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Frontiers in Genetics 2024Small RNAs (sRNAs) are important non-coding RNA regulators that play key roles in the development and pathogenesis of plant pathogens, as well as in other biological...
Small RNAs (sRNAs) are important non-coding RNA regulators that play key roles in the development and pathogenesis of plant pathogens, as well as in other biological processes. However, whether these abundant and varying sRNAs are involved in development or infection remains enigmatic. In this study, sRNA sequencing of 4 asexual stages of (), namely, as mycelia (HY), sporangia (SP), zoospores (ZO), cysts (CY), and pepper infected with (IN), were performed, followed by sRNA analysis, microRNA (miRNA) identification, and miRNA target prediction. sRNAs were mainly distributed at 25-26 nt in HY, SP, and ZO but distributed at 18-34 nt in CY and IN. 92, 42, 176, 39, and 148 known miRNAs and 15, 19, 54, 13, and 1 novel miRNA were identified in HY, SP, ZO, CY, and IN, respectively. It was found that the expression profiles of known miRNAs vary greatly at different stages and could be divided into 4 categories. Novel miRNAs mostly belong to part I. Gene ontology (GO) analysis of known miRNA-targeting genes showed that they are involved in the catalytic activity pathway, binding function, and other biological processes. Kyoto Encyclopedia of Gene and Genome (KEGG) analysis of novel miRNA-targeting genes showed that they are involved in the lysine degradation pathway. The expression of candidate miRNAs was validated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), and miRNAs were downregulated in or mutants. To further explore the function of the detected miRNAs, the precursor of a novel miRNA, miR91, was knockout by CRISPR-Cas9, the mutants displayed decreased mycelial growth, sporangia production, and zoospore production. It was found that 503142 (Inositol polyphosphate 5-phosphatase and related proteins) can be predicted as a target of miR91, and the interaction between miR91 and 503142 was verified using the tobacco transient expression system. Overall, our results indicate that the diverse and differentially expressed sRNAs are involved in the development and pathogenesis of
PubMed: 38919951
DOI: 10.3389/fgene.2024.1296533 -
Frontiers in Plant Science 2024Enhancing grain yield is a primary goal in the cultivation of major staple crops, including wheat. Recent research has focused on identifying the physiological and...
Enhancing grain yield is a primary goal in the cultivation of major staple crops, including wheat. Recent research has focused on identifying the physiological and molecular factors that influence grain weight, a critical determinant of crop yield. However, a bottleneck has arisen due to the trade-off between grain weight and grain number, whose underlying causes remain elusive. In a novel approach, a wheat expansin gene, , known for its expression in root tissues, was engineered to express in the grains of the spring wheat cultivar Fielder. This modification led to increases in both grain weight and yield without adversely affecting grain number. Conversely, a triple mutant line targeting the gene , a known negative regulator of grain weight, resulted in increased grain weight but decreased grain number, potentially offsetting yield gains. This study aimed to evaluate the two aforementioned modified wheat genotypes ( and ) alongside their respective wild-type counterparts. Conducted in southern Chile, the study employed a Complete Randomized Block Design with four replications, under well-managed field conditions. The primary metrics assessed were grain yield, grain number, and average grain weight per spike, along with detailed measurements of grain weight and dimensions across the spike, ovary weight at pollination (Waddington's scale 10), and post-anthesis expression levels of and . Results indicated that both the and the triple mutant lines achieved significantly higher average grain weights compared to their respective wild types. Notably, the line did not exhibit a reduction in grain number, thereby enhancing grain yield per spike. By contrast, the triple mutant line showed a reduced grain number per spike, with no significant change in overall yield. expression peaked at 10 days after anthesis (DAA), and its effect on grain weight over the WT became apparent after 15 DAA. In contrast, gene disruption in the triple mutant line increased ovary size at anthesis, leading to improved grain weight above the WT from the onset of grain filling. These findings suggest that the trade-off between grain weight and number could be attributed to the overlapping of the critical periods for the determination of these traits.
PubMed: 38919825
DOI: 10.3389/fpls.2024.1380429 -
Frontiers in Plant Science 2024Anthracnose, white mold, powdery mildew, and root rot caused by , , spp., and , respectively, are among the most frequent diseases that cause significant production...
Anthracnose, white mold, powdery mildew, and root rot caused by , , spp., and , respectively, are among the most frequent diseases that cause significant production losses worldwide in common bean ( L.). Reactions against these four fungal diseases were investigated under controlled conditions using a diversity panel of 311 bean lines for snap consumption (Snap bean Panel). The genomic regions involved in these resistance responses were identified based on a genome-wide association study conducted with 16,242 SNP markers. The highest number of resistant lines was observed against the three isolates evaluated: 156 lines were resistant to CL124 isolate, 146 lines resistant to CL18, and 109 lines were resistant to C531 isolate. Two well-known anthracnose resistance clusters were identified, the Co-2 on chromosome Pv11 for isolates CL124 and CL18, and the Co-3 on chromosome Pv04 for isolates CL124 and C531. In addition, other lesser-known regions of anthracnose resistance were identified on chromosomes Pv02, Pv06, Pv08, and Pv10. For the white mold isolate tested, 24 resistant lines were identified and the resistance was localized to three different positions on chromosome Pv08. For the powdery mildew local isolate, only 12 resistant lines were identified, and along with the two previous resistance genes on chromosomes Pv04 and Pv11, a new region on chromosome Pv06 was also identified. For root rot caused by , 31 resistant lines were identified and two main regions were located on chromosomes Pv04 and Pv05. Relevant information for snap bean breeding programs was provided in this work. A total of 20 lines showed resistant or intermediate responses against four or five isolates, which can be suitable for sustainable farm production and could be used as resistance donors. Potential genes and genomic regions to be considered for targeted improvement were provided, including new or less characterized regions that should be validated in future works. Powdery mildew disease was identified as a potential risk for snap bean production and should be considered a main goal in breeding programs.
PubMed: 38919821
DOI: 10.3389/fpls.2024.1386877 -
Frontiers in Plant Science 2024, belonging to the family and genus , is used in traditional Chinese medicine and is rich in beneficial components, such as flavonoids. As its abundant medicinal value...
, belonging to the family and genus , is used in traditional Chinese medicine and is rich in beneficial components, such as flavonoids. As its abundant medicinal value has become increasingly recognized, its excessive development poses a considerable challenge to wild germplasm resources, necessitating artificial cultivation and domestication. Considering these factors, a high-quality genome of was assembled and the evolutionary relationships within were compared, based on which 58 individual samples of were re-sequenced. We found that the samples could be categorized into three purebred populations and regions distributed at distinct elevations. Our varieties were cultivated from the parental populations of the subpopulation in central Yunnan. is speculated to have originated in the high-altitude Tibetan Plateau region, and that its combination with flavonoids can protect plants against ultraviolet radiation; this infers a subpopulation with a high accumulation of flavonoids. This study assembled a high-quality genome and provided a theoretical foundation for the future introduction, domestication, and development of cultivated varieties of .
PubMed: 38919820
DOI: 10.3389/fpls.2024.1380157 -
Frontiers in Plant Science 2024The pH of the solution in the rhizosphere is an important factor that determines the availability and mobility of nutrients for plant uptake. Solution pH may also affect...
The pH of the solution in the rhizosphere is an important factor that determines the availability and mobility of nutrients for plant uptake. Solution pH may also affect the root distribution and architecture of apple rootstocks. In this study, we evaluated the effect of solution pH on root system development of apple rootstocks using an aeroponics system designed and developed at Cornell AgriTech Geneva, USA. Four Geneva apple rootstocks (G.210, G.214, G.41, and G.890) were grown in an aeroponic system under nutrient solution misting featuring continuously adjusted pH levels to three pH treatments (5.5, 6.5, and 8.0). Root development was monitored for 30 days and evaluated regularly for distribution and root mass. Images of the developed roots grown in the aeroponic system were collected at the end of the experiment using a high-resolution camera and analyzed using GiA Roots software, which generates root architecture parameter values in a semi-automated fashion. The resulting root architecture analysis showed that the Geneva rootstocks were significantly different for two architecture parameters. The length-to-width ratio analysis represented by two GiA Roots parameters (minor-to-major ellipse ratio and network width-to-depth ratio) showed that G.210 was flatter than G.890, which had a greater tendency to grow downward. Rootstocks G.214 and G.41 displayed similar growth values. The solution pH affected most root architecture parameter measurements where overall root growth was higher at pH 8 than at pH 5.5 and 6.5, which showed similar growth. In general, the average root width tended to decrease at higher pH values. While there were no significant differences in the leaf nutrient concentrations of P, K, Ca, Mg, S, B, Zn, Cu, and Fe within the four rootstocks, the pH level of the solution had a significant effect on P, Ca, and Mn. This study is the first of its kind to investigate the effect of pH on root architecture in a soil-free (aeroponic) environment and may have implications for apple root behavior under field conditions where pH levels are different.
PubMed: 38919817
DOI: 10.3389/fpls.2024.1351679 -
Frontiers in Plant Science 2024Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy...
Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy traits. Previous studies have shown that black seeds have a very low germination rate under natural conditions, but exogenous GA effectively enhanced the germination rate of black seeds. However, the physiological and molecular mechanisms underlying the effects of GA on black seeds are still unclear. In this study, transcriptomic profiles of seeds at different germination stages with and without GA treatment were analyzed and compared, and the TTF, HO, O , starch, and soluble sugar contents of the corresponding seed samples were determined. The results indicated that exogenous GA treatment significantly increased seed vigor, HO, and O contents but decreased starch and soluble sugar contents of black seeds during seed dormancy release. RNA-seq results showed that a total of 1136 DEGs were identified in three comparison groups and were involved mainly in plant hormone signal transduction, diterpenoid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and carbohydrate metabolism pathway. Among them, the DEGs related to diterpenoid biosynthesis (, and ) and ABA signal transduction () could play important roles during seed dormancy release. Most genes involved in phenylpropanoid biosynthesis were activated under GA treatment conditions, especially many genes encoding peroxidase. In addition, exogenous GA treatment also significantly enhanced the expression of genes involved in flavonoid synthesis, which might be beneficial to seed dormancy release. In accordance with the decline in starch and soluble sugar contents, 15 genes involved in carbohydrate metabolism were significantly up-regulated during GA-induced dormancy release, such as , , and , etc. In a word, exogenous GA effectively increased the germination rate and seed vigor of black seeds by mediating the metabolic process or signal transduction of plant hormones, phenylpropanoid and flavonoid biosynthesis, and carbohydrate metabolism processes. Our results provide novel insights into the transcriptional regulation mechanism of exogenous GA on the dormancy release of black seeds. The candidate genes identified in this study may be further studied and used to enrich our knowledge of seed dormancy and germination.
PubMed: 38919815
DOI: 10.3389/fpls.2024.1354141 -
AIMS Microbiology 2024Fruit and vegetable industries face a major environmental challenge with food loss and waste. Broccoli stems, comprising 38% of the plant's total weight, are usually...
Fruit and vegetable industries face a major environmental challenge with food loss and waste. Broccoli stems, comprising 38% of the plant's total weight, are usually discarded by the industry producing fourth-range and ready-to-use products, despite being rich in antioxidants, vitamins, fiber, carotenoids, phenolic compounds, and glucosinolates. Addressing the challenge of reducing waste in this sector includes the production of stable and nutrient-concentrated powders, which can be consumed directly or used as ingredients in functional food formulation. This study investigated fermentation with lactic acid bacteria (, , and ) as a pretreatment for enhancing antioxidant and probiotic potential in broccoli stem powders. Results showed maximum counts 24 h after inoculation, and no effect of the previous disruption intensity on microbial growth was observed. Fermenting broccoli stems for 24 h with the three microbial strains led to a significant increase in total phenols and flavonoids but to a general reduction in the samples' capacity to scavenge DPPH and ABTS free radicals. Overall, ground broccoli stems exhibited the most favorable antioxidant properties following the 24 h fermentation step. The subsequent freeze-drying and final grinding had minimal impact on the microbial population but significantly enhanced the extractability of the antioxidant compounds. This study offers a valuable reference for researchers and stakeholders exploring the development of new products and innovations from vegetable waste.
PubMed: 38919719
DOI: 10.3934/microbiol.2024013 -
Ecology and Evolution Jun 2024Many species of have excellent ornamental, culinary, and medicinal values. , is an ornamental and highly medicinal perennial herb endemic to the prefecture-level city...
Many species of have excellent ornamental, culinary, and medicinal values. , is an ornamental and highly medicinal perennial herb endemic to the prefecture-level city of Zhangjiajie in Hunan Province, China, with a narrow geographical distribution. However, currently, it has only been assessed as a Critically Endangered species according to the IUCN classification criteria, but its conservation has not yet been studied. This study investigated the distribution and niche characteristics of , and compared the differences in growth, flowering characteristics, and soil nutrients between the wild and ex situ populations. We also analyzed the effects of soil nutrients on plant growth and flowering characteristics. During the survey, we found 274 individuals on a rock approximately 200 m from ZEFR1. Nevertheless, were still restricted in three populations, TNFP, TGM, and ZEFR in Zhangjiajie City, with a total of about 500 plants and less than 250 mature individuals. Our results show that aspects such as adverse environmental conditions, low seedling renewal rate, a lack of soil nutrients, and competition for the characteristic niche of this and other dominant plants in the natural community are the main ecological factors affecting the growth, flowering, and geographic distribution of . Based on the results of field surveys, we recommend that (1) be classified as Critically Endangered C2b and China's List of Plant Species with Extremely Small Populations. (2) Comprehensive conservation strategies were developed, such as the establishment of nature reserves, reintroduction, public education, and institutional development to provide management recommendations related to the conservation of and other endangered plants.
PubMed: 38919643
DOI: 10.1002/ece3.11629 -
Frontiers in Immunology 2024Colorectal cancer exhibits a notable prevalence and propensity for metastasis, but the current therapeutic interventions for metastatic colorectal cancer have yielded... (Review)
Review
Colorectal cancer exhibits a notable prevalence and propensity for metastasis, but the current therapeutic interventions for metastatic colorectal cancer have yielded suboptimal results. ICIs can decrease tumor development by preventing the tumor's immune evasion, presenting cancer patients with a new treatment alternative. The increased use of immune checkpoint inhibitors (ICIs) in CRC has brought several issues. In particular, ICIs have demonstrated significant clinical effectiveness in patients with MSI-H CRC, whereas their efficacy is limited in MSS. Acquired resistance can still occur in patients with a positive response to ICIs. This paper describes the efficacy of ICIs currently in the clinical treatment of CRC, discusses the mechanisms by which acquired resistance occurs, primarily related to loss and impaired presentation of tumor antigens, reduced response of IFN-λ and cytokine or metabolic dysregulation, and summarizes the incidence of adverse effects. We posit that the future of ICIs hinges upon the advancement of precise prediction biomarkers and the implementation of combination therapies. This study aims to elucidate the constraints associated with ICIs in CRC and foster targeted problem-solving approaches, thereby enhancing the potential benefits for more patients.
Topics: Humans; Colorectal Neoplasms; Immune Checkpoint Inhibitors; Animals; Drug Resistance, Neoplasm
PubMed: 38919624
DOI: 10.3389/fimmu.2024.1403533 -
Horticulture Research Jun 2024To date, there has been no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding efforts to improve grape cultivars. This...
To date, there has been no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding efforts to improve grape cultivars. This study presents ~522 Mb of the () genome sequence containing 27 635 coding genes. Phylogenetic analysis indicated that () may have first split from the other two species, and (). Divergent numbers of duplicated genes reserved among grapes suggests that the core eudicot-common hexaploidy (ECH) and the subsequent genome instability still play a non-negligible role in species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in , resulting in a more robust network of regulatory cold resistance genes, explaining why it is extremely cold-tolerant compared with and . In contrast, has preserved many fewer nucleotide binding site (NBS) disease resistance genes than the other grapes. Notably, multi-omics analysis identified one -cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during berry development. A selective sweep analysis revealed a hypothetical sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related to sex determination in . The content and arrangement order of genes in the putative SDR of female were similar to those of female . However, the putative SDR of female has lost one flavin-containing monooxygenase (FMO) gene and contains one extra protein-coding gene uncharacterized so far. These findings will improve the understanding of biology and contribute to the improvement of grape breeding.
PubMed: 38919553
DOI: 10.1093/hr/uhae117