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1.
Proc Natl Acad Sci U S A ; 120(24): e2222041120, 2023 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-37276420

RESUMO

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis vinifera ssp. sylvestris) and cultivated (V. vinifera ssp. vinifera) grapes. Based on machine learning-based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources.


Assuntos
Domesticação , Vitis , Europa (Continente) , Genômica , Análise de Sequência de DNA , Vitis/genética
2.
Plant Physiol ; 195(2): 1401-1413, 2024 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-38285049

RESUMO

Plant domestication are evolutionary experiments conducted by early farmers since thousands years ago, during which the crop wild progenitors are artificially selected for desired agronomic traits along with dramatic genomic variation in the course of moderate to severe bottlenecks. However, previous investigations are mainly focused on small-effect variants, while changes in gene contents are rarely investigated due to the lack of population-level assemblies for both the crop and its wild relatives. Here, we applied comparative genomic analyses to discover gene gain and loss during grapevine domestication using long-read assemblies of representative population samples for both domesticated grapevines (V. vinifera ssp. vinifera) and their wild progenitors (V. vinifera ssp. sylvestris). Only ∼7% of gene families were shared by 16 Vitis genomes while ∼8% of gene families were specific to each accession, suggesting dramatic variations of gene contents in grapevine genomes. Compared to wild progenitors, the domesticated accessions exhibited an increased presence of genes associated with asexual reproduction, while the wild progenitors showcased a higher abundance of genes related to pollination, revealing the transition from sexual reproduction to clonal propagation during domestication processes. Moreover, the domesticated accessions harbored fewer disease-resistance genes than wild progenitors. The SVs occurred frequently in aroma and disease-resistance related genes between domesticated grapevines and wild progenitors, indicating the rapid diversification of these genes during domestication. Our study provides insights and resources for biological studies and breeding programs in grapevine.


Assuntos
Domesticação , Genoma de Planta , Genômica , Vitis , Vitis/genética , Genômica/métodos , Genes de Plantas , Produtos Agrícolas/genética
3.
Plant Physiol ; 195(4): 2799-2814, 2024 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-38743633

RESUMO

The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies and breeding programs. In this study, we assembled a haplotype-resolved telomere-to-telomere (T2T) reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on 12 assemblies from wild and cultivated species to investigate the dynamic changes of functional genes. Our results revealed the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Our analyses also demonstrated a higher prevalence of different types of resistance gene analogs (RGAs) in cultivars than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR, NB-ARC-LRR, and CC-NB-ARC-LRR genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding.


Assuntos
Domesticação , Genoma de Planta , Malus , Telômero , Malus/genética , Genoma de Planta/genética , Telômero/genética , Genes de Plantas , Haplótipos/genética , Resistência à Doença/genética
4.
J Integr Plant Biol ; 66(7): 1408-1426, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38578160

RESUMO

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.


Assuntos
Vitis , Vitis/genética , Adaptação Fisiológica/genética , Genoma de Planta/genética , Genética Populacional , Polimorfismo de Nucleotídeo Único/genética , Tolerância ao Sal/genética , Variação Estrutural do Genoma/genética , Genômica , Genes de Plantas
5.
Mol Carcinog ; 62(3): 293-302, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36342357

RESUMO

Dihydroartemisinin (DHA) has recently attracted increasing attention for its low toxicity and high antitumor activity. DHA has been reported to have synergistic anticancer effects with a variety of drugs in the clinic; however, the molecular mechanism by which DHA inhibits tumorigenesis and improves oxaliplatin cytotoxicity in colon cancer cells is still not well understood. In this study, we found that DHA can inhibit cell proliferation and colony formation in a dose-dependent manner. Prohibitin 2 (PHB2) is a potential target by which DHA exerts its antitumor and cytotoxic effects. The function and molecular mechanism of PHB2 in colon cancer tumorigenesis were fully studied to determine the regulatory mechanism between DHA and PHB2. We found that PHB2, a mitochondrial inner membrane scaffold protein, has a higher expression level in colon cancer tissues than in adjacent nontumor tissues and is mainly localized in mitochondria. Overexpression of PHB2 can promote cell proliferation and colony formation in vitro and accelerate tumor growth in vivo. We also found that the expression level of PHB2 was inversely related to the cytotoxicity of DHA and oxaliplatin in colon cancer cells. The molecular mechanism of PHB2 in tumorigenesis and cancer therapy was further studied. The results showed that 20 µM DHA can downregulate PHB2 expression in a ubiquitylation-dependent manner and subsequently block PHB2-induced RCHY1 upregulation and p53 and p21 downregulation. In this process, RCHY1 is necessary for PHB2 to play a tumor-promoting role. Thus, PHB2 and RCHY1 are effective targets for colon cancer therapy, and DHA has synergistic anticancer effects with oxaliplatin via promoting PHB2 degradation in colon cancer cells.


Assuntos
Antineoplásicos , Neoplasias do Colo , Humanos , Oxaliplatina/farmacologia , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Transdução de Sinais , Neoplasias do Colo/tratamento farmacológico , Carcinogênese , Linhagem Celular Tumoral , Ubiquitina-Proteína Ligases
6.
Genet Res (Camb) ; 2022: 9282484, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36101744

RESUMO

Sirtuin 2 (SIRT2), as a member of the sirtuin family, has representative features of evolutionarily highly conserved nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase activity. In addition, SIRT2, as the only sirtuin protein colocalized with tubulin in the cytoplasm, has its own functions and characteristics. In recent years, studies have increasingly shown that SIRT2 can participate in the regulation of gene expression and regulate signal transduction in the metabolic pathway mainly through its post-translational modification of target genes; thus, SIRT2 has become a key centre in the metabolic pathway and participates in the pathological process of metabolic disorder-related diseases. In this paper, it is discussed that SIRT2 can regulate all aspects of gene expression, including epigenetic modification, replication, transcription and translation, and post-translational modification, which enables SIRT2 to participate in energy metabolism in life activities, and it is clarified that SIRT2 is involved in metabolic process-specific signal transduction mechanisms. Therefore, SIRT2 can be involved in metabolic disorder-related inflammation and oxidative stress, thereby triggering the occurrence of metabolic disorder-related diseases, such as neurodegenerative diseases, tumours, diabetes, and cardiovascular diseases. Currently, although the role of SIRT2 in some diseases is still controversial, given the multiple roles of SIRT2 in regulating physiological and pathological signal transduction, SIRT2 has become a key target for disease treatment. It is believed that with increasing research, the clinical application of SIRT2 will be promoted.


Assuntos
Doenças Neurodegenerativas , Sirtuína 2 , Humanos , Doenças Neurodegenerativas/genética , Doenças Neurodegenerativas/metabolismo , Estresse Oxidativo , Processamento de Proteína Pós-Traducional/genética , Transdução de Sinais/genética , Sirtuína 2/genética , Sirtuína 2/metabolismo
7.
Nucleic Acids Res ; 48(8): e44, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32128590

RESUMO

Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source, which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased the valid-pairs ratio from ∼40% to ∼80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.


Assuntos
Cromossomos de Mamíferos , Exodesoxirribonucleases , Genômica/métodos , Animais , Linhagem Celular , Células Cultivadas , Cromatina , Camundongos
8.
Geneva Risk Insur Rev ; 47(1): 98-121, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-34690612

RESUMO

We conducted in-the-field choice experiments in China to investigate farmers' willingness to pay for crop insurance and to determine how objective and subjective beliefs affect Willingness to Pay (WTP). We deploy three variants of the choice experiment using a priming mechanism on objective and subjective beliefs plus a control. We find that the cuing frame matters in that there are differences in WTP within five attributes and across variants. In terms of practical policy, our results suggest that farmers' frame of reference toward objective and subjective risks can affect insurance demand.

9.
BMC Genomics ; 22(1): 857, 2021 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-34837950

RESUMO

BACKGROUND: As a powerful tool, RNA-Seq has been widely used in various studies. Usually, unmapped RNA-seq reads have been considered as useless and been trashed or ignored. RESULTS: We develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse transcription primers design and high throughput sequencing. In this study, we salvage 36 unmapped reads from standard RNA-Seq data and randomly select one 149 bp read as a model. Specific reverse transcription primers are designed to amplify its both ends, followed by next generation sequencing. Then we design a statistical model based on power law distribution to estimate its integrality and significance. Further, we validate it by Sanger sequencing. The result shows that the full length is 1556 bp, with insertion mutations in microsatellite structure. CONCLUSION: We believe this method would be a useful strategy to extract the sequences information from the unmapped RNA-seq data. Further, it is an alternative way to get the full length sequence of unknown cDNA.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , DNA Complementar , RNA-Seq , Análise de Sequência de RNA , Sequenciamento do Exoma
10.
Mikrochim Acta ; 187(5): 308, 2020 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-32356133

RESUMO

A colorimetric method was developed using G-quadruplex and gold nanoparticles (AuNPs) for determination of Escherichia coli K88 (ETEC K88). It was composed of two modules: (1) an aptamer as biorecognizing element and (2) a capturing DNA (modified with AuNPs at 5') as a transducer. In the absence of target bacteria, the aptamer can form stable double strands with capturing DNA, preventing the binding of capturing DNA to the G-quadruplex. However, the double strands of capturing DNA and aptamer are untied due to the stronger binding of aptamers to bacteria in the presence of target bacteria. As a result, the G-quadruplex binds to capture DNA and leads to the aggregation and color change of AuNPs, which can be monitored by a spectrophotometer or visualization. The quantitative determination was achieved by monitoring the optical density change of AuNPs solution at 524 nm after target addition. Under optimal conditions, the method has a low detection limit (1.35 × 102 CFU mL-1) and a linear response in the range 102 to 106 CFU mL-1. Graphical abstract The manuscripts describe a colorimetric method for the detection of ETEC K88 by using intermolecular G-quadruplex to induce the agglomeration of gold nanoparticles, which can be directly used to determine the presence of bacteria with our naked eyes.


Assuntos
Aptâmeros de Nucleotídeos/química , Colorimetria/métodos , DNA/química , Escherichia coli/isolamento & purificação , Quadruplex G , Nanopartículas Metálicas/química , Técnicas Biossensoriais/métodos , Ouro/química , Humanos , Limite de Detecção , Lagoas/microbiologia , Espectrofotometria/métodos , Urina/microbiologia , Poluentes da Água/análise
11.
Opt Express ; 24(20): 22596-22605, 2016 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-27828330

RESUMO

A kind of grating-type mid-infrared light absorber based on silicon carbide (SiC) material is designed and its absorption properties are studied using the finite-difference frequency-domain (FDFD) method. The results show that, its absorption mechanism is the excitation of surface plasmon and magnetic polariton as well as the loss of materials. Due to the optical characteristics of the SiC material in the mid-infrared band and the truncated pyramid structure in the grating, in the range of 10.5-12.5µm and 0-80°, absorptivity of higher than 80% can be obtained with optimized structural parameters. Among six structural parameters, the layer number of the composite layers has a relatively great influence on the absorption properties, while the thickness of the dielectric layer has less influence on the absorption properties.

12.
Am J Bot ; 102(10): 1676-84, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26437885

RESUMO

PREMISE OF THE STUDY: Biological responses to climatic change usually leave imprints on the genetic diversity and structure of plants. Information on the current genetic diversity and structure of dominant tree species has facilitated our general understanding of phylogeographical patterns. METHODS: Using amplified fragment length polymorphism (AFLPs), we compared genetic diversity and structure of 384 adults of P. tarapacana with those of 384 seedlings across 32 forest sites spanning a latitudinal gradient of 600 km occurring between 4100 m and 5000 m a.s.l. in Polylepis tarapacana (Rosaceae), one of the world's highest treeline species endemic to the central Andes. KEY RESULTS: Moderate to high levels of genetic diversity and low genetic differentiation were detected in both adults and seedlings, with levels of genetic diversity and differentiation being almost identical. Four slightly genetically divergent clusters were identified that accorded to differing geographical regions. Genetic diversity decreased from south to north and with increasing precipitation for adults and seedlings, but there was no relationship to elevation. CONCLUSIONS: Our study shows that, unlike the case for other Andean treeline species, recent human activities have not affected the genetic structure of P. tarapacana, possibly because its inhospitable habitat is unsuitable for agriculture. The current genetic pattern of P. tarapacana points to a historically more widespread distribution at lower altitudes, which allowed considerable gene flow possibly during the glacial periods of the Pleistocene epoch, and also suggests that the northern Argentinean Andes may have served as a refugium for historical populations.


Assuntos
Variação Genética , Rosaceae/genética , Árvores/genética , Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Bolívia , Chile , Clima , Camada de Gelo
13.
Proc Natl Acad Sci U S A ; 109(20): 7793-8, 2012 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-22550176

RESUMO

Most extant genus-level radiations in gymnosperms are of Oligocene age or younger, reflecting widespread extinction during climate cooling at the Oligocene/Miocene boundary [∼23 million years ago (Ma)]. Recent biogeographic studies have revealed many instances of long-distance dispersal in gymnosperms as well as in angiosperms. Acting together, extinction and long-distance dispersal are likely to erase historical biogeographic signals. Notwithstanding this problem, we show that phylogenetic relationships in the gymnosperm family Cupressaceae (162 species, 32 genera) exhibit patterns expected from the Jurassic/Cretaceous breakup of Pangea. A phylogeny was generated for 122 representatives covering all genera, using up to 10,000 nucleotides of plastid, mitochondrial, and nuclear sequence per species. Relying on 16 fossil calibration points and three molecular dating methods, we show that Cupressaceae originated during the Triassic, when Pangea was intact. Vicariance between the two subfamilies, the Laurasian Cupressoideae and the Gondwanan Callitroideae, occurred around 153 Ma (124-183 Ma), when Gondwana and Laurasia were separating. Three further intercontinental disjunctions involving the Northern and Southern Hemisphere are coincidental with or immediately followed the breakup of Pangea.


Assuntos
Cupressaceae/fisiologia , Demografia/história , Fósseis , Filogenia , Sequência de Bases , Teorema de Bayes , Cupressaceae/genética , Evolução Molecular , Geografia , História Antiga , Funções Verossimilhança , Modelos Genéticos , Dados de Sequência Molecular , Filogeografia , Análise de Sequência de DNA , Especificidade da Espécie
14.
Biotechnol J ; 19(3): e2300516, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38472100

RESUMO

Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. We report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-ß stimulated mouse embryonic fibroblasts (MEFs). The data clearly discriminate two IFN-ß stimulated MEFs. Moreover, our results indicate 81% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on Cap-Analysis Gene Expression (CAGE) (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future.


Assuntos
Fibroblastos , Estudo de Associação Genômica Ampla , Animais , Camundongos , Regiões Promotoras Genéticas , Genoma , Genômica , Mamíferos/genética
15.
Hortic Res ; 11(1): uhad252, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38269295

RESUMO

The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.

16.
Hortic Res ; 11(6): uhae109, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38883333

RESUMO

The economically significant genus Prunus includes fruit and nut crops that have been domesticated for shared and specific agronomic traits; however, the genomic signals of convergent and divergent selection have not been elucidated. In this study, we aimed to detect genomic signatures of convergent and divergent selection by conducting comparative population genomic analyses of the apricot-peach-plum-mei (APPM) complex, utilizing a haplotype-resolved telomere-to-telomere (T2T) genome assembly and population resequencing data. The haplotype-resolved T2T reference genome for the plum cultivar was assembled through HiFi and Hi-C reads, resulting in two haplotypes 251.25 and 251.29 Mb in size, respectively. Comparative genomics reveals a chromosomal translocation of ~1.17 Mb in the apricot genomes compared with peach, plum, and mei. Notably, the translocation involves the D locus, significantly impacting titratable acidity (TA), pH, and sugar content. Population genetic analysis detected substantial gene flow between plum and apricot, with introgression regions enriched in post-embryonic development and pollen germination processes. Comparative population genetic analyses revealed convergent selection for stress tolerance, flower development, and fruit ripening, along with divergent selection shaping specific crop, such as somatic embryogenesis in plum, pollen germination in mei, and hormone regulation in peach. Notably, selective sweeps on chromosome 7 coincide with a chromosomal collinearity from the comparative genomics, impacting key fruit-softening genes such as PG, regulated by ERF and RMA1H1. Overall, this study provides insights into the genetic diversity, evolutionary history, and domestication of the APPM complex, offering valuable implications for genetic studies and breeding programs of Prunus crops.

17.
Mol Plant ; 17(6): 867-883, 2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38678365

RESUMO

Given the escalating impact of climate change on agriculture and food security, gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change. Alfalfa (Medicago sativa subsp. sativa), the queen of forages, shows remarkable adaptability across diverse global environments, making it an excellent model for investigating species responses to climate change. In this study, we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa's climatic adaptation and genetic susceptibility to future climate change. We found that interspecific genetic exchange has contributed to the gene pool of alfalfa, particularly enriching defense and stress-response genes. Intersubspecific introgression between M. sativa subsp. falcata (subsp. falcata) and alfalfa not only aids alfalfa's climatic adaptation but also introduces genetic burden. A total of 1671 genes were associated with climatic adaptation, and 5.7% of them were introgressions from subsp. falcata. By integrating climate-associated variants and climate data, we identified populations that are vulnerable to future climate change, particularly in higher latitudes of the Northern Hemisphere. These findings serve as a clarion call for targeted conservation initiatives and breeding efforts. We also identified pre-adaptive populations that demonstrate heightened resilience to climate fluctuations, illuminating a pathway for future breeding strategies. Collectively, this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars, contributing to effective agricultural strategies for facing future climate change.


Assuntos
Mudança Climática , Medicago sativa , Medicago sativa/genética , Medicago sativa/fisiologia , Adaptação Fisiológica/genética , Genômica , Genoma de Planta
18.
Curr Biol ; 2024 Jul 30.
Artigo em Inglês | MEDLINE | ID: mdl-39094571

RESUMO

Seedlessness is a crucial quality trait in table grape (Vitis vinifera L.) breeding. However, the development of seeds involved intricate regulations, and the polygenic basis of seed abortion remains unclear. Here, we combine comparative genomics, population genetics, quantitative genetics, and integrative genomics to unravel the evolution and polygenic basis of seedlessness in grapes. We generated the haplotype-resolved genomes for two seedless grape cultivars, "Thompson Seedless" (TS, syn. "Sultania") and "Black Monukka" (BM). Comparative genomics identified a ∼4.25 Mb hemizygous inversion on Chr10 specific in seedless cultivars, with seedless-associated genes VvTT16 and VvSUS2 located at breakpoints. Population genomic analyses of 548 grapevine accessions revealed two distinct clusters of seedless cultivars, and the identity-by-descent (IBD) results indicated that the origin of the seedlessness trait could be traced back to "Sultania." Introgression, rather than convergent selection, shaped the evolutionary history of seedlessness in grape improvement. Genome-wide association study (GWAS) analysis identified 110 quantitative trait loci (QTLs) associated with 634 candidate genes, including previously unidentified candidate genes, such as three 11S GLOBULIN SEED STORAGE PROTEIN and two CYTOCHROME P450 genes, and well-known genes like VviAGL11. Integrative genomic analyses resulted in 339 core candidate genes categorized into 13 functional categories related to seed development. Machine learning-based genomic selection achieved a remarkable prediction accuracy of 97% for seedlessness in grapevines. Our findings highlight the polygenic nature of seedlessness and provide candidate genes for molecular genetics and an effective prediction for seedlessness in grape genomic breeding.

19.
Sci Rep ; 13(1): 14595, 2023 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-37670039

RESUMO

SVIL is a member of the villin/gelsolin superfamily and is responsible for encoding supervillin. It has been reported to be closely related to the occurrence and development of various tumors. However, the mechanism of SVIL in bladder cancer has not been reported yet. In this research, we evaluated the relationship between SVIL expression and bladder cancer in public dataset and examined the expression of SVIL in bladder cancer cell lines, tissue microarrays and patients in our cohort. Our work determined that the expression of SVIL in bladder cancer tissue was significantly lower than that in normal tissue. However, in bladder cancer tissues, the high expression of SVIL is significantly associated with poor prognosis. This kind of duality is very novel and has great research value. The expression level of SVIL can well predict the survival time of bladder cancer patients, and is an independent risk factor of bladder cancer patients. The expression of SVIL is also closely related to the immune tumor microenvironment of bladder cancer. Our research provides a basis for personalized therapeutic targets for bladder cancer.


Assuntos
Neoplasias da Bexiga Urinária , Humanos , Linhagem Celular , Gelsolina , Fatores de Risco , Microambiente Tumoral , Proteínas de Membrana , Proteínas dos Microfilamentos
20.
Chemosphere ; 336: 139310, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37354959

RESUMO

Solar interfacial evaporation is a potential technology to produce clean water due to its simplicity and being driven by renewable clean energy, but it still requires further development to break through the bottleneck of removing volatile organic compounds (VOCs), especially in wastewater treatment. Herein, we proposed a dual-functional hydrogel evaporator that coupled solar interfacial evaporation with Fenton reaction to simultaneously remove VOCs and non-volatile pollutants from water with low energy consumption and high efficiency. The evaporator was composed with ß-FeOOH and polydopamine (PDA) on an electrospun nanofibrous hydrogel. Arising from the PDA with excellent photothermal properties, the evaporator revealed a high light absorption characteristics (∼90%) and photothermal efficiency (83.4%), which ensured a favorable evaporation rate of 1.70 kg m-2 h-1 under one solar irradiation. More importantly, benefited from the coupled Fenton reaction, the VOCs removal rate of ß-FeOOH@PDA/polyvinyl alcohol nanofibrous hydrogel (ß-FeOOH@PPNH) reached 95.8%, which was 6.5 times than that of sole solar interfacial evaporation (14.8%). In addition, the evaporator exhibited an outstanding non-volatile pollutant removal capability and stable removal performance for organic pollutants over a long period of operation. The prepared ß-FeOOH@PPNH evaporator provides a promising idea for simultaneous removal of non-volatile pollutants and volatile pollutants performance in long-term water purification.


Assuntos
Poluentes Ambientais , Compostos Orgânicos Voláteis , Purificação da Água , Hidrogéis , Fenômenos Físicos , Água
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