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Pod size is a key agronomic trait that influences peanut yield greatly. However, our understanding of the mechanisms underlying pod size is limited. In this study, we employed a segregating population derived from a cross between the small-pod line ND_S and the large-pod line ND_L to map quantitative trait loci (QTL) associated with pod size. Initial mapping performed using bulk segregant analysis revealed a candidate interval on chromosome A05 referred to as qPSW05. We refined this interval to a 256.9 kb genomic region using newly developed molecular markers. Through sequence and expression analyses, we identified the candidate gene AhXE45GC, which encodes an AN1 zinc finger protein. We discovered a 33-bp insertion in the intron of AhXE45GC in ND_S. Accessions that lack this insertion, such as ND_L, had significantly larger pods than those with the insertion, including ND_S. To facilitate marker-assisted selection for peanut pod size, we developed a molecular marker associated with this polymorphism. This marker could provide a valuable genetic resource for breeding high-yielding peanut varieties.

Peanut (Arachis hypogaea L.) is an important oil crop. Oleic acid is a major factor that determines the quality of peanuts. Therefore, the high oleic and high oleic to linoleic acid ratio are the target traits in an advanced peanut breeding program. This study provided an extensive evaluation of the genetic and physical characteristics as well as disease resistance of 220 high oleic peanut varieties in China. Notably, these varieties clustered into five major categories based on their traits. A majority of these varieties have been bred using interspecific hybridization or selected from mutants of self-crossed parents, with the main parent varieties being Kaixuan 016 and CTWE. Analysis of disease resistance showed that most high oleic peanut varieties could resist two or three diseases. However, those varieties with resistance to multiple diseases were relatively scarce. Moreover, some high oleic peanut varieties showed no disease resistance or inadequate testing. The results further indicate that the genetic basis for high oleic peanut breeding is insufficient, highlighting the need for its further development. Importantly, our findings lay a critical foundation for future high oleic peanut breeding and promote better understanding of the genetic and trait diversity offered by these varieties.

Abstract Background Protein–protein interactions are the primary means through which proteins carry out their functions. These interactions thus have crucial roles in life activities. The wide availability of fully sequenced animal and plant genomes has facilitated establishment of relatively complete global protein interaction networks for some model species. The genomes of cultivated and wild peanut (Arachis hypogaea L.) have also been sequenced, but the functions of most of the encoded proteins remain unclear. Results We here used homologous mapping of validated protein interaction data from model species to generate complete peanut protein interaction networks for A. hypogaea cv. ‘Tifrunner’ (282,619 pairs), A. hypogaea cv. ‘Shitouqi’ (256,441 pairs), A. monticola (440,470 pairs), A. duranensis (136,363 pairs), and A. ipaensis (172,813 pairs). A detailed analysis was conducted for a putative disease-resistance subnetwork in the Tifrunner network to identify candidate genes and validate functional interactions. The network suggested that DX2UEH and its interacting partners may participate in peanut resistance to bacterial wilt; this was preliminarily validated with overexpression experiments in peanut. Conclusion Our results provide valuable new information for future analyses of gene and protein functions and regulatory networks in peanut.

Abstract How organisms respond to environmental stress is a key topic in evolutionary biology. This study focused on the genomic evolution of Laburnicola rhizohalophila, a dark-septate endophytic fungus from roots of a halophyte. Chromosome-level assemblies were generated from five representative isolates from structured subpopulations. The data revealed significant genomic plasticity resulting from chromosomal polymorphisms created by fusion and fission events, known as dysploidy. Analyses of genomic features, phylogenomics, and macrosynteny have provided clear evidence for the origin of intraspecific diploid-like hybrids. Notably, one diploid phenotype stood out as an outlier and exhibited a conditional fitness advantage when exposed to a range of abiotic stresses compared with its parents. By comparing the gene expression patterns in each hybrid parent triad under the four growth conditions, the mechanisms underlying growth vigor were corroborated through an analysis of transgressively upregulated genes enriched in membrane glycerolipid biosynthesis and transmembrane transporter activity. In vitro assays suggested increased membrane integrity and lipid accumulation, as well as decreased malondialdehyde production under optimal salt conditions (0.3 M NaCl) in the hybrid. These attributes have been implicated in salinity tolerance. This study supports the notion that hybridization-induced genome doubling leads to the emergence of phenotypic innovations in an extremophilic endophyte.

Aiming at the problems of Flow Direction Algorithm (FDA), such as premature convergence and tendency to fall into local optimum, this paper proposes an efficient improved version named FDA_CPR. Firstly, the embedding of the topological structure of cellular automata to increase the population diversity of the algorithm. Then, Lévy flight is used to replace the D8 algorithm of FDA and a position update strategy based on Sine Cosine Algorithm to slow down the convergence of the algorithm. Furthermore, a new concept of “potential energy” is introduced to calculate the energy score of the flow and determine the new direction of movement to improve the search efficiency of the algorithm. Finally, a “rockfall strategy” based on dynamic opposite learning is designed to help the algorithm jump out of the local optimum. FDA_CPR is compared with eight well-known algorithms on CEC2017 and several feature selection problems to evaluate its performance. Qualitative analysis, Friedman's test and Wilcoxon signed rank test confirmed the effectiveness of the improvement in different ways. Various experimental results show that FDA_CPR has considerable advantages in solving both discrete and continuous problems, and its comprehensive performance is better than that of FDA and other comparison algorithms.

Abstract Background To analyze the relationship between lipid metabolism, coagulation function, and bone metabolism and the contributing factor and staging of non-traumatic femoral head necrosis, and to further investigate the factors influencing the blood indicators related to the staging of non-traumatic femoral head necrosis. Methods The medical records of patients with femoral head necrosis were retrieved from the inpatient medical record management system, and the lipid metabolism, bone metabolism, and coagulation indices of non-traumatic femoral head necrosis (including alcoholic, hormonal, and idiopathic group) were obtained according to the inclusion and exclusion criteria, including Low-Density Lipoprotein Cholesterol, Triglycerides, Non-High-Density Lipoprotein Cholesterol, Apolipoprotein A1, Apolipoprotein (B), Apolipoprotein (E), Uric Acid, Alkaline Phosphatase, Bone-specific Alkaline Phosphatase, Activated Partial Thromboplastin Time, Prothrombin Time, D-dimer, Platelet count. The relationship between these blood indices and the different stages under different causative factors was compared, and the factors influencing the stages of non-traumatic femoral head necrosis were analyzed using multivariate logistic regression. Results (i) Gender, Age and BMI stratification, Low-density Lipoprotein Cholesterol, Triglycerides, Non-High-density Lipoprotein Cholesterol, Apolipoprotein (B), Apolipoprotein (E), Uric Acid, Bone-specific Alkaline Phosphatase, Activated Partial Thromboplastin Time, Plasminogen Time, D-dimer, and Platelet count of the alcohol group were statistically different when compared among the different ARCO staging groups; (ii) The differences in Age and BMI stratification, Triglycerides, Non-High-density Lipoprotein Cholesterol, Apolipoprotein A1, Apolipoprotein B, Apolipoprotein E, Uric Acid, Bone-specific Alkaline Phosphatase, Activated Partial Thromboplastin Time, Plasminogen Time, D-dimer, and Platelet count were statistically significant when compared among the different phases in the hormone group (P

Peanut (Arachis hypogaea L.) is an oilseed crop grown worldwide. Flavonoids have profound benefits for plant growth and development because of their powerful antioxidant properties. Seed vigor is an important indicator of seed quality. However, how flavonoids impact seed vigor formation in large-seed peanuts is still poorly understood. Here, we profiled flavonoids, phytohormones, and transcriptomes of developing seeds of large-seed peanut varieties with low (ZP06) and high (H8107) seed vigor. A total of 165 flavonoids were identified, 51 of which were differentially accumulated in ZP06 and H8107. Lower levels of dihydromyricetin (0.28 times) and hesperetin-7-O-glucoside (0.26 times) were observed in ZP06 seeds than in H8107. All flavonoid biosynthesis structural genes were down-regulated in ZP06. The different hormone levels found in ZP06 and H8107 seeds could be associated with the expression of flavonoid biosynthesis genes via MYB and bHLH transcription factors. Dihydromyricetin could relate to ZP06′s poor seed vigor by impacting its seed antioxidant properties. Thus, the presence of flavonoids in large-seed peanuts could contribute to their physiological quality and germination potential through controlling the accumulation of reactive oxygen species to improve seed antioxidant properties.

Plant architecture is a target of crop improvement. The soybean mutant ideal type 1 (it1) displays a pleiotropic phenotype characterized by compact plant architecture, reduced plant height, shortened petioles, wrinkled leaves, and indented seeds. Genetic analysis revealed that the pleiotropic phenotype was controlled by an incomplete dominant gene. We characterized the cellular phenotypes of it1 and positionally cloned the it1 locus. Detailed morphogenetic analysis of the it1 mutant revealed an excess of xylem cells and expanded phloem, and polygonal pavement cells. Positional cloning showed that the phenotype was caused by a G-to-A mutation in the second exon of the α-tubulin gene (Glyma.05G157300). The mutation altered microtubule arrangement in pavement cells, changing their morphology. Overexpression of Gmit1 resulted in an it1-like phenotype and polygonal pavement cells and microtubules of overexpressors were parallel or slightly inclined. Five suppressor mutants able to suppress the phenotype of it1 were obtained by EMS mutagenesis in the it1 background. All these mutants carried an additional mutation in the it1 gene. These results suggest that the pleiotropic phenotype of it1 is caused by the mutation in the α-tubulin gene.

Summary: Cytosine methylation is an important epigenetic modification involved in regulation of plant development. However, the epigenetic mechanisms governing peanut seed development remain unclear. Herein, we generated DNA methylation profiles of developmental seeds of peanut H2014 and its smaller seed mutant H1314 at 15 and 60 days after pegging (DAP, S1, S4). Accompanying seed development, globally elevated methylation was observed in both lines. The mutant had a higher methylation level of 31.1% than wild type at S4, and 27.1–35.9% of the differentially methylated regions (DMRs) between the two lines were distributed in promoter or genic regions at both stages. Integrated methylome and transcriptome analysis revealed important methylation variations closely associated with seed development. Furthermore, some genes showed significantly negative correlation of expression with the methylation level within promoter or gene body. The results provide insights into the roles of DNA methylation in peanut seed development.

Peanut (Arachis hypogea L.) bacterial wilt (BW) is a devastating disease caused by Ralstonia solanacearum that results in severe yield and quality losses. Plant defensins are short cysteine-rich peptides with antimicrobial activity. The role of defensin genes (AhDef) in peanut is unclear. A genome-wide investigation of AhDef genes was undertaken, and 12 identified AhDef genes were classified into two groups containing the gamma-thionin domain formed by four disulfide pairs: Cys1-Cys8, Cys2-Cys5, Cys3-Cys6, and Cys4-Cys7. In silico analysis revealed that AhDef genes showed highly conserved architectural features and contained cis-elements associated with phytohormone signaling and defense responses. A highly resistant cultivar, H108 (R) and a susceptible accession, H107 (S) were tested by R. solanacearum inoculation. H108 (R) showed fewer symptoms than H107 (S) owing to inhibition of bacterial reproduction and spread in the vascular bundles of roots and stems. In a transcriptomic expression profile, AhDef genes, particularly AhDef1.6 and AhDef2.2, were up-regulated in H108 (R) compared with H107 (S) under R. solanacearum infection and phytohormone treatment. Subcellular localization showed that the AhDef1.6 and AhDef2.2 proteins were both expressed specifically on the plasma membrane. Overexpression of protein fusion AhDef2.2-YFP in Nicotiana benthamiana and peanut leaves increased resistance to R. solanacearum, suggesting its role in response to BW infection. AhDef2.2 may be valuable for peanut resistance breeding.

Abstract Background Bernese periacetabular osteotomy (PAO) is an effective treatment for patients with developmental dysplasia of the hip (DDH). PAO has been widely used in China, but few follow-up outcomes have been reported in the international community. Moreover, the risk factors affecting patient-reported outcomes have not been discussed in recent studies. In this study, patient-reported outcomes after PAO were reported, and risk factors affecting patient-reported outcomes were analyzed. Methods Patients who underwent PAO for DDH from January 2014 to January 2020 were selected as the study subjects, and 66 hips were included in the analysis after screening (59 patients, with an average follow-up time of 3.01 years). The Harris Hip Score (HHS) and International Hip Outcome Instrument-12 (iHOT-12) were used to assess hip function and patient quality of life. The changes of preoperative and latest follow-up HHSs less than 9 were defined as symptomatic hips, that is, an adverse outcome; otherwise, the score indicates preserved hips. Also, the changes of preoperative and latest follow-up iHOT-12 were defined as symptomatic hips and preserved hips. Multivariate logistic regression analysis was used to predict the risk factors influencing the patient-reported outcomes, and receiver operating characteristic (ROC) curve analysis was performed on the risk factors to determine their sensitivity, specificity and cutoff value. Results Clinical outcome analysis demonstrates marked improvements in patient-reported outcomes. The multivariate logistic regression analysis showed that when the postoperative LCEA was > 38°, adverse outcomes were much more likely. However, a Tönnis angle of − 10° to 0° was a protective factor. In addition, hips with fair or poor joint congruency were more likely to develop negative outcomes. The ROC curve analysis showed that the optimal thresholds for the LCEA and Tönnis angles used to predict outcomes after PAO were 38.2° and − 9°, respectively. Based on the results of the ROC curve analysis, among hips with poor or fair joint congruency preoperatively treated by surgeons who obtained the improper postoperative LCEAs and Tönnis angles, bad patient-reported outcomes will most likely be obtained. Conclusions Our results demonstrate marked improvements in patient-reported outcomes. Among hips with preoperative excellent or good joint congruency treated by experienced surgeons who obtain the proper postoperative LCEA and Tönnis angles, good patient-reported outcomes can be expected.

Abstract Background Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. Conclusions Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.

Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.

Herein we performed bioinformatics analysis of patatin-like protein (PLP) family genes, including gene numbers, gene structure, chromosomal distribution, and expression levels, in order to establish a theoretical foundation for genes encoding PLPs in peanut (Arachis hypogaea L.). In total, 49 PLP family members were identified: 26 in A. hypogaea, 11 in A. duranansis (AA), and 12 in A. ipaënsis (BB). They were classified into four categories (class II, III, V and VI), and unevenly distributed on 20 chromosomes. Gene structure analysis revealed that the exon numbers varied from 2 to 14, and the length of amino acid ranged from 157 to 812 aa with isoelectric point (pI) ranged from 4.55 to 8.74. All the PLP family members contained the conserved patatin-like phospholipase domain, but none of them contained signal peptides, and only four contained transmembrane domains. Promoter analysis showed that PLP-encoding genes contained cis-acting regulatory elements related to hormone responses, environmental adaptability and stress response induction. RNA-seq data showed that these genes were expressed under different spatiotemporal conditions. The relative expression levels of PLP-encoding genes in different tissues were detected using quantitative real-time polymerase chain reaction (qRT-PCR). AhPLP1 and AhPLP10 expression levels in flowers were relatively high, while AhPLP4 expression level in roots, stems, and flowers was extremely low, which indicated the potential functions of PLPs in peanut.

Multiple object tracking based on tracking-by-detection is the most common method used in addressing illumination change and occlusion problems. In this paper, we present a tracking algorithm based on Edge Multi-channel Gradient Model. We first use the canny operator to extract the edges of the image, and establish a biologically inspired Multi-channel Gradient Model that integrate the spatio-temporal-spectral information of the edge to detect moving multiple objects. Under this model, the ORB feature is introduced to solve the problem of matching the object with the object library. Therefore, we can achieve object consistency, and the threshold classification method can solve the problem of multiple object occlusion in the process of persistent multiple object tracking. The experimental results show that the proposed method can effectively deal with the problems of occlusion and illumination changes. Compared with other state-of-the-art algorithms, the proposed algorithm achieves better performance on MOTA, MOTP, and IDF1. In particular, it performs best on IDSW on MOT2015 dataset, with an average improvement ratio of 28.99% over the second-place algorithm. In addition, our algorithm has a better performance in running time, achieving a good compromise between the speed and the accuracy.

Abstract Background Knee osteoarthritis (KOA), with a high incidence in old-age population, adversely affects their life quality. The valgus knee bracing is an important physical therapy for KOA, but its clinical effects on pain release and functional improvement remained unclear. This meta-analysis is to systematically evaluate the clinical outcomes of valgus knee bracing in patients with KOA. Methods A meta-analysis of clinical randomized controlled trials (RCTs) on pain and functional changes in patients with KOA after using valgus knee braces. The search period was ranged from the inception of the database to May 2020. The enrolled research databases included PubMed, Embase, and Web of Science databases. Two investigators independently formulated inclusion criteria and exclusion criteria and screened and determined the final enrolled literature. Then the outcome indicators were extracted and organized from the included literature, and the risk of bias was assessed by Cochrane Handbook 5.0.1. Results A total of 10 articles were included in this study, including 739 patients. Eight articles were related to the visual analog scale (VAS) pain score, and the results showed that RR = − 0.29, 95% CI − 0.73, 0.15], P = 0.20; four articles were related to the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) function score, and the results showed that RR = − 0.15, 95% CI [− 0.41, 0.11], P = 0.26; two articles were related to the Knee Injury and Osteoarthritis Outcome Score (KOOS), and the results showed that RR = 0.58, 95% CI [− 4.25, 5.42], P = 0.81; and three articles were related to the KOOS Activities of Daily Living (KOOS-ADL), and the results showed that RR = 0.04, 95% CI [− 0.62, 0.69], P = 0.91. These results indicated that the valgus knee bracing has no statistical significance in pain and functional activity improvement of patients with KOA. The subgroup analysis showed that the follow-up time was the source of the heterogeneity of the VAS pain score. Conclusion Our current evidence suggests that valgus knee bracing may not improve pain release and function activates in KOA patients in the long-term period, but only being beneficial to the short-term rehabilitation.

Abstract Background Long noncoding RNAs (lncRNAs) have several known functions involving various biological regulatory processes in plant. However, the possible roles of lncRNAs during peanut seed development have not been fully explored. Results In this study, two peanut recombinant inbred lines (RIL8) that differ in seed size were used to investigate comprehensive lncRNA profiles derived from the seed development at 15 and 35 days after flowering (DAF). We identified a total of 9388 known and 4037 novel lncRNAs, from which 1437 were differentially expressed lncRNAs. Interestingly, the expression patterns of a number of lncRNAs can be very different between two closely related inbred lines and these lncRNAs were expressed predominantly in only one RIL at 35 DAF. Some differentially expressed lncRNAs were found related to putative cis-acting target genes and predicted to be involved in transcription, transport, cell division, and plant hormone biosynthesis. The expression patterns of several representative lncRNAs and 12 protein-coding genes were validated by qPCR. Same expression pattern was observed between most lncRNAs and their target genes. 11 lncRNAs, XR_001593099.1, MSTRG.18462.1, MSTRG.34915.1, MSTRG.41848.1, MSTRG.22884.1, MSTRG.12404.1, MSTRG.26719.1, MSTRG.35761.1, MSTRG.20033.1, MSTRG.13500.1, and MSTRG.9304.1 and their cis-acting target genes may play key roles in peanut seed development. Conclusions These results provided new information on lncRNA-mediated regulatory roles in peanut seed development, contributing to the comprehensive understanding of the molecular mechanisms involved in peanut seed development.

Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I–VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.

Abstract Background Circular RNAs (circRNAs), a class of widely expressed endogenous regulatory RNAs, are involved in diverse physiological and developmental processes in eukaryotic cells. However, there have been no related studies on the number of circRNAs and their overall characteristics including circRNA abundance and expression profiles in peanut, which is one of the most important edible oil seed crops in the world. Results We performed a genome-wide identification of circular RNAs using ribosomal-depleted RNA-sequencing from the seeds of two peanut eighth-generation recombinant inbred lines (RIL8): ‘RIL 8106’ (a medium-pod variety) and ‘RIL 8107’ (a super-pod variety), at 15 and 35 days after flowering (DAF), respectively. A total of 347 circRNA candidates were detected by two computational pipelines: CIRCexplorer and CIRI, with at least two supporting junction reads. All these circRNAs were generated from exons of annotated genes, and widespread on the 20 peanut chromosomes. The expression profiles revealed that circRNAs were differentially expressed between two stages and between two lines. GO enrichment analysis of the host genes produced differentially-expressed circRNAs suggested that circRNAs are involved in seed development and regulation of seed size. Fifteen circRNAs were experimentally analyzed by qRT-PCR with divergent primers, and six circRNAs were resistant to digestion with RNase R exonuclease, and the back-splicing sites were further validated by Sanger DNA sequencing. Conclusions We present the first systematical investigation of the genomic characteristics and expression profiles of circRNAs in peanut. The results revealed that circRNAs are abundant and widespread in peanut, and the differentially-expressed circRNAs between two lines suggested that they might play regulatory roles in peanut seeds development.

Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8–34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.

Abstract Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. However, little is known about A. monticola and its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV‐associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance.

Triptolide, the main active ingredient in Tripterygium wilfordiiHook. f. (Celastraceae), has shown promising effects against a variety of tumors. However, the molecular pharmacological mechanisms explaining the action of triptolide remain unknown. In this study, the CT26 colon tumor cell line was inoculated subcutaneously into BALB/c mice, and plasma samples were subjected to 1H NMR metabolomics analysis. The metabolic signature identified five metabolites whose levels were lower and 15 whose levels were higher in CT26 tumor-bearing mice than in normal control mice. Triptolide treatment significantly reversed the levels of nine of these metabolites, including isoleucine, glutamine, methionine, proline, 3-hydroxybutyric acid, 2-hydroxyisovalerate, 2-hydroxyisobutyrate, and low-density lipoprotein/very low-density lipoprotein. Based on the identities of these potential biomarkers, we conclude that the antitumor mechanism of triptolide might rely on correcting perturbations in branched-chain amino acid metabolism, serine/glycine/methionine biosynthesis, and ketone bodies metabolism.

Objective: To evaluate the efficacy of traditional Chinese herbs on heart failure (HF) using nuclear magnetic resonance (NMR) metabolomics. Methods: Plasma metabolomics was conducted on both patients with HF and healthy controls. The partial least squares model was applied to determine potential metabolic markers and related metabolic pathways of the disease. HF patients with the traditional Chinese syndrome pattern of qi deficiency and blood stasis were divided into two groups, and treated, respectively, with conventional medicine and a combination of conventional and Chinese herbs, aimed at tonifying qi and activating blood. Healthy participants served as a control group for comparison. Results and conclusion: Both conventional and herbal treatments appear to regulate disorders of amino acid and glucose metabolism. Combined treatment appears to be more comprehensive, indicating that herbal and conventional medicines exert their effects through different mechanisms in treating HF. It can be further inferred that herbs that tonify qi and activate blood may regulate different essential metabolites.

“RenqingMangjue” pill (RMP), as an effective prescription of Traditional Tibetan Medicine (TTM), has been widely used in treating digestive diseases and ulcerative colitis for over a thousand years. In certain classical Tibetan Medicine, heavy metal may add as an active ingredient, but it may cause contamination unintentionally in some cases. Therefore, the toxicity and adverse effects of TTM became to draw public attention. In this study, 48 male Wistar rats were orally administrated with different dosages of RMP once a day for 15 consecutive days, then half of the rats were euthanized on the 15th day and the remaining were euthanized on the 30th day. Plasma, kidney and liver samples were acquired to 1H NMR metabolomics analysis. Histopathology and ICP-MS were applied to support the metabolomics findings. The metabolic signature of plasma from RMP-administrated rats exhibited increasing levels of glucose, betaine, and creatine, together with decreasing levels of lipids, 3-hydroxybutate, pyruvate, citrate, valine, leucine, isoleucine, glutamate, and glutamine. The metabolomics analysis results of liver showed that after RMP administration, the concentrations of valine, leucine, proline, tyrosine, and tryptophan elevated, while glucose, sarcosine and 3-hydroxybutyrate decreased. The levels of metabolites in kidney, such as, leucine, valine, isoleucine and tyrosine, were increased, while taurine, glutamate, and glutamine decreased. The study provides several potential biomarkers for the toxicity mechanism research of RMP and shows that RMP may cause injury in kidney and liver and disturbance of several pathways, such as energy metabolism, oxidative stress, glucose and amino acids metabolism.

A new swarm intelligence optimization algorithm is proposed to simulate the long-distance flight process of dandelion seeds as a function of wind by the dandelion optimizer (DO). An improved version of DO, called IDO, is proposed to overcome the shortcomings of slow optimization speed and vulnerability to local optimum of the algorithm. In the landing stage of the dandelion seeds, IDO introduces the elite pool roulette wheel selection mechanism to maintain the diversity of the dandelion population, which enables the algorithm to maintain a better optimization ability. In the rising stage, a gamma distribution is introduced to make the algorithm population more diverse, thus improving its optimization capabilities. Finally, the mirror reversal strategy is introduced to search for the mirror solutions of inferior particles in the population surrounding the optimal individual, which helps the population to escape from local optima. The performance of the proposed improved IDO algorithm was tested against the CEC-2017, CEC-2020, and CEC-2022 benchmark functions. Finally, three engineering design problems were optimized, namely, three-bar truss design, cantilever design, and pressure vessel design. The experimental results show that the proposed IDO algorithm significantly improves the convergence rate and optimization accuracy. The experimental results show that the proposed IDO algorithm optimizes the exploitation and exploration process, improves the convergence rate and optimization accuracy. [ABSTRACT FROM AUTHOR]