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[学术文献 ] Diploid inbred-based hybrids: fast-forward breeding approach in potatoes 进入全文
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
Following the identification of the self-compatibility gene (Sli) in diploid potatoes two decades ago, the breeding of inbred based diploid hybrid potatoes made its way. Tetraploid potatoes have a long history of cultivation through domestication and selection. Tetrasomic inheritance, heterozygosity and clonal propagation complicate genetic studies, resulting in a low genetic gain in potato breeding. Diploid hybrid TPS potato breeding, similar to the developments in hybrid maize, was pursued as an alternative to the genetic improvement of potatoes. However, several challenges, like self-incompatibility and high inbreeding depression associated with diploid potatoes, must be overcome to develop inbred lines in potatoes. Moreover, the inbred lines must retain good fertility and vigour for hybrid breeding. Good progress has been made by creating di-haploids of popular varieties, mapping self-incompatibility inhibitor gene, understanding the genetic basis of inbreeding depression, and identifying genomic regions for deleterious alleles and fertility. Further, the genome sequencing of diploid inbred lines has revealed the genetics of key traits associated with potato breeding. This article discussed these insights and summarized the progress of diploid hybrid TPS potato breeding. Recent advances in genetic and genomic research and genome editing technology have shown promise for this technology's success and far-reaching implications.
[学术文献 ] Ubiquitin Ligase U-Box51 Positively Regulates Drought Stress in Potato (Solanum tuberosum L.) 进入全文
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
The ubiquitin-proteasome system (UPS) is a key protein degradation pathway in eukaryotes, in which E3 ubiquitin ligases mediate protein ubiquitination, directly or indirectly targeting substrate proteins to regulate various biological processes, including plant growth, hormone signaling, immune responses, and adaptation to abiotic stress. In this study, we identified plant U-box protein 51 in Solanum tuberosum (StPUB51) as an E3 ubiquitin ligase through transcriptomic analysis, and used it as a candidate gene for gene-function analysis. Quantitative real-time PCR (qRT-PCR) was used to examine StPUB51 expression across different tissues, and its expression patterns under simulated drought stress induced by polyethylene glycol (PEG 6000) were assessed. Transgenic plants overexpressing StPUB51 and plants with down-regulated StPUB51 expression were generated to evaluate drought tolerance. The activities of key antioxidant enzymes-superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) as well as malondialdehyde (MDA) content in transgenic plants' leaves were measured under drought conditions. Protein-protein interactions involving StPUB51 were explored via yeast two-hybrid (Y2H) screening, with interaction verification by bimolecular fluorescence complementation (BiFC). StPUB51 was predominantly expressed in stems, with lower expression observed in tubers, and its expression was significantly upregulated in response to 20% PEG-6000 simulated drought. Subcellular localization assays revealed nuclear localization of the StPUB51 protein. Under drought stress, StPUB51-overexpressing plants exhibited enhanced SOD, POD, and CAT activities and reduced MDA levels, in contrast to plants with suppressed StPUB51 expression. Y2H and BiFC analyses identified two interacting proteins, StSKP2A and StGATA1, which may be functionally linked to StPUB51. Collectively, these findings suggest that StPUB51 plays a positive regulatory role in drought tolerance, enhancing resilience in potato growth and stress adaptation.
[学术文献 ] The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging 进入全文
Nature Communications
In the era of synthetic biology, design, construction, and utilization of synthetic chromosomes with unique features provide a strategy to study complex cellular processes such as aging. Herein, we successfully construct the 884 Kb synXIII of Saccharomyces cerevisiae to investigate replicative aging using these synthetic strains. We verify that up-regulation of a rRNA-related transcriptional factor, RRN9, positively influence replicative lifespan. Using SCRaMbLE system that enables inducible whole-genome rearrangement on synXIII, we obtain 20 SCRaMbLEd synXIII strains with extended lifespan. Transcriptome analysis reveal the expression of genes involve in global protein synthesis is up-regulated in longer-lived strains. We establish causal links between genotypic change and the long-lived phenotype via reconstruction of some key structural variations observed in post-SCRaMbLE strains and further demonstrate combinatorial effects of multiple aging regulators on lifespan extension. Our findings underscore the potential of synthetic yeasts in unveiling the function of aging-related genes.
[学术文献 ] Chromosome Engineering: Technologies, Applications, and Challenges 进入全文
Annu Rev Anim Biosci
Chromosome engineering is a transformative field at the cutting edge of biological science, offering unprecedented precision in manipulating large-scale genomic DNA within cells. This discipline is central to deciphering how the multifaceted roles of chromosomes-guarding genetic information, encoding sequence positional information, and influencing organismal traits-shape the genetic blueprint of life. This review comprehensively examines the technological advancements in chromosome engineering, which center on engineering chromosomal rearrangements, generating artificial chromosomes, de novo synthesizing chromosomes, and transferring chromosomes. Additionally, we introduce the application progress of chromosome engineering in basic and applied research fields, showcasing its capacity to deepen our knowledge of genetics and catalyze breakthroughs in therapeutic strategies. Finally, we conclude with a discussion of the challenges the field faces and highlight the profound implications that chromosome engineering holds for the future of modern biology and medical applications.
[学术文献 ] Orthogonal and multiplexable genetic perturbations with an engineered prime editor and a diverse RNA array 进入全文
Nature Communications
Programmable and modular systems capable of orthogonal genomic and transcriptomic perturbations are crucial for biological research and treating human genetic diseases. Here, we present the minimal versatile genetic perturbation technology (mvGPT), a flexible toolkit designed for simultaneous and orthogonal gene editing, activation, and repression in human cells. The mvGPT combines an engineered compact prime editor (PE), a fusion activator MS2–p65–HSF1 (MPH), and a drive-and-process multiplex array that produces RNAs tailored to different types of genetic perturbation. mvGPT can precisely edit human genome via PE coupled with a prime editing guide RNA and a nicking guide RNA, activate endogenous gene expression using PE with a truncated single guide RNA containing MPH-recruiting MS2 aptamers, and silence endogenous gene expression via RNA interference with a short-hairpin RNA. We showcase the versatility of mvGPT by simultaneously correcting a c.3207C>A mutation in the ATP7B gene linked to Wilson’s disease, upregulating the PDX1 gene expression to potentially treat Type I diabetes, and suppressing the TTR gene to manage transthyretin amyloidosis. In addition to plasmid delivery, we successfully utilize various methods to deliver the mvGPT payload, demonstrating its potential for future in vivo applications.
[学术文献 ] Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing 进入全文
Nature Genetics
Crop genomes accumulate deleterious mutations—a phenomenon known as the cost of domestication. Precision genome editing has been proposed to eliminate such potentially harmful mutations; however, experimental demonstration is lacking. Here we identified a deleterious mutation in the tomato transcription factor SUPPRESSOR OF SP2 (SSP2), which became prevalent in the domesticated germplasm and diminished DNA binding to genome-wide targets. We found that the action of SSP2 is partially redundant with that of its paralog SSP in regulating shoot and inflorescence architecture. However, redundancy was compromised during tomato domestication and lost completely in the closely related species Physalis grisea, in which a single ortholog regulates shoot branching. We applied base editing to directly repair the deleterious mutation in cultivated tomato and obtained plants with compact growth that provide an early fruit yield. Our work shows how deleterious variants have sensitized modern genotypes for phenotypic tuning and illustrates how repairing deleterious mutations with genome editing may allow predictable crop improvement.