJ)'s articular disc were checked before, during and after the treatment by MRI, and the anterior and posterior spaces of TMJ were measured with an electronic measuring ruler. Pre- and post-treatment alterations in the Visual Analogue Scale (VAS) score, TMJ clicking, maximum mouth opening (MMO), and Fricton's indexes (TMJ dysfunction index, DI; palpation index, PI; craniomandibular index, CMI) of the patients were comparatively analyzed. The Oral Health Impact Profile questionnaire was employed for QoL assessment before and after treatment. RESULTS: On MRI, patients with TMDs presented clear changes in TMJ disc position, morphology, thickness and joint effusion, while those with pain symptoms also had condylar degeneration. In addition to a reduced VAS score, the line distance of the TMJ anterior space increased significantly, while the posterior space line distance decreased significantly after treatment, as compared with the baseline (before treatment). Before orthodontic treatment, a total of 46 TMD patients were accompanied by associated TMJ clicking, including 8 severe cases and 38 mild cases. The clicking disappeared in 39 cases after treatment, but mild unilateral clicking, mild bilateral clicking, and severe clicking were still observed in 5, 1, and 1 case(s), respectively. The patients exhibited an increase in MMO and a decrease in Fricton's indexes with significantly enhanced QoL after the orthodontic treatment. CONCLUSIONS: Patients with TMDs exhibit diverse clinical features, and MRI can accurately reflect changes in the position, morphology and thickness of the articular disc as the disease progresses, which can improve the accuracy of clinical diagnosis. In addition, orthodontic treatment for TMD patients can effectively alleviate adverse clinical symptoms and improve their QoL.

Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.

Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties.

Whole Genome Resequencing of 20 Accessions of Rice Landraces Reveals Javanica Genomic Structure Variation and Allelic Genotypes of a Grain Weight Gene TGW2.

The landraces preserved by indigenous worldwide exhibited larger variation in the phenotypes and adaption to different environments, which suggests that they comprise rich resources and can be served as a gene pool for rice improvement. Despite extensive studies on cultivated rice, the variations and relationships between landraces and modern cultivated rice remain unclear. In this study, a total of 20 varieties that include 10 Oryza javanica collected from different countries worldwide and 10 Oryza indica from China were genotyped and yielded a sum of 99.9-Gb resequencing raw data. With the genomic sequence of the japonica cultivar Nipponbare as a reference, the following genetic features of single-nucleotide polymorphism (SNP) ranged from 861,177 to 1,044,617, insertion-deletion polymorphisms (InDels) ranged from 164,018 to 211,135, and structural variation (SV) ranged from 3,313 to 4,959 were identified in Oryza javanica. Variation between the two subspecies was also determined that 584,104 SNPs, 75,351 InDels, 104,606 SNPs, and 19,872 InDels specific to Oryza indica and Oryza javanica, respectively. Furthermore, Gene Ontology (GO) and KEGG of Oryza javanica-specific SNP-related genes revealed that they participated in DNA metabolic process, DNA replication, and DNA integration. The sequence variation and candidate grain shape-related gene TGW2 were identified through Fst and sweep selective analysis. Hap4 of TGW2 is performed better than others. The whole genome sequence data and genetic variation information illustrated in this study will serve as an important gene pool for molecular breeding and facilitate genetic analysis of Oryza javanica varieties.

[Particle Size Distribution of PM Emission from In-use Gasoline and Diesel Vehicles].

Particle size distribution and emission factors from 9 State 3-5 light-duty gasoline vehicles (LDGVs) and 15 State 3-5 heavy-duty diesel vehicles (HDDVs) were tested in this study using a constant volume sampling (CVS) system on a dynamometer. The influences of driving cycles and emission control level on the PM emission factors and particle size distribution were analyzed. The results show that the PM emission factors of the tested LDGVs and HDDVs were (4.1±4.0)×1014 and (5.7±4.3)×1015 kg-1, respectively; the HDDV PM emission factor was (14±7) times less than that of LDGVs. Regarding LDGVs, the PM emission factor under the extra high speed condition was much more than that of the other speed conditions at (5.1±5.0)×1013 km-1, 11.7, 14.1, and 7.3 times more than that under the low, medium, and high speed conditions, respectively. Regarding HDDVs, the emission factor under the high speed condition was 2.5 and 1.4 times that under the low and medium speed conditions, respectively, and was mostly of nuclei-mode particles. At the emission control level of State 3-5, the PM emission factors of LDGVs were (2.7±1.7)×1013, (2.6±1.3)×1013, and (1.6±1.2)×1013 km-1, respectively, and those of HDDVs were (2.2±1.2)×1015, 2.0×1015, and (7.1±2.1)×1014 km-1, respectively. With improvement in emission control level, the particle number emission control of LDGVs and HDDVs generally showed a good downward trend. However, the emission of PM above 110 nm from LDGVs did not improve with the emission control level. Although the quantity emission factor of HDDVs with particle size above 110 nm is relatively low, its harm to the environment cannot be ignored, which should justify necessary attention.

Effects of external Mn2+ activities on OsNRAMP5 expression level and Cd accumulation in indica rice.

Manganese (Mn) transporter OsNRAMP5 was widely reported to regulate cadmium (Cd) uptake in rice. However, the relationship between OsNRAMP5 expression level and Cd accumulation, impacts of external ion activities on OsNRAMP5 expression level and Cd accumulation are still unclear. Investigations of the relationship between OsNRAMP5 expression level and Cd accumulation in three indica rice genotypes were conducted under various external Mn2+ activities ranging from Mn deficiency to toxicity in EGTA-buffered nutrient solution. Results in this work indicated that OsNRAMP5 expression level in roots significantly up-regulated at Mn phytotoxicity compared to that at Mn deficiency, which may stimulate by the increasing uptake of Mn. Our work also demonstrated that root Cd concentration of all the tested rice decreased notably when external Mn2+ activity reached the level of toxicity. This may explain by the increasing competition between the excess Mn2+ and Cd2+ as well as the disorder of element absorption caused by root damage at Mn toxicity. Our work also revealed that the relationship between OsNRAMP5 expression level in roots and Cd accumulation in roots was insignificant for all the tested genotypes. Besides, OsNRAMP5 expression level in roots seemed more related to root Mn accumulation. The fact that function of OsNRAMP5 mainly focuses on Mn uptake, together with the fact that many transporter genes involved in Cd uptake might result in the insignificant correlation between OsNRAMP5 expression level and Cd accumulation in roots. At last, multi-level regulating and processing of the process from gene expression to protein translation might account for the inconsistent relationship between root OsNRAMP5 expression level and Cd accumulation in roots.

Mechanisms and uncertainties of Zn supply on regulating rice Cd uptake.

Application of Zinc (Zn) is considered an effective measure to reduce Cadmium (Cd) uptake and toxicity in Cd-contaminated soils for many plant species. However, interaction between Zn and Cd in rice plant is complex and uncertain. In this study, four indica rice cultivars were selected to evaluate the effect of Zn exposure in an EGTA-buffered nutrient solution under varying Zn activities and a field level of Cd activity to characterize the interaction between Zn and Cd in rice. Severe depression in shoots' biomass, tiller number, and SPAD (Soil and Plant Analyzer Development) value were found at both Zn deficiency and Zn phytotoxicity levels among four tested rice cultivars. There existed a strong antagonism interaction between Zn and Cd in both shoot and root from Zn deficiency to Zn phytotoxicity. The reduction of Cd accumulation in roots and shoots could be explained by the competition between Zn and Cd as well as the dilution effect of increasing biomass. The conflicting effect of Zn supply on Cd uptake may be attributed to the increasing transfer ratio of Cd from root to shoot with the increasing Zn2+ activities and the strong depression of Fe and Mn in shoots with the increasing Zn2+ activities as well as the variation of genotypes. Balance between Zn and Cd should be considered in field application.