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International Journal of Molecular... Feb 2023Rind color is an economically important agronomic trait in eggplant that impacts consumer preferences. In this study, bulked segregant analysis and competitive...
Rind color is an economically important agronomic trait in eggplant that impacts consumer preferences. In this study, bulked segregant analysis and competitive allele-specific PCR were employed to identify the candidate gene for eggplant rind color through constructing a 2794 F population generated from a cross between "BL01" (green pericarp) and "B1" (white pericarp). Genetic analysis of rind color revealed that a single dominant gene controls green color of eggplant peel. Pigment content measurement and cytological observations demonstrated that chlorophyll content and chloroplast number in BL01 were higher than in B1. A candidate gene (EGP19168.1) was fine-mapped to a 20.36 Kb interval on chromosome 8, which was predicted to encode the two-component response regulator-like protein Arabidopsis pseudo-response regulator2 (). Subsequently, allelic sequence analysis revealed that a SNP deletion (ACT→AT) in white-skinned eggplant led to a premature termination codon. Genotypic validation of 113 breeding lines using the Indel marker closely linked to could predict the skin color (green/white) trait with an accuracy of 92.9%. This study will be valuable for molecular marker-assisted selection in eggplant breeding and provides theoretical foundation for analyzing the formation mechanism of eggplant peel color.
Topics: Chromosome Mapping; Solanum melongena; Plant Breeding; Phenotype
PubMed: 36834473
DOI: 10.3390/ijms24043059 -
Frontiers in Oncology 2023Progressive enhancement predicted poor survival in ACRIN 6677/RTOG 0625, a multi-center trial of bevacizumab with irinotecan or temozolomide in recurrent glioblastoma,...
BACKGROUND
Progressive enhancement predicted poor survival in ACRIN 6677/RTOG 0625, a multi-center trial of bevacizumab with irinotecan or temozolomide in recurrent glioblastoma, but pseudoresponse likely limited enhancement-based survival prognostication in T1 non-progressors. We aimed to determine whether early change in cerebral blood volume from baseline (ΔCBV) could further stratify the T1 non-progressors according to overall (OS) and progression-free (PFS) survival.
METHODS
37/123 enrolled patients had DSC-MRI, including 13, 15, and 8 patients without 2D-T1 progression at 2, 8, and 16 weeks post-treatment initiation, respectively. Mean CBV normalized to white matter (nRCBV) and mean standardized CBV (sRCBV) were extracted from enhancing tumor. ROC curves were derived for ΔCBV using six-month PFS and one-year OS as reference standards. Kaplan-Meier survival estimates and log-rank test compared PFS and OS for both ΔCBV (increase vs. decrease) and T1 response status (stable vs. decreasing enhancement).
RESULTS
PFS and OS were significantly worse for increasing CBV at 2 weeks (p=0.003 and p=0.002 for nRCBV, and p=0.03 and p=0.03 for sRCBV, respectively), but not for 2D-T1 patients with stable vs. decreasing enhancement (p=0.44 and p=0.86, respectively). ΔCBV at week 2 was also a good prognostic marker for OS-1 and PFS-6 using ROC analysis. By contrast, 2D-T1 response status at weeks 2, 8, and 16 was not associated with PFS-6. ΔCBV at 16 weeks (p=0.008 for sRCBV) but not 8 weeks (p=0.74 for nRCBV and p=0.56 for sRCBV) was associated with significant difference in median survival, but no difference in survival was observed for 2D-T1 patients with stable vs. decreasing enhancement at 8 weeks (p=0.69) or 16 weeks (p=0.21). At 16 weeks, OS did not differ significantly between 2D-T1 progressors and 2D-T1 non-progressors with increasing CBV (median survival 3.3 months post week 16 scan vs. 9.2 months, respectively; p=0.13), suggesting that 2D-T1 non-progressors with increasing CBV may have a prognosis like that of 2D-T1 progressors.
CONCLUSION
After 2 weeks of anti-angiogenic therapy, ΔCBV in 2D-T1 non-progressors significantly prognosticated PFS and OS, whereas 2D-T1 response status did not, identifying a subpopulation that benefits from bevacizumab. Combining 2D-T1 progression and ΔCBV may yield a response assessment paradigm with 3-tiered OS stratification.
PubMed: 36776298
DOI: 10.3389/fonc.2023.1061502 -
Plant, Cell & Environment May 2023Plants adapt to high temperature stresses through thermomorphogenesis, a process that includes stem elongation and hyponastic leaf growth. Thermomorphogenesis is gated...
Plants adapt to high temperature stresses through thermomorphogenesis, a process that includes stem elongation and hyponastic leaf growth. Thermomorphogenesis is gated by the circadian clock through two evening-expressed clock components, TIMING OF CAB EXPRESSION1 (TOC1) and PSEUDO-RESPONSE REGULATORS5 (PRR5). These proteins directly interact with and inhibit PHYTOCHROME INTERACTING FACTOR4 (PIF4), a basic helix-loop-helix transcription factor that promotes thermoresponsive growth. PIF4-mediated thermoresponsive growth is positively regulated by ZEITLUPE (ZTL), a central clock component, but the molecular mechanisms underlying this are poorly understood. Here, we show that ZTL regulates thermoresponsive growth through TOC1 and PRR5. Genetic analyses reveal that ZTL regulates PIF4 activity as well as PIF4 expression. In Arabidopsis thaliana, ztl mutants exhibit highly accumulated TOC1 and PRR5 and unresponsive expression of PIF4 target genes under exposure to high temperatures. Mutations in TOC1 and PRR5 restore thermoactivation of PIF4 target genes and thermoresponsive growth in ztl mutants. We also show that the molecular chaperone heat-shock protein 90 promotes thermoresponsive growth through the ZTL-TOC1/PRR5 signaling module. Further, we show that ZTL protein stability is increased at high temperatures. Taken together, our results demonstrate that ZTL-mediated degradation of TOC1 and PRR5 enhances the sensitivity of hypocotyl growth to high temperatures.
Topics: Transcription Factors; Arabidopsis Proteins; Circadian Rhythm; Arabidopsis; Basic Helix-Loop-Helix Transcription Factors; Gene Expression Regulation, Plant
PubMed: 36655421
DOI: 10.1111/pce.14542 -
Plant & Cell Physiology Mar 2023The circadian clock allows plants to anticipate and adapt to periodic environmental changes. Organ- and tissue-specific properties of the circadian clock and...
The circadian clock allows plants to anticipate and adapt to periodic environmental changes. Organ- and tissue-specific properties of the circadian clock and shoot-to-root circadian signaling have been reported. While this long-distance signaling is thought to coordinate physiological functions across tissues, little is known about the feedback regulation of the root clock on the shoot clock in the hierarchical circadian network. Here, we show that the plant circadian clock conveys circadian information between shoots and roots through sucrose and K+. We also demonstrate that K+ transport from roots suppresses the variance of period length in shoots and then improves the accuracy of the shoot circadian clock. Sucrose measurements and qPCR showed that root sucrose accumulation was regulated by the circadian clock. Furthermore, root circadian clock genes, including PSEUDO-RESPONSE REGULATOR7 (PRR7), were regulated by sucrose, suggesting the involvement of sucrose from the shoot in the regulation of root clock gene expression. Therefore, we performed time-series measurements of xylem sap and micrografting experiments using prr7 mutants and showed that root PRR7 regulates K+ transport and suppresses variance of period length in the shoot. Our modeling analysis supports the idea that root-to-shoot signaling contributes to the precision of the shoot circadian clock. We performed micrografting experiments that illustrated how root PRR7 plays key roles in maintaining the accuracy of shoot circadian rhythms. We thus present a novel directional signaling pathway for circadian information from roots to shoots and propose that plants modulate physiological events in a timely manner through various timekeeping mechanisms.
Topics: Circadian Clocks; Arabidopsis Proteins; Arabidopsis; Circadian Rhythm; Signal Transduction; Gene Expression Regulation, Plant; Plant Roots
PubMed: 36631969
DOI: 10.1093/pcp/pcad003 -
Plant Physiology Mar 2023There is a close regulatory relationship between the circadian clock and the abscisic acid (ABA) signaling pathway in regulating many developmental processes and stress...
There is a close regulatory relationship between the circadian clock and the abscisic acid (ABA) signaling pathway in regulating many developmental processes and stress responses. However, the exact feedback regulation mechanism between them is still poorly understood. Here, we identified the rice (Oryza sativa) clock component PSEUDO-RESPONSE REGULATOR 95 (OsPRR95) as a transcriptional regulator that accelerates seed germination and seedling growth by inhibiting ABA signaling. We also found that OsPRR95 binds to the ABA receptor gene REGULATORY COMPONENTS OF ABA RECEPTORS10 (OsRCAR10) DNA and inhibits its expression. Genetic analysis showed OsRCAR10 acts downstream of OsPRR95 in mediating ABA responses. In addition, the induction of OsPRR95 by ABA partly required a functional OsRCAR10, and the ABA-responsive element-binding factor ABSCISIC ACID INSENSITIVE5 (OsABI5) bound directly to the promoter of OsPRR95 and activated its expression, thus establishing a regulatory feedback loop between OsPRR95, OsRCAR10, and OsABI5. Taken together, our results demonstrated that the OsRCAR10-OsABI5-OsPRR95 feedback loop modulates ABA signaling to fine-tune seed germination and seedling growth, thus establishing the molecular link between ABA signaling and the circadian clock.
Topics: Abscisic Acid; Oryza; Circadian Clocks; Arabidopsis; Germination; Seedlings; Seeds; Gene Expression Regulation, Plant
PubMed: 36493391
DOI: 10.1093/plphys/kiac548 -
International Journal of Molecular... Oct 2022Floral initiation is a major phase change in the spermatophyte, where developmental programs switch from vegetative growth to reproductive growth. It is a key phase of...
Floral initiation is a major phase change in the spermatophyte, where developmental programs switch from vegetative growth to reproductive growth. It is a key phase of flowering in tea-oil trees that can affect flowering time and yield, but very little is known about the molecular mechanism of floral initiation in tea-oil trees. A 12-year-old (cultivar 'changlin53') was the source of experimental materials in the current study. Scanning electron microscopy was used to identify the key stage of floral initiation, and transcriptome analysis was used to reveal the transcriptional regulatory network in old leaves involved in floral initiation. We mined 5 DEGs related to energy and 55 DEGs related to plant hormone signal transduction, and we found floral initiation induction required a high level of energy metabolism, and the phytohormones signals in the old leaves regulate floral initiation, which occurred at stage I and II. Twenty-seven rhythm-related DEGs and 107 genes associated with flowering were also identified, and the circadian rhythm interacted with photoperiod pathways to induce floral initiation. Unigene0017292 (), Unigene0046809 (), Unigene0009932 (), Unigene0001842 (), and Unigene0084708 () were the key genes in the circadian rhythm-photoperiod regulatory network. In conjunction with morphological observations and transcriptomic analysis, we concluded that the induction of floral initiation by old leaves in 'changlin53' mainly occurred during stages I and II, floral initiation was completed during stage III, and rhythm-photoperiod interactions may be the source of the main signals in floral initiation induced by old leaves.
Topics: Camellia; Trees; Gene Expression Profiling; Flowers; Plant Leaves; Plant Growth Regulators; Tea; Transcriptome; Gene Expression Regulation, Plant
PubMed: 36361817
DOI: 10.3390/ijms232113021 -
Frontiers in Plant Science 2022Wax gourd (), a popular fruit of the Cucurbitaceae (cucurbits) family, contains many nutrients with health benefits and is widely grown in China and other tropical...
Wax gourd (), a popular fruit of the Cucurbitaceae (cucurbits) family, contains many nutrients with health benefits and is widely grown in China and other tropical areas. In this study, a wax gourd mutant with light-color pericarp was obtained through ethane methylsulfonate (EMS) mutagenesis. Integrative analysis of the metabolome and transcriptome identified 31 differentially accumulated flavonoids (DAFs; flavonoids or flavonoid glycosides) and 828 differentially expressed genes (DEGs) between the mutant and wild-type 'BWT'. Furthermore, BSA-seq and kompetitive allele specific PCR (KASP) analysis suggested that the light-color pericarp and higher flavonoid content was controlled by a single gene (), a typical two-component system (TCS) pseudo-response regulator (PRR). Genetic analysis detected only one nonsynonymous mutation (C-T) in the second exon region of the . Weighted correlation network analysis (WGCNA) identified the downstream target genes of , probably regulated by light and were intermediated in the regulatory enzyme reaction of flavonoid biosynthetic pathway. Thus, these results speculated that the transcription factor , interacting with multiple genes, regulates the absorption of light signals and thereby changes the pericarp color and synthesis of flavonoids in wax gourd.
PubMed: 36226283
DOI: 10.3389/fpls.2022.1019787 -
Nature Communications Sep 2022Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this...
Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean.
Topics: Chromatin; Genomics; Humans; Phylogeny; Plant Breeding; Vigna
PubMed: 36175442
DOI: 10.1038/s41467-022-33515-2 -
The Plant Cell Jan 2023Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a...
Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a reduction of its photoperiod sensitivity. In this study, we cloned a quantitative trait locus (QTL) regulating flowering time in maize and show that the maize ortholog of Arabidopsis thaliana EARLY FLOWERING3, ZmELF3.1, is the causal locus. We demonstrate that ZmELF3.1 and ZmELF3.2 proteins can physically interact with ZmELF4.1/4.2 and ZmLUX1/2, to form evening complex(es; ECs) in the maize circadian clock. Loss-of-function mutants for ZmELF3.1/3.2 and ZmLUX1/2 exhibited delayed flowering under long-day and short-day conditions. We show that EC directly represses the expression of several flowering suppressor genes, such as the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes ZmCCT9 and ZmCCT10, ZmCONSTANS-LIKE 3, and the PSEUDORESPONSE REGULATOR (PRR) genes ZmPRR37a and ZmPRR73, thus alleviating their inhibition, allowing florigen gene expression and promoting flowering. Further, we identify two closely linked retrotransposons located in the ZmELF3.1 promoter that regulate the expression levels of ZmELF3.1 and may have been positively selected during postdomestication spread of maize from tropical to temperate regions during the pre-Columbian era. These findings provide insights into circadian clock-mediated regulation of photoperiodic flowering in maize and new targets of genetic improvement for breeding.
Topics: Zea mays; Flowers; Plant Proteins; Adaptation, Physiological; Acclimatization; Photoperiod; Arabidopsis; Gene Expression Regulation, Plant
PubMed: 36173348
DOI: 10.1093/plcell/koac296 -
Genetics and Molecular Biology 2022PSEUDO-RESPONSE PROTEINS (PRRs) are a gene family vital for the generation of rhythms by the circadian clock. Plants have circadian clocks, or circadian oscillators, to...
PSEUDO-RESPONSE PROTEINS (PRRs) are a gene family vital for the generation of rhythms by the circadian clock. Plants have circadian clocks, or circadian oscillators, to adapt to a rhythmic environment. The circadian clock system can be divided into three parts: the core oscillator, the input pathways, and the output pathways. The PRRs have a role in all three parts. These nuclear proteins have an N-terminal pseudo receiver domain and a C-terminal CONSTANS, CONSTANS-LIKE, and TOC1 (CCT) domain. The PRRs can be identified from green algae to monocots, ranging from one to >5 genes per species. Arabidopsis thaliana, for example, has five genes: PRR9, PRR7, PRR5, PRR3 and TOC1/PRR1. The PRR genes can be divided into three clades using protein homology: TOC1/PRR1, PRR7/3, and PRR9/5 expanded independently in eudicots and monocots. The PRRs can make protein complexes and bind to DNA, and the wide variety of protein-protein interactions are essential for the multiple roles in the circadian clock. In this review, the history of PRR research is briefly recapitulated, and the diversity of PRR genes in green and recent works about their role in the circadian clock are discussed.
PubMed: 36125163
DOI: 10.1590/1678-4685-GMB-2022-0137