Therapeutic Efficacy, Safety and Predictive Indicators of Eribulin Plus Anti-Angiogenic Medicine for Metastatic Breast Cancer.

OBJECTIVE: To evaluate the efficacy and safety of eribulin plus anti-angiogenic medicine in metastatic breast cancer (MBC), and explore the potential biomarkers. STUDY DESIGN: Observational study. Place and Duration of the Study: Department of Medical Oncology, Xi'an International Medical Centre Hospital, Xi'an, China, from May 2022 to 2023. METHODOLOGY: A total of 40 MBC patients treated with eribulin were enrolled. Patients were divided into two groups based on whether they received eribulin monotherapy or combined therapy. Median progression-free survival (mPFS), the time from the start of erbium treatment to the time of disease progression, was calculated using the Kaplan-Meier method. RESULTS: The eribulin plus anti-angiogenic medicine treatment group had a significantly prolonged mPFS compared to the group without anti-angiogenic medicine treatment (7.0 months vs. 2.0 months, p <0.001). The multivariate analysis identified that the combination of anti-angiogenic therapy (HR = 0.043, p = 0.004) and the occurrence of grade 3-4 neutropenia after the treatment were two predictive factors for longer PFS (HR = 0.322, p = 0.009). In contrast, prior resistance to taxane was predictive of shorter PFS (HR = 4.583, p = 0.019). Other clinic-pathological factors were not significantly associated with PFS. Fisher's exact test showed no significant increase in treatment-related adverse events (all grades) after combination with anti-angiogenic medicine. CONCLUSION: The eribulin plus anti-angiogenic combination may act as a potential therapy for late-line MBC patients with clinically beneficial therapeutic effects. KEY WORDS: Metastatic breast cancer, Eribulin, Anti-angiogenic therapy, Predictive indicators of efficacy.

Clpf encodes pentatricopeptide repeat protein (PPR5) and regulates pink flesh color in watermelon (Citrullus lanatus L.).

KEY MESSAGE: The gene controlling pink flesh in watermelon was finely mapped to a 55.26-kb region on chromosome 6. The prime candidate gene, Cla97C06G122120 (ClPPR5), was identified through forward genetics. Carotenoids offer numerous health benefits; while, they cannot be synthesized by the human body. Watermelon stands out as one of the richest sources of carotenoids. In this study, genetic generations derived from parental lines W15-059 (red flesh) and JQ13-3 (pink flesh) revealed the presence of the recessive gene Clpf responsible for the pink flesh (pf) trait in watermelon. Comparative analysis of pigment components and microstructure indicated that the disparity in flesh color between the parental lines primarily stemmed from variations in lycopene content, as well as differences in chromoplast number and size. Subsequent bulk segregant analysis (BSA-seq) and genetic mapping successfully narrowed down the Clpf locus to a 55.26-kb region on chromosome 6, harboring two candidate genes. Through sequence comparison and gene expression analysis, Cla97C06G122120 (annotated as a pentatricopeptide repeat, PPR) was predicted as the prime candidate gene related to pink flesh trait. To further investigate the role of the PPR gene, its homologous gene in tomato was silenced using a virus-induced system. The resulting silenced fruit lines displayed diminished carotenoid accumulation compared with the wild-type, indicating the potential regulatory function of the PPR gene in pigment accumulation. This study significantly contributes to our understanding of the forward genetics underlying watermelon flesh traits, particularly in relation to carotenoid accumulation. The findings lay essential groundwork for elucidating mechanisms governing pigment synthesis and deposition in watermelon flesh, thereby providing valuable insights for future breeding strategies aimed at enhancing fruit quality and nutritional value.

Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction.

The development and function of the immune system are controlled by temporospatial gene expression programs, which are regulated by cis-regulatory elements, chromatin structure, and trans-acting factors. In this study, we cataloged the dynamic histone modifications and chromatin interactions at regulatory regions during T helper (Th) cell differentiation. Our data revealed that the H3K4me1 landscape established by MLL4 in naive CD4+ T cells is critical for restructuring the regulatory interaction network and orchestrating gene expression during the early phase of Th differentiation. GATA3 plays a crucial role in further configuring H3K4me1 modification and the chromatin interaction network during Th2 differentiation. Furthermore, we demonstrated that HSS3-anchored chromatin loops function to restrict the activity of the Th2 locus control region (LCR), thus coordinating the expression of Th2 cytokines. Our results provide insights into the mechanisms of how the interplay between histone modifications, chromatin looping, and trans-acting factors contributes to the differentiation of Th cells.

Identification of Chromosomal Regions and Candidate Genes for Round leaf Locus in Cucumis melo L.

Leaf morphology plays a crucial role in plant classification and provides a significant model for studying plant diversity while directly impacting photosynthetic efficiency. In the case of melons, leaf shape not only influences production and classification but also represents a key genetic trait that requires further exploration. In this study, we utilized forward genetics to pinpoint a recessive locus, dubbed Cmrl (Round leaf), which is responsible for regulating melon leaf shape. Through bulked segregant analysis sequencing and extensive evaluation of a two-year F2 population, we successfully mapped the Cmrl locus to a 537.07 kb region on chromosome 8 of the melon genome. Subsequent genetic fine-mapping efforts, leveraging a larger F2 population encompassing 1322 plants and incorporating F2:3 phenotypic data, further refined the locus to an 80.27 kb interval housing five candidate genes. Promoter analysis and coding sequence cloning confirmed that one of these candidates, MELO3C019152.2 (Cmppr encoding a pentatricopeptide repeat-containing family protein, Cmppr), stands out as a strong candidate gene for the Cmrl locus. Notably, comparisons of Cmrl expressions across various stages of leaf development and different leaf regions suggest a pivotal role of Cmrl in the morphogenesis of melon leaves.

Deciphering the Genomic Characterization of the GGP Gene Family and Expression Verification of CmGGP1 Modulating Ascorbic Acid Biosynthesis in Melon Plants.

Ascorbic acid (AsA), also known as vitamin C, is a well-known antioxidant found in living entities that plays an essential role in growth and development, as well as in defensive mechanisms. GDP-L-galactose phosphorylase (GGP) is a candidate gene regulating AsA biosynthesis at the translational and transcriptional levels in plants. In the current study, we conducted genome-wide bioinformatic analysis and pinpointed a single AsA synthesis rate-limiting enzyme gene in melon (CmGGP1). The protein prediction analysis depicted that the CmGGP1 protein does not have a signaling peptide or transmembrane structure and mainly functions in the chloroplast or nucleus. The constructed phylogenetic tree analysis in multispecies showed that the CmGGP1 protein has a highly conserved motif in cucurbit crops. The structural variation analysis of the CmGGP1 gene in different domesticated melon germplasms showed a single non-synonymous type-base mutation and indicated that this gene was selected by domestication during evolution. Wild-type (WT) and landrace (LDR) germplasms of melon depicted close relationships to each other, and improved-type (IMP) varieties showed modern domestication selection. The endogenous quantification of AsA content in both the young and old leaves of nine melon varieties exhibited the major differentiations for AsA synthesis and metabolism. The real-time quantitative polymerase chain reaction (qRT-PCR) analysis of gene co-expression showed that AsA biosynthesis in leaves was greater than AsA metabolic consumption, and four putative interactive genes (MELO3C025552.2, MELO3C007440.2, MELO3C023324.2, and MELO3C018576.2) associated with the CmGGP1 gene were revealed. Meanwhile, the CmGGP1 gene expression pattern was noticed to be up-regulated to varying degrees in different acclimated melons. We believe that the obtained results would provide useful insights for an in-depth genetic understanding of the AsA biosynthesis mechanism, aimed at the development of improving crop plants for melon.

Molecular Mapping of Putative Genomic Regions Controlling Fruit and Seed Morphology of Watermelon.

The genetic regulatory basis of qualitative and quantitative phenotypes of watermelon is being investigated in different types of molecular and genetic breeding studies around the world. In this study, biparental F2 mapping populations were developed over two experimental years, and the collected datasets of fruit and seed traits exhibited highly significant correlations. Whole-genome resequencing of comparative parental lines was performed and detected single nucleotide polymorphism (SNP) loci were converted into cleaved amplified polymorphic sequence (CAPS) markers. The screened polymorphic markers were genotyped in segregating populations and two genetic linkage maps were constructed, which covered a total of 2834.28 and 2721.45 centimorgan (cM) genetic lengths, respectively. A total of 22 quantitative trait loci (QTLs) for seven phenotypic traits were mapped; among them, five stable and major-effect QTLs (PC-8-1, SL-9-1, SWi-9-1, SSi-9-1, and SW-6-1) and four minor-effect QTLs (PC-2-1 and PC-2-2; PT-2-1 and PT-2-2; SL-6-1 and SSi-6-2; and SWi-6-1 and SWi-6-2) were observed with 3.77-38.98% PVE. The adjacent QTL markers showed a good fit marker-trait association, and a significant allele-specific contribution was also noticed for genetic inheritance of traits. Further, a total of four candidate genes (Cla97C09G179150, Cla97C09G179350, Cla97C09G180040, and Cla97C09G180100) were spotted in the stable colocalized QTLs of seed size linked traits (SL-9-1 and SWi-9-1) that showed non-synonymous type mutations. The gene expression trends indicated that the seed morphology had been formed in the early developmental stage and showed the genetic regulation of seed shape formation. Hence, we think that our identified QTLs and genes would provide powerful genetic insights for marker-assisted breeding aimed at improving the quality traits of watermelon.

Clorf Encodes Carotenoid Isomerase and Regulates Orange Flesh Color in Watermelon (Citrullus lanatus L.).

Flesh color is a significant characteristic of watermelon. Although various flesh-color genes have been identified, the inheritance and molecular basis of the orange flesh trait remain relatively unexplored. In the present study, the genetic analysis of six generations derived from W1-1 (red flesh) and W1-61 (orange flesh) revealed that the orange flesh color trait was regulated by a single recessive gene, Clorf (orange flesh). Bulk segregant analysis (BSA) locked the range to ∼4.66 Mb, and initial mapping situated the Clorf locus within a 688.35-kb region of watermelon chromosome 10. Another 1,026 F2 plants narrowed the Clorf locus to a 304.62-kb region containing 32 candidate genes. Subsequently, genome sequence variations in this 304.62-kb region were extracted for in silico BSA strategy among 11 resequenced lines (one orange flesh and ten nonorange flesh) and finally narrowed the Clorf locus into an 82.51-kb region containing nine candidate genes. Sequence variation analysis of coding regions and gene expression levels supports Cla97C10G200950 as the most possible candidate for Clorf, which encodes carotenoid isomerase (Crtiso). This study provides a genetic resource for investigating the orange flesh color of watermelon, with Clorf malfunction resulting in low lycopene accumulation and, thus, orange flesh.

The N-terminus of Spt16 anchors FACT to MCM2-7 for parental histone recycling.

Parental histone recycling is vital for maintaining chromatin-based epigenetic information during replication, yet its underlying mechanisms remain unclear. Here, we uncover an unexpected role of histone chaperone FACT and its N-terminus of the Spt16 subunit during parental histone recycling and transfer in budding yeast. Depletion of Spt16 and mutations at its middle domain that impair histone binding compromise parental histone recycling on both the leading and lagging strands of DNA replication forks. Intriguingly, deletion of the Spt16-N domain impairs parental histone recycling, with a more pronounced defect observed on the lagging strand. Mechanistically, the Spt16-N domain interacts with the replicative helicase MCM2-7 and facilitates the formation of a ternary complex involving FACT, histone H3/H4 and Mcm2 histone binding domain, critical for the recycling and transfer of parental histones to lagging strands. Lack of the Spt16-N domain weakens the FACT-MCM interaction and reduces parental histone recycling. We propose that the Spt16-N domain acts as a protein-protein interaction module, enabling FACT to function as a shuttle chaperone in collaboration with Mcm2 and potentially other replisome components for efficient local parental histone recycling and inheritance.

MiR-199a-3p promotes repair of myocardial infarction by targeting NACC2.

OBJECTIVE: Myocardial infarction (MI) has gained widespread interest due to its high death and disability rate worldwide. Some miRNAs are markers of heart disease. Therefore, it is necessary to understand the mechanism for repairing MI injury. METHODS: Here, we evaluated the relative expression levels of miR-199a-3p in mouse and human myocardial cell models of injury, and its effect on myocardial cells viability using Cell Counting Kit-8 (CCK-8) assay, 5-ethynyl-2'-deoxyuridline (EdU) assay, and flow cytometry assay as well as western blot in vitro. Furthermore, we performed bioinformatic online analysis to investigate the role that miR-199a-3p plays in cardiomyocyte injury, measured by dual-luciferase reporter assay. RESULTS: The results showed that miR-199a-3p significantly increased the growth rate of cardiomyocytes after treating them with hydrogen peroxide (H2O2). miR-199a-3p also acted as an inhibitor that directly targeted NACC2, resulting in a higher NACC2 expression level in the injury model of cardiomyocytes than normal myocardial cells and thus preventing miR-199a-3p-induced proliferation promotion in model cardiomyocytes. CONCLUSION: Our results demonstrate that miR-199a-3p may be a prognostic biomarker in myocardial injury.

Non-invasive hemodynamic diagnosis based on non-linear pulse wave theory applied to four limbs.

Introduction: Hemodynamic diagnosis indexes (HDIs) can comprehensively evaluate the health status of the cardiovascular system (CVS), particularly for people older than 50 years and prone to cardiovascular disease (CVDs). However, the accuracy of non-invasive detection remains unsatisfactory. We propose a non-invasive HDIs model based on the non-linear pulse wave theory (NonPWT) applied to four limbs. Methods: This algorithm establishes mathematical models, including pulse wave velocity and pressure information of the brachial and ankle arteries, pressure gradient, and blood flow. Blood flow is key to calculating HDIs. Herein, we derive blood flow equation for different times of the cardiac cycle considering the four different distributions of blood pressure and pulse wave of four limbs, then obtain the average blood flow in a cardiac cycle, and finally calculate the HDIs. Results: The results of the blood flow calculations reveal that the average blood flow in the upper extremity arteries is 10.78 ml/s (clinically: 2.5-12.67 ml/s), and the blood flow in the lower extremity arteries is higher than that in the upper extremity. To verify model accuracy, the consistency between the clinical and calculated values is verified with no statistically significant differences (p < 0.05). Model IV or higher-order fitting is the closest. To verify the model generalizability, considering the risk factors of cardiovascular diseases, the HDIs are recalculated using model IV, and thus, consistency is verified (p < 0.05 and Bland-Altman plot). Conclusion: We conclude our proposed algorithmic model based on NonPWT can facilitate the non-invasive hemodynamic diagnosis with simpler operational procedures and reduced medical costs.

PANDEMIC: Occupancy driven predictive ventilation control to minimize energy consumption and infection risk.

During the SARS-CoV-2 (COVID-19) pandemic, governments around the world have formulated policies requiring ventilation systems to operate at a higher outdoor fresh air flow rate for a sufficient time, which has led to a sharp increase in building energy consumption. Therefore, it is necessary to identify an energy-efficient ventilation strategy to reduce the risk of infection. In this study, we developed an occupant-number-based model predictive control (OBMPC) algorithm for building ventilation systems. First, we collected the occupancy and Heating, ventilation, and air conditioning system (HVAC) data from March to July 2021. Then, four different models (Auto regression moving average-based multilayer perceptron (ARMA_MLP), Recurrent neural networks (RNN), Long short-term memory networks (LSTM), and Nonhomogeneous Markov with change points detection (NH_Markov)) were used to predict the number of room occupants from 15 min to 24 h ahead with an interval output. We found that each model could predict the number of occupants with 85 % accuracy using a one-person offset. The accuracy of 15 min of the ahead prediction could reach 95 % with a one-person offset, but none of them could track abrupt changes. The occupancy prediction results were used to calculate the ventilation demand using the Wells-Riley equation, and the upper bound can maintain an infection risk lower than 2 % for 93 % of the day. This OBMPC model could reduce the coil load by 52.44 % and shift the peak load by 3 h up to 5 kW compared with 24 × 7 h full outdoor air (OA) system when people wear masks in the space. The occupancy prediction uncertainty could cause a 9 % to 26 % difference in demand ventilation, a 0.3 °C to 2.4 °C difference in zone temperature, a 28.5 % to 44.5 % difference in outdoor airflow rate, and a 10.7 % to 28.2 % difference in coil load.

Nationwide evaluation of energy and indoor air quality predictive control and impact on infection risk for cooling season.

Since the coronavirus disease 2019, the extended time indoors makes people more concerned about indoor air quality, while the increased ventilation in seeks of reducing infection probability has increased the energy usage from heating, ventilation, and air-conditioning systems. In this study, to represent the dynamics of indoor temperature and air quality, a coupled grey-box model is developed. The model is identified and validated using a data-driven approach and real-time measured data of a campus office. To manage building energy usage and indoor air quality, a model predictive control strategy is proposed and developed. The simulation study demonstrated 18.92% energy saving while maintaining good indoor air quality at the testing site. Two nationwide simulation studies assessed the overall energy saving potential and the impact on the infection probability of the proposed strategy in different climate zones. The results showed 20%-40% energy saving in general while maintaining a predetermined indoor air quality setpoint. Although the infection risk is increased due to the reduced ventilation rate, it is still less than the suggested threshold (2%) in general. Electronic Supplementary Material ESM: The Appendix is available in the online version of this article at 10.1007/s12273-022-0936-6.

Single-cell RNA-seq reveals early heterogeneity during aging in yeast.

The budding yeast Saccharomyces cerevisiae (S. cerevisiae) has relatively short lifespan and is genetically tractable, making it a widely used model organism in aging research. Here, we carried out a systematic and quantitative investigation of yeast aging with single-cell resolution through transcriptomic sequencing. We optimized a single-cell RNA sequencing (scRNA-seq) protocol to quantitatively study the whole transcriptome profiles of single yeast cells at different ages, finding increased cell-to-cell transcriptional variability during aging. The single-cell transcriptome analysis also highlighted key biological processes or cellular components, including oxidation-reduction process, oxidative stress response (OSR), translation, ribosome biogenesis and mitochondrion that underlie aging in yeast. We uncovered a molecular marker of FIT3, indicating the early heterogeneity during aging in yeast. We also analyzed the regulation of transcription factors and further characterized the distinctive temporal regulation of the OSR by YAP1 and proteasome activity by RPN4 during aging in yeast. Overall, our data profoundly reveal early heterogeneity during aging in yeast and shed light on the aging dynamics at the single cell level.

Transcriptomic Analysis of Fusarium oxysporum Stress-Induced Pathosystem and Screening of Fom-2 Interaction Factors in Contrasted Melon Plants.

Fusarium wilt is one of the most destructive and less controllable diseases in melon, which is usually caused by fusarium oxysporum. In this study, transcriptome sequencing and Yeast Two-Hybrid (Y2H) methods were used for quantification of differentially expressed genes (DEGs) involved in fusarium oxysporum (f. sp. melonis race 1) stress-induced mechanisms in contrasted melon varieties (M4-45 "susceptible" and MR-1 "resistant"). The interaction factors of Fom-2 resistance genes were also explored in response to the plant-pathogen infection mechanism. Transcriptomic analysis exhibited total 1,904 new genes; however, candidate DEGs analysis revealed a total of 144 specific genes (50 upregulated and 94 downregulated) for M4-45 variety and 104 specific genes (71 upregulated and 33 downregulated) for MR-1 variety, respectively. The analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway depicted some candidate DEGs, including Phenylalanine metabolism, phenylpropane biosynthesis, plants-pathogen interaction, and signal transduction of plant hormones, which were mainly involved in disease resistance metabolic pathways. The weighted gene co-expression network analysis (WGCNA) analysis revealed a strong correlation module and exhibited the disease resistance-related genes encoding course proteins, transcription factors, protein kinase, benzene propane biosynthesis path, plants-pathogen interaction pathway, and glutathione S-transferase. Meanwhile, the resistance-related specific genes expression was relatively abundant in MR-1 compared to the M4-45, and cell wall-associated receptor kinases (MELO3C008452 and MELO3C008453), heat shock protein (Cucumis_melo_newGene_172), defensin-like protein (Cucumis_melo_newGene_5490), and disease resistance response protein (MELO3C016325), activator response protein (MELO3C021623), leucine-rich repeat receptor protein kinase (MELO3C024412), lactyl glutathione ligase (Cucumis_melo_newGene_36), and unknown protein (MELO3C007588) were persisted by exhibiting the upregulated expressions. At the transcription level, the interaction factors between the candidate genes in response to the fusarium oxysporum induced stress, and Y2H screening signified the main contribution of MYB transcription factors (MELO3C009678 and MELO3C014597), BZIP (MELO3C011839 and MELO3C019349), unknown proteins, and key enzymes in the ubiquitination process (4XM334FK014). The candidate genes were further verified in exogenously treated melon plants with f. oxysporum (Fom-2, Race 1), Abscisic acid (ABA), Methyl Jasmonite (MeJA), and Salicylic acid (SA), using the fluorescence quantitative polymerase chain reaction (qRT-PCR) analysis. The overall expression results indicated that the SA signal pathway is involved in effective regulation of the Fom-2 gene activity.

Development of Whole Genome SNP-CAPS Markers and Preliminary QTL Mapping of Fruit Pedicel Traits in Watermelon.

Fruit pedicel (FP) is an important determinant of premium fruit quality that directly affects commercial market value. However, in-depth molecular and genetic basis of pedicel-related traits has not been identified in watermelon. Herein, a quantitative trait locus (QTL) mapping strategy was used to identify the potential genetic regions controlling FP traits based on newly derived whole-genome single nucleotide polymorphism based cleaved amplified polymorphism sequence (SNP-CAPS) markers. Next-generation sequencing based whole-genome re-sequencing of two watermelon parent lines revealed 98.30 and 98.40% of average coverage, 4,989,869 SNP variants, and 182,949 CAPS loci pairs across the reference genome, respectively. A total of 221 sets of codominant markers exhibited 46.42% polymorphism rate and were effectively genotyped within 100-F2:3 derived mapping population. The developed linkage map covered a total of 2,630.49 cM genetic length with averaged 11.90 cM, and depicted a valid marker-trait association. In total, 6 QTLs (qFPL4.1, qFPW4.1, qFPD2.1, qFPD2.2, qFPD8.1, qFPD10.1) were mapped with five major effects and one minor effect between the whole genome adjacent markers positioned over distinct chromosomes (02, 04, 08, 10), based on the ICIM-ADD mapping approach. These significant QTLs were similarly mapped in delimited flanking regions of 675.10, 751.38, 859.24, 948.39, and 947.51 kb, which collectively explained 8.64-13.60% PVE, respectively. A highly significant and positive correlation was found among the observed variables. To our knowledge, we first time reported the mapped QTLs/genes affecting FP traits of watermelon, and our illustrated outcomes will deliver the potential insights for fine genetic mapping as well as functional gene analysis through MAS-based breeding approaches.

Mapping of genetic loci controlling fruit linked morphological traits of melon using developed CAPS markers.

BACKGROUND: Fruit morphology traits are important commercial traits that directly affect the market value. However, studying the genetic basis of these traits in un-explored botanical groups is a fundamental objective for crop genetic improvement through marker-assisted breeding. METHODS AND RESULTS: In this study, a quantitative trait loci (QTLs) mapping strategy was used for dissecting the genomic regions of fruit linked morphological traits by single nucleotide polymorphism (SNP) based cleaved amplified polymorphism sequence (CAPS) molecular markers. Next-generation sequencing was done for the genomic sequencing of two contrasted melon lines (climacteric and non-climacteric), which revealed 97% and 96% of average coverage over the reference melon genome database, respectively. A total of 57.51% non-synonymous SNPs and 42.49% synonymous SNPs were found, which produced 149 sets of codominant markers with a 24% polymorphism rate. Total 138-F2 derived plant populations were genotyped for linkage mapping and composite interval mapping based QTL mapping exposed 6 genetic loci, positioned over distinct chromosomes (02, 04, 08, 09, and 12) between the flanking intervals of CAPS markers, which explained an unlinked polygenic architecture in genome. Three minor QTLs of fruit weight (FWt2.1, FWt4.1, FWt9.1), one major QTL of fruit firmness (FrFir8.1), one major QTL of fruit length (FL12.1), and one major QTL of fruit shape (FS12.1) were determined and collectively explained the phenotypic variance from 5.64 to 15.64%. Fruit phenotypic correlation exhibited the significant relationship and principal component analysis also identified the potential variability. Multiple sequence alignments also indicated the significant base-mutations in the detected genetic loci, respectively. CONCLUSION: In short, our illustrated genetic loci are expected to provide the reference insights for fine QTL mapping and candidate gene(s) mining through molecular genetic breeding approaches aimed at developing the new varieties.

Genome-Wide Analysis of the Peroxidase Gene Family and Verification of Lignin Synthesis-Related Genes in Watermelon.

Watermelon (Citrullus lanatus) is an important horticultural crop worldwide, but peel cracking caused by peel hardness severely decreases its quality. Lignification is one of the important functions of class III peroxidase (PRX), and its accumulation in the plant cell wall leads to cell thickening and wood hardening. For in-depth physiological and genetical understanding, we studied the relationship between peel hardness and lignin accumulation and the role of PRXs affecting peel lignin biosynthesis using genome-wide bioinformatics analysis. The obtained results showed that lignin accumulation gradually increased to form the peel stone cell structure, and tissue lignification led to peel hardness. A total of 79 ClPRXs (class III) were identified using bioinformatics analysis, which were widely distributed on 11 chromosomes. The constructed phylogenetics indicated that ClPRXs were divided into seven groups and eleven subclasses, and gene members of each group had highly conserved intron structures. Repeated pattern analysis showed that deletion and replication events occurred during the process of ClPRX amplification. However, in the whole-protein sequence alignment analysis, high homology was not observed, although all contained four conserved functional sites. Repeated pattern analysis showed that deletion and replication events occurred during ClPRXs' amplification process. The prediction of the promoter cis-acting element and qRT-PCR analysis in four tissues (leaf, petiole, stem, and peel) showed different expression patterns for tissue specificity, abiotic stress, and hormone response by providing a genetic basis of the ClPRX gene family involved in a variety of physiological processes in plants. To our knowledge, we for the first time report the key roles of two ClPRXs in watermelon peel lignin synthesis. In conclusion, the extensive data collected in this study can be used for additional functional analysis of ClPRXs in watermelon growth and development and hormone and abiotic stress response.

CmPMRl and CmPMrs are responsible for resistance to powdery mildew caused by Podosphaera xanthii race 1 in Melon.

KEY MESSAGE: Two genes for resistance to Podosphaera xanthii race 1 in melon were identified on chromosomes 10 and 12 of the Cucumis melo cultivar MR-1. Cucumis melo L. is an economically important crop, the production of which is threatened by the prevalence of melon powdery mildew (PM) infections. We herein utilized the MR-1 (P1; resistant to PM) and M4-7 (P2; susceptible to PM) accessions to assess the heritability of PM (race 1) resistance in these melon plants. PM resistance in MR-1 leaves was linked to a dominant gene (CmPMRl), whereas stem resistance was under the control of a recessive gene (CmPMrs), with the dominant gene having an epistatic effect on the recessive gene. The CmPMRl gene was mapped to a 50 Kb interval on chromosome 12, while CmPMrs was mapped to an 89 Kb interval on chromosome 10. The CmPMRl candidate gene MELO3C002441 and the CmPMrs candidate gene MELO3C012438 were identified through sequence alignment, functional annotation, and expression pattern analyzes of all genes within these respective intervals. MELO3C002441 and MELO3C012438 were both localized to the cellular membrane and were contained conserved NPR gene-like and MLO domains, respectively, which were linked to PM resistance. In summary, we identified patterns of PM resistance in the disease-resistant MR-1 melon cultivar and identified two putative genes linked to resistance. Our results offer new genetic resources and markers to guide future marker-assisted breeding for PM resistance in melon.

Nucleotide variation in the phytoene synthase (ClPsy1) gene contributes to golden flesh in watermelon (Citrullus lanatus L.).

KEY MESSAGE: A gene controlling golden flesh trait in watermelon was discovered and fine mapped to a 39.08 Kb region on chromosome 1 through a forward genetic strategy, and Cla97C01G008760 (annotated as phytoene synthase protein, ClPsy1 ) was recognized as the most likely candidate gene. Vitamin A deficiency is a worldwide public nutrition problem, and ß-carotene is the precursor for vitamin A synthesis. Watermelon with golden flesh (gf, which occurs due to an accumulated abundance of ß-carotene) is an important germplasm resource. In this study, a genetic analysis of segregated gf gene populations indicated that gf was controlled by a single recessive gene. BSA-seq (Bulked segregation analysis) and an initial linkage analysis placed the gf locus in a 290-Kb region on watermelon chromosome 1. Further fine mapping in a large population including over 1000 F2 plants narrowed this region to 39.08 Kb harboring two genes, Cla97C01G008760 and Cla97C01G008770, which encode phytoene synthase (ClPsy1) and GATA zinc finger domain-containing protein, respectively. Gene sequence alignment and expression analysis between parental lines revealed Cla97C01G008760 as the best possible candidate gene for the gf trait. Nonsynonymous SNP mutations in the first exon of ClPsy1 between parental lines co-segregated with the gf trait only among individuals in the genetic population and were not related to flesh color in natural watermelon panels. Promoter sequence analysis of 26 watermelon accessions revealed two SNPs in the cis-acting element sequences corresponding to MYB and MYC2 transcription factors. RNA-seq data and qRT-PCR verification showed that two MYBs exhibited expression trends similar to that of ClPsy1 in the parental lines and may regulate the ClPsy1 expression. Further research findings indicate that the gf trait is determined not only by ClPsy1 but also by ClLCYB, ClCRTISO and ClNCED7, which play important roles in watermelon ß-carotene accumulation.