农学最新文献

{"title":"plantGIR: a genomic database of plants.","authors":"Zhuo Liu, Chenhao Zhang, Jinghua He, Chunjin Li, Yanhong Fu, Yongfeng Zhou, Rui Cao, Haibin Liu, Xiaoming Song","doi":"10.1093/hr/uhae342","DOIUrl":"https://doi.org/10.1093/hr/uhae342","url":null,"abstract":"","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 12","pages":"uhae342"},"PeriodicalIF":7.6,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple ancestral components and complex origins of the Yugur people in Gansu province revealing by 35 Y-STR.","authors":"Xian-Peng Zhang, Hui-Xin Yu, Jie Zhang, Xin-Yi Jia, Xiao-Fei He, Bo-Feng Zhu, Lan-Hai Wei, Hong-Bing Yao","doi":"10.16288/j.yczz.24-136","DOIUrl":"https://doi.org/10.16288/j.yczz.24-136","url":null,"abstract":"<p><p>The Yugur people represent one of the ethnic groups residing within the Hexi Corridor, distinguishable by their small population size, linguistic diversity, intricate ancestral components, serving as a quintessential exemplar of the populations inhabiting this corridor. There are still many controversial issues in the academic community regarding the origin, migration, and formation process of the Yugur. In this study, we explored the formation process of the Yugur from the perspective of molecular anthropology, based on the paternal genetic characteristics of the Yugur people. And the study will synthesize multiple disciplines, encompassing ethnology, history and linguistics, in order to offer a thorough analysis. Within this research endeavor, a high-resolution kit comprising 35 Y-STRs was employed to examine 237 male specimens from the Yugur people in Gansu province. Y-SNP haplogroups were deduced through the utilization of Y-STR data. The paternal genetic data from diverse populations documented in published literature were merged to construct a 16 Y-STR dataset, a 25 Y-STR dataset, and a dataset detailing haplogroup frequencies. In this study, we employed haplotype network analysis, principal component analysis, multidimensional scaling analysis, phylogenetic tree construction, and genetic distance calculations to delve into the genetic structure, haplotype distribution, and genetic relationship with neighboring populations of the Yugur people. The findings of this study reveal that the Yugur people are a blend of ancestral lineages from both Eastern and Western Eurasian origins, with approximately 13% of their genetic component traced back to Western Eurasian populations. The Yugur people in Gansu province exhibits a more intimate genetic relationship with the Han, Tibetan, and Mongolian populations inhabiting nearby regions, while showing distinct genetic differences with Turkic-speaking groups like the Uyghur. Based on the merged data, we identified Q1b1a3-L330 and R1a1a-M17 shared with Turkic-speaking people, C2a1a1-F1756, C2a1a3-M504, C2a1a3a-F3796, C2a1a2-M48 and C2b1a1a1a-M407 shared with Mongolic-speaking people, D1a1a-M15 and D1a1b1-P47 shared with Tibetans, and multiple paternal lineages shared with Han people, which are the main paternal lineages of Yugur people, indicating multiple ancestral components and complex origins of Yugur. In this study, we provided a clearer genetic landscape which further supports the formation process and population characteristics of the Yugur people recorded in history, ethnology, and linguistics, and lays the foundation for more detailed studies on population genetics and forensic genetics in the future.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 12","pages":"1042-1054"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening and validation of downstream target genes of SLC25A21 based on bioinformatics.","authors":"Yao Chen, Xin Wen, Fang-Yuan Yuan, Chao-Ling Peng, Cui-Zhe Wang, Jun Zhang, Ping-Ping Meng","doi":"10.16288/j.yczz.24-230","DOIUrl":"https://doi.org/10.16288/j.yczz.24-230","url":null,"abstract":"<p><p>Solute carrier 25 member 21 (<i>SLC25A21</i>) serves as an oxodicarboxylate carrier, which mainly conveys 2-oxoadipate from the cytoplasm to the mitochondria <i>via</i> a reverse exchange mechanism. Previous studies have indicated that the capacity for glucose consumption is significantly enhanced in 3T3-L1 cells overexpressing <i>SLC25A21</i>. In this study, we upregulate <i>SLC25A21</i> in 3T3-L1 cells to further probe into the downstream key metabolic genes of <i>SLC25A21</i>. Through high-throughput sequencing combined with bioinformatics analysis, differentially expressed genes are obtained, and the expression of key genes is verified by qRT-PCR. The results demonstrat that: (1) There are 26 up-regulated genes and 66 down-regulated genes in the adipocytes overexpressing <i>SLC25A21</i>; (2) GO (gene ontology) analysis indicates that the biological functions of differentially expressed genes are predominantly involved in lipid synthesis and metabolism, and KEGG (Kyoto encyclopedia of genes and genomes) and GSEA (gene set enrichment analysis) analyses reveal that differentially expressed genes are mainly concentrated in sphingolipid metabolism, secretion and synthesis of insulin and glucagon-like peptide 1; (3) By means of cytoHubba, 10 key genes with the highest scores, such as <i>GRB2, SOS1, SHC1, CBL, HRAS, SOS2, EGFR, MET, PLCG2</i> and <i>KRAS</i>, were screened out and they are mainly involved in the sugar and lipid metabolism processes of cells; (4) <i>SLC25A21</i> is overexpressed in adipocytes, and the qRT-PCR verification results show that the mRNA expression levels of other genes increased correspondingly, except for <i>KRAS</i> expression, which exhibits no significant change. These results provide a theoretical basis for further investigations on the role and mechanism of SLC25A21 in the process of glucose and lipid metabolism.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 12","pages":"1055-1065"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A non-synonymous variant of C21R in the <i>ABCG2</i> gene is significantly associated with brown eggshell color of Lueyang black-boned chicken.","authors":"De-Yang Zhang, Wen-Chuan Zhou, Jia-le Li, Zhe-Peng Wang","doi":"10.16288/j.yczz.24-225","DOIUrl":"https://doi.org/10.16288/j.yczz.24-225","url":null,"abstract":"<p><p>Eggshell colors have a significant effect on sale of eggs. The aim of this study is to identify sequence variants associated with color variation of chicken brown eggs in the <i>ABCG2</i>, a protoporphyrin transport-related gene. Three successive eggs were collected from each of 381 Lueyang black-boned hens at the 31 weeks old. Eggshell color was quantified via the L*a*b color space. g.18378442T>C (a non-synonymous mutation C21R), g.18383682A>G and g.18391548A>T were genotyped <i>via</i> the MassARRAY platform. The associations of genotypes with color indexes were tested by one-way ANOVA. The conservation of the C21R locus was analyzed by multiple alignment of 52 avian genomes from the UCSC database. We predicted 3D structures of ABCG2 with C²¹ and R²¹ by homology modelling using the MODELLER program to analyze effect of C21R on protein structures. Results showed that g.18378442T>C was significantly associated with L and b values. The L value (75.3±4.0) of CC was significantly lower than ones of CT (76.6±4.3) and TT (78.0±4.4) genotypes. The b value (16.2±3.5) of CC was significantly higher than ones of CT (15.7±3.6) and TT (15.7±3.6). g.18383682A>G was only associated with the L value (<i>P</i><0.05). There was no any association between g.18391548A>T and three color indexes (<i>P</i>>0.05)。The C²¹ was completely conserved among 45 bird species. In contrast, the R²¹ was only present in two species of Psittaciformes. Structure comparisons showed that C21R potentially cause 468 structure alternations, of which 49.6% belong to hydrogen bond alternations, 38.8% for solvent accessible, 8.1% for positive φ angle and 3.5% for changes of secondary structures. In conclusion, this study identifies C21R as a molecular marker that is associated with color variation of chicken brown eggs and has a potential effect on protein structures. The CC genotype of C21R is associated with dark brown color and the TT for light brown.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 12","pages":"1066-1075"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mechanism and related research progress of GLP-1 receptor agonists in treating Alzheimer's disease.","authors":"Xiao-Cheng Zhu, Yi-Wen Wang, Hong-Wen Zhou","doi":"10.16288/j.yczz.24-178","DOIUrl":"https://doi.org/10.16288/j.yczz.24-178","url":null,"abstract":"<p><p>GLP-1 receptor agonists are primarily used clinically for the treatment of type 2 diabetes and have the potential for weight loss, while they are currently expanding their horizons in the treatment of hypertension, non-alcoholic liver disease, depression, and neurodegenerative diseases. In particular, in the treatment of Alzheimer's disease, a large number of animal models and a handful of clinical studies have demonstrated the potential efficacy of GLP-1 receptor agonists, making it highly probable that they will become a new entrant in the drug list for Alzheimer's disease. At present, the research on the mechanism of GLP-1 receptor agonist in the treatment of Alzheimer's disease is mainly based on in-depth analysis of the pathogenesis of Alzheimer's disease and exploration of the mechanism of its comorbidity with diabetes. This article mainly reviews the latest advances in the mechanism of GLP-1 receptor agonists in the treatment of Alzheimer's disease, introduces the latest achievements in animal studies and clinical studies, and aims to provide reference for the subsequent relevant basic research and clinical application.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 12","pages":"1017-1027"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The carboxy-terminal domain of RNA polymerase II large subunit: simple repeats are not simple.","authors":"Qi Li, Zhi-Cheng Dong, Min Liu","doi":"10.16288/j.yczz.24-200","DOIUrl":"https://doi.org/10.16288/j.yczz.24-200","url":null,"abstract":"<p><p>Transcription, as a crucial step in the transmission of genetic information, is completed by DNA-dependent RNA polymerase. In eukaryotes, the transcription of protein-coding genes is completed by RNA polymerase II (Pol II). A distinctive feature of Pol II is the carboxy-terminal domain (CTD) of its largest subunit, RPB1, which is composed of a series of heptapeptide repeats that play a vital role in transcription. Here, we provide a comprehensive review and summary of the sequence characteristics and evolutionary trajectory of the eukaryotic RPB1 CTD, as well as its regulatory function within the transcription cycle. We particularly focus on the mechanisms by which the CTD participates in the regulation of transcription and co-transcriptional processing through post-translational modifications. This deepens our understanding of the intricate regulatory mechanisms governing gene transcription in eukaryotes and lays the groundwork for further investigation into the role of the RPB1 CTD.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 12","pages":"1028-1041"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Progress on molecular mechanisms of bacterial transcription termination.","authors":"Lin-Lin You, Yu Zhang","doi":"10.16288/j.yczz.24-244","DOIUrl":"https://doi.org/10.16288/j.yczz.24-244","url":null,"abstract":"<p><p>Transcription is the process by which genetic information is copied from DNA to RNA, and it can be divided into three stages: transcription initiation, elongation, and termination. Transcription termination is the last step of gene transcription and is crucial for accurate gene expression. Two prevailing modes of transcription termination exist in bacteria: Rho-dependent termination and intrinsic termination (Rho-independent termination). Transcription termination is positively and negatively regulated by bacterial or bacteriophage proteins. In this review, we summarize the research progress of bacterial transcription and its regulation, with the aim of providing a theoretical foundation for further studies and understanding of transcription termination process.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 12","pages":"982-994"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research progresses on non-coding DNA regulatory elements in the evolution of animal adaptive traits.","authors":"Xiu-Hong Wu, Ya-Jun Wang, Li-Feng Che, Xiao-Ping Wang","doi":"10.16288/j.yczz.24-272","DOIUrl":"https://doi.org/10.16288/j.yczz.24-272","url":null,"abstract":"<p><p>Driven by adaptive evolution, animals have developed a variety of adaptive traits that are critical to their survival and reproduction. Unraveling the molecular mechanisms of adaptive evolution is of key significance for understanding important biological phenomena such as species diversification and phenotypic convergence, etc. With the development and maturation of multi-omics technologies, genomic non-coding DNA regulatory elements have been proven to play important regulatory roles in the evolution of adaptive traits in animals. In this review, we summarize the characteristics and mechanisms of non-coding DNA regulatory elements and reviews their molecular mechanisms in the evolution of adaptive traits in animals from three aspects: adaptive traits of animal appendages, traits for adaptation to extreme environments, and other special phenotypic adaptive traits. It offers significant insights for understanding the molecular mechanisms of adaptive trait evolution in animals.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 12","pages":"995-1016"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an RNA virus vector for non-transgenic genome editing in tobacco and generation of berberine bridge enzyme-like mutants with reduced nicotine content","authors":"Haiying Xiang,&nbsp;Binhuan Chen,&nbsp;Shuo Wang,&nbsp;Wanli Zeng,&nbsp;Jiarui Jiang,&nbsp;Weisong Kong,&nbsp;Haitao Huang,&nbsp;Qili Mi,&nbsp;Shuang Ni,&nbsp;Qian Gao,&nbsp;Zhenghe Li","doi":"10.1007/s42994-024-00188-y","DOIUrl":"10.1007/s42994-024-00188-y","url":null,"abstract":"<div><p>Tobacco (<i>Nicotiana tabacum</i>) plants synthesize the psychoactive pyridine alkaloid nicotine, which has sparked growing interest in reducing nicotine levels through genome editing aiming at inactivating key biosynthetic genes. Although stable transformation-mediated genome editing is effective in tobacco, its polyploid nature complicates the complete knockout of genes and the segregation of transgenes from edited plants. In this study, we developed a non-transgenic genome editing method in tobacco by delivering the CRISPR/Cas machinery via an engineered negative-strand RNA rhabdovirus vector, followed by the regeneration of mutant plants through tissue culture. Using this method, we targeted six <i>berberine bridge enzyme-like protein</i> (<i>BBL</i>) family genes for mutagenesis, which are implicated in the last steps of pyridine alkaloid biosynthesis, in the commercial tobacco cultivar Hongda. We generated a panel of 16 mutant lines that were homozygous for mutations in various combinations of <i>BBL</i> genes. Alkaloid profiling revealed that lines homozygous for <i>BBLa</i> and <i>BBLb</i> mutations exhibited drastically reduced nicotine levels, while other <i>BBL</i> members played a minor role in nicotine synthesis. The decline of nicotine content in these lines was accompanied by reductions in anatabine and cotinine levels but increases in nornicotine and its derivative myosmine. Preliminary agronomic evaluation identified two low-nicotine lines with growth phenotypes comparable to those of wild-type plants under greenhouse and field conditions. Our work provides potentially valuable genetic materials for breeding low-nicotine tobacco and enhances our understanding of alkaloid biosynthesis.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"449 - 464"},"PeriodicalIF":4.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00188-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary administration of probiotic Bacillus coagulans and Mentha piperita can protect histological architecture and DNA damage in Catla catla (Hamilton, 1822)","authors":"","doi":"10.1016/j.aaf.2023.02.002","DOIUrl":"10.1016/j.aaf.2023.02.002","url":null,"abstract":"<div><div>The present experimental investigation was executed to evaluate the combined effect of probiotic bacterium <em>Bacillus coagulans</em> along with herb <em>Mentha piperita</em> on histological architecture; and extent of DNA damage after challenge trial with pathogenic bacterium <em>Aeromonas hydrophila</em> in <em>Catla catla</em>. In this experiment, six dietary treatments in triplicate were formulated; C0, M3 and M6 in which <em>M. piperita</em> was supplemented at 0, 3, 6 g kg⁻¹ of feed, while in dietary treatments CP, MP3 and MP6; supplementation of probiotic bacterium <em>B. coagulans</em> at the rate of 3000 CFU g⁻¹ was done along with different inclusion level of <em>M. piperita</em> (0, 3, 6 g kg⁻¹ of feed). Fishes were fed for 60 days on different dietary treatments. Growth performance, histological study and extent of DNA damage using comet assay was examined. Significantly (<em>p</em> &lt; 0.05) high growth % gain in BW was observed in treatment MP6 followed by treatment M6. The histological analysis clearly revealed that dietary <em>M. piperita</em> without or with probiotic bacterium can protect the histoarchitecture of intestinal layers and liver even after challenge with <em>A. hydrophila</em>. Analysis of various comet parameters (tail length, olive moment, tail DNA, head DNA) affirmed that <em>M. piperita</em> supplemented diet can reduce the extent of DNA damage in fishes after challenge trial with <em>A. hydrophila</em>, however dietary supplementation of probiotic bacterium along with <em>M. piperita</em> can reduce the DNA damage up to larger extent confirming its combined protective effect of supplemented diets.</div></div>","PeriodicalId":36894,"journal":{"name":"Aquaculture and Fisheries","volume":"9 6","pages":"Pages 948-956"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86798169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}