genetic analysis

遗传分析
  • 文章类型: Journal Article
    目标:科罗拉多马铃薯甲虫,Leptinotarsadecemlineata(说)(鞘翅目:菊科)是造成重大经济损失的最广泛的害虫,尤其是土豆。由于大量使用杀虫剂,这个物种现在能抵抗大多数杀虫剂,构成了重大的控制挑战。频繁施用农药还会伤害非目标生物,环境,和人类健康。因此,利用昆虫病原真菌(EPF)等生物防治剂为害虫管理提供了可行的替代方案。这项研究的目的是鉴定和表征从土壤样品中分离出的新EPF菌株,并在实验室条件下评估其对成年L.decemlineata的功效。
    结果:在捷克共和国的马铃薯田或与田地相邻的未耕种区域中收集了土壤样品,并使用改良的Tenebrio诱饵方法分离了EPF菌株。共分离出20株真菌菌株,并使用基于28SrRNA的形态学和分子标记进行鉴定,ITS和延伸因子1-α基因序列作为球孢白僵菌(Bals。-Criv.)Vuill。,白僵菌(Sacc。)凡夫子和冬虫夏草(威兹)开普勒,B.Shrestha&Spatafora(Hyproreales:Cordycipitaceae),紫丁香纯病菌(Thom。)Luangsa-ard,Houbraken,Hywel-Jones&Samson(Hypecreales:蛇尾科),褐煤(Petch)和褐煤。,Rehner&Humber(Hyprocreales:木耳科)。生物测定法显示,这些菌株对L.decemlineata的毒力之间存在高度差异,在M.robertsii菌株MAN3b中死亡的中值时间最短(LT50=5.0天)。
    结论:结果表明,一些EPF菌株,尤其是绿僵菌属,可以成为对抗科罗拉多马铃薯甲虫的有前途的生物防治剂。
    OBJECTIVE: The Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae) is the most widespread insect pest that causes major economic losses, especially on potatoes. Due to heavy insecticide use, this species now resists most pesticides, posing a significant control challenge. Frequent pesticide application also harms non-target organisms, the environment, and human health. Hence, utilizing biocontrol agents like entomopathogenic fungi (EPF) offers a viable alternative for pest management. The aim of this study was to identify and characterize new EPF strains isolated from soil samples and evaluate their efficacy against adult L. decemlineata under laboratory conditions.
    RESULTS: Soil samples were collected in potato fields or uncultivated areas adjacent to the field in the Czech Republic and EPF strains were isolated using a modified Tenebrio bait method. A total of 20 fungal strains were isolated and identified using morphological and molecular markers based on the 28S rRNA, ITS and elongation factor 1-alpha gene sequences as Beauveria bassiana (Bals.-Criv.) Vuill., Beauveria brongniartii (Sacc.) Petch and Cordyceps fumosorosea (Wize) Kepler, B. Shrestha & Spatafora (Hypocreales: Cordycipitaceae), Purpureocillium lilacinum (Thom.) Luangsa-ard, Houbraken, Hywel-Jones & Samson (Hypocreales: Ophiocordycipitaceae), Metarhizium brunneum (Petch) and Metarhizium robertsii Bisch., Rehner & Humber (Hypocreales: Clavicipitaceae). The bioassays revealed high variability among virulence of these strains against L. decemlineata with the shortest median time to death (LT50 = 5.0 days) in M. robertsii strain MAN3b.
    CONCLUSIONS: Results shown that some EPF strains, particularly those of genera Metarhizium, can be promising biocontrol agents against the Colorado potato beetle.
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  • 文章类型: Journal Article
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  • 文章类型: Journal Article
    OBJECTIVE: The objective is to develop a natural and stable anti-oxidative stress and anti-ageing ingredient. In this study, we evaluated the changes in white tea leaves fermented with Eurotium cristatum PLT-PE and Saccharomyces boulardii PLT-HZ and their efficacy against skin oxidative stress.
    METHODS: We employed untargeted metabolomics technology to analyse the differential metabolites between tea extract (TE) and fermented tea extract (FTE). In vitro, using H2O2-induced HaCaT cells, we evaluated cell vitality, ROS, and inflammatory factors (TNF-α, IL-1β, and IL-6). Additionally, we verified the effects on the extracellular matrix and nuclear DNA using fibroblasts or reconstructed skin models. We measured skin hydration, elasticity, wrinkle area, wrinkle area ratio, erythema area, and erythema area ratio in volunteers after using an emulsion containing 3% FTE for 28 and 56 days.
    RESULTS: Targeted metabolomics analysis of white tea leaves yielded more than 20 differential metabolites with antioxidant and anti-inflammatory activities, including amino acids, polypeptides, quercetin, and liquiritin post-fermentation. FTE, compared to TE, can significantly reduce reactive oxygen species (ROS) and protect against oxidative stress-induced skin damage in H2O2-induced HaCaT cells. FTE can inhibit H2O2-induced collagen degradation by suppressing the MAPK/c-Jun signalling pathway and can also mitigate the reactive oxygen species damage to nuclear DNA. Clinical studies showed that the volunteers\' stratum corneum water content, skin elasticity, wrinkle area, wrinkle area ratio, erythema area, and erythema area ratio significantly improved from the baseline after 28 and 56 days of FTE use.
    CONCLUSIONS: This study contributes to the growing body of literature supporting the protective effects against skin oxidative stress and ageing from fermented plant extracts. Moreover, our findings might inspire multidisciplinary efforts to investigate new fermentation techniques that could produce even more potent anti-ageing solutions.
    OBJECTIVE: L\'objectif est de développer un ingrédient naturel et stable contre le stress oxydatif et anti‐âge. Dans cette étude, nous avons évalué les modifications dans les feuilles de thé blanc fermentées avec la PLT‐PE Eurotium cristatum et la PLT‐HZ Saccharomyces boulardii et leur efficacité contre le stress oxydatif cutané. MÉTHODES: Nous avons utilisé une technologie de métabolomique non ciblée pour analyser les métabolites différentiels entre l\'extrait de thé (ET) et l\'extrait de thé fermenté (ETF). In vitro, à l\'aide de cellules HaCaT induites par l\'H2O2, nous avons évalué la vitalité cellulaire, les ERO et les facteurs inflammatoires (TNF‐α, IL‐1β, and IL‐6). Nous avons également vérifié les effets sur la matrice extracellulaire et l\'ADN nucléaire à l\'aide de fibroblastes ou de modèles cutanés reconstruits. Nous avons mesuré l\'hydratation de la peau, l\'élasticité, la surface de rides, le rapport des surfaces de rides, la surface d\'érythème, et le rapport des surfaces d\'érythème chez des volontaires ayant utilisé une émulsion contenant 3% d\'ETF pendant 28 et 56 jours. RÉSULTATS: L\'analyse métabolomique ciblée des feuilles de thé blanc a révélé plus de 20 métabolites différentiels ayant des activités antioxydantes et anti‐inflammatoires, notamment des acides aminés, des polypeptides, de la quercétine et de la liquiritine après fermentation. Par rapport à l\'ET, l\'ETF peut réduire significativement les espèces réactives de l\'oxygène (ERO) et protéger contre les lésions cutanées induites par le stress oxydatif dans les cellules HaCaT induites par l\'H2O2. L\'ETF peut inhiber la dégradation du collagène induite par l\'H2O2 en supprimant la voie de signalization MAPK/c‐Jun et peut également atténuer les dommages causés par les espèces réactives de l\'oxygène à l\'ADN nucléaire. Les études cliniques ont montré que la teneur en eau de la couche cornée des volontaires, l\'élasticité de la peau, la surface de rides, le rapport des surfaces de rides, la surface d\'érythème et le rapport des surfaces d\'érythème se sont significativement améliorés par rapport à la référence après 28 et 56 jours d\'utilisation d\'ETF.
    CONCLUSIONS: Cette étude contribue au corpus croissant de littérature soutenant les effets protecteurs des extraits de plantes fermentées contre le stress oxydatif cutané et le vieillissement. En outre, nos résultats pourraient inspirer des efforts pluridisciplinaires pour étudier de nouvelles techniques de fermentation susceptibles de produire des solutions anti‐âge encore plus puissantes.
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  • 文章类型: Journal Article
    血浆蛋白是中风的有希望的生物标志物和潜在的药物靶标。本研究旨在使用孟德尔随机化(MR)方法探讨血浆蛋白与卒中亚型之间是否存在因果关系。采用双样本双向孟德尔随机化方法来研究血浆蛋白与中风之间的因果关系。血浆蛋白的数据来自三项研究,包括INTERVAL,合并的中风信息来自MEGASTROKE联盟和英国生物银行数据集,涵盖中风的四种亚型。MR分析主要使用方差逆加权进行,并进行了敏感性分析.最后,使用双向MR评估潜在的反向因果关系.我们确定了两种与中风有因果关系的蛋白质:一种是潜在的治疗靶点,另一种是保护因子。发现CXCL8与大动脉粥样硬化(LAA)卒中的风险呈正相关(OR,1.005;95%CI1.001至1.010;p=0.022),而TNFRSF11b与发生LAA卒中的风险呈负相关(OR,0.937;95%CI0.892至0.984;p=0.010),独立于其他中风亚型。反向双变量分析未显示缺血性卒中与CXCL8和TNFRSF11b有因果关系。CXCL8和TNFRSF11b与左心耳卒中有因果关系,独立于其他亚型。这项研究为中风的遗传学研究提供了新的视角。
    Plasma proteins are promising biomarkers and potential drug targets for stroke. This study aimed to explore whether there is a causal relationship between plasma proteins and subtypes of stroke using a Mendelian randomization (MR) approach. A two-sample bidirectional Mendelian randomization approach was employed to investigate the causal link between plasma proteins and stroke. Data on plasma proteins were obtained from three studies, including INTERVAL, and pooled stroke information was sourced from the MEGASTROKE consortium and the UK Biobank dataset, covering four subtypes of stroke. MR analyses were primarily conducted using inverse variance weighting, and sensitivity analyses were also performed. Finally, potential reverse causality was assessed using bidirectional MR. We identified two proteins causally associated with stroke: one as a potential therapeutic target and another as a protective factor. CXCL8 was found to be positively associated with the risk of developing large-artery atherosclerotic (LAA) stroke (OR, 1.005; 95% CI 1.001 to 1.010; p = 0.022), whereas TNFRSF11b was negatively correlated with the risk of developing LAA stroke (OR, 0.937; 95% CI 0.892 to 0.984; p = 0.010), independently of other stroke subtypes. Reverse bivariate analysis did not indicate that ischemic stroke was causally associated with CXCL8 and TNFRSF11b. There is a causal relationship between CXCL8 and TNFRSF11b with LAA stroke, independent of other subtypes. This study offers a new perspective on the genetics of stroke.
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  • 文章类型: Journal Article
    背景:隐匿性黄斑营养不良(OMD),主要由色素性视网膜炎1样1(RP1L1)变体引起,是一种复杂的视网膜疾病,其特征是进行性视力丧失和正常的眼底外观。本研究旨在探讨OMD在中国患者中的不同表型表达和基因型相关性。包括一例罕见的与RP1L1相关的卵形黄斑营养不良(VMD)。
    方法:我们分析了7名OMD患者和1名VMD患者,所有具有杂合致病性RP1L1变体。临床评估包括最佳矫正视力(BCVA),视野测试,谱域光学相干断层扫描(SD-OCT)多焦视网膜电图(mfERGs),和显微视野。下一代测序用于遗传分析。
    结果:OMD患者表现出一系列的表型变异性。大多数(7个中的5个)具有RP1L1变体c.133C>T;p.R45W,与中心视力丧失和SD-OCT和mfERG的特定模式相关。两名患者表现出不同的RP1L1变体(c.3599G>T;p.G1200V和c.2880G>C;p.W960C),呈现温和的表型。SD-OCT显示光感受器层变化,大多数患者在中央环中显示mfERG反应降低。有趣的是,观察到与RP1L1变体相关的VMD的独特病例,与传统的OMD演示不同。
    结论:这项研究强调了OMD内的表型多样性和更广泛的RP1L1相关黄斑营养不良,包括与VMD的新颖联系。研究结果强调了RP1L1变异在确定临床表现时的复杂性。强调需要对黄斑营养不良进行全面的遗传和临床评估。
    BACKGROUND: Occult Macular Dystrophy (OMD), primarily caused by retinitis pigmentosa 1-like 1 (RP1L1) variants, is a complex retinal disease characterised by progressive vision loss and a normal fundus appearance. This study aims to investigate the diverse phenotypic expressions and genotypic correlations of OMD in Chinese patients, including a rare case of Vitelliform Macular Dystrophy (VMD) associated with RP1L1.
    METHODS: We analysed seven OMD patients and one VMD patient, all with heterozygous pathogenic RP1L1 variants. Clinical assessments included Best Corrected Visual Acuity (BCVA), visual field testing, Spectral Domain Optical Coherence Tomography (SD-OCT), multifocal Electroretinograms (mfERGs), and microperimetry. Next-generation sequencing was utilised for genetic analysis.
    RESULTS: The OMD patients displayed a range of phenotypic variability. Most (5 out of 7) had the RP1L1 variant c.133 C > T; p.R45W, associated with central vision loss and specific patterns in SD-OCT and mfERG. Two patients exhibited different RP1L1 variants (c.3599G > T; p.G1200V and c.2880G > C; p.W960C), presenting milder phenotypes. SD-OCT revealed photoreceptor layer changes, with most patients showing decreased mfERG responses in the central rings. Interestingly, a unique case of VMD linked to the RP1L1 variant was observed, distinct from traditional OMD presentations.
    CONCLUSIONS: This study highlights the phenotypic diversity within OMD and the broader spectrum of RP1L1-associated macular dystrophies, including a novel association with VMD. The findings emphasise the complexity of RP1L1 variants in determining clinical manifestations, underscoring the need for comprehensive genetic and clinical evaluations in macular dystrophies.
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  • 文章类型: Journal Article
    尽管已经描述了尿镁(Mg2)排泄的年龄依赖性变化,潜在的机制仍然难以捉摸。由于遗传力显着导致尿Mg2排泄的变化,我们在一组遗传变量多样性远交(DO)小鼠中测量了不同年龄的尿Mg2排泄。与6个月大的动物相比,在12个月和18个月时观察到Mg2+排泄增加.数量性状基因座(QTL)分析显示,10号染色体上的基因座与6个月大的Mg2排泄有关,以Oit3(编码癌蛋白诱导的转录本3;OIT3)作为我们的主要候选基因。为了研究OIT3在肾脏Mg2+处理中的可能作用,我们产生并表征Oit3敲除(Oit3-/-)小鼠。尽管在雄性Oit3-/-小鼠中存在略低的血清Mg2浓度,在雌性Oit3-/-小鼠中未观察到这种作用。此外,Oit3-/-小鼠的尿Mg2排泄和肾磁化基因的表达没有改变。对于12个月和18个月大的动物,QTL分析显示与19号染色体上的一个基因座相关,该基因座包含编码TRPM6的基因,TRPM6是一种已知的Mg2通道,参与肾脏Mg2重吸收。与RNAseq数据的比较表明,Trpm6mRNA表达与QTL效应呈负相关,这意味着TRPM6可能与小鼠尿Mg2排泄的年龄依赖性变化有关。总之,我们在这里显示Oit3和Trpm6的变异体在生命的不同时期与尿Mg2+排泄有关,虽然OIT3不太可能影响肾脏Mg2+处理。
    Although age-dependent alterations in urinary magnesium (Mg2+) excretion have been described, the underlying mechanism remains elusive. As heritability significantly contributes to variations in urinary Mg2+excretion, we measured urinary Mg2+ excretion at different ages in a cohort of genetically variable Diversity Outbred (DO) mice. Compared to animals aged 6 months, an increase in Mg2+ excretion was observed at 12 and 18 months. Quantitative trait locus (QTL) analysis revealed an association of a locus on chromosome 10 with Mg2+ excretion at 6 months of age, with Oit3 (encoding oncoprotein-induced transcript 3; OIT3) as our primary candidate gene. To study the possible role of OIT3 in renal Mg2+ handling, we generated and characterized Oit3 knockout (Oit3-/-) mice. Although a slightly lower serum Mg2+ concentration was present in male Oit3-/- mice, this effect was not observed in female Oit3-/- mice. Additionally, urinary Mg2+ excretion and the expression of renal magnesiotropic genes was unaltered in Oit3-/- mice. For animals aged 12 and 18 months, QTL analysis revealed an association with a locus on chromosome 19, which contains the gene encoding TRPM6, a known Mg2+ channel involved in renal Mg2+ reabsorption. Comparison with RNAseq data revealed that Trpm6 mRNA expression is inversely correlated with the QTL effect, implying that TRPM6 may be involved in age-dependent changes in urinary Mg2+ excretion in mice. In conclusion, we show here that variants in Oit3 and Trpm6 are associated with urinary Mg2+ excretion at distinct periods in life, although OIT3 is unlikely to affect renal Mg2+ handling.
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  • 文章类型: Case Reports
    人类蛔虫病是一种土壤传播的蠕虫病,仍然是一种被忽视的热带病。蛔虫有可能导致人和猪之间的交叉感染。在这项研究中,我们介绍了一例罕见的无症状的蛔虫感染患者。一名66岁的男性接受了结肠镜检查,在肝曲中发现了一个白色的线性蠕虫体。通过抽吸收集蠕虫,并将其提交给实验室进行寄生虫鉴定。患者没有与寄生虫感染相关的症状。高度怀疑该蠕虫是A虫属。由于形态学分类的困难,进行遗传分析。从PCR限制性片段长度多态性结果和内部转录的间隔区1区的序列分析,它被确定为A.suum。通过进行遗传分析来快速分化A.suum的经验将有助于将来检查寄生虫感染。
    Human ascariasis is a soil-transmitted helminthiasis and remains a neglected tropical disease. Ascaris suum has the potential to cause cross-infections between humans and pigs. In this study, we present a rare case of a patient with asymptomatic infection by Ascaris suum. A 66-year-old male underwent colonoscopy, and a white linear worm body was found in the hepatic curvature. The worm was collected by aspiration and submitted to the laboratory for parasite identification. The patient had no symptoms related to parasitic infection. The worm was highly suspected to be of the genus Ascaris. Because of the difficulty of morphological classification, genetic analysis was performed. From PCR-restriction fragment length polymorphism results and sequence analysis of the internal transcribed spacer-1 region, it was determined to be A. suum. The experience with rapid differentiation of A. suum by performing genetic analysis will be useful for future examinations of parasitic infections.
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  • 文章类型: Journal Article
    本研究旨在研究原发性干燥综合征(SS)和多发性硬化症(MS)之间的因果关系,使用双样本孟德尔随机化(MR)分析,以提供对其共同机制和治疗策略的影响的见解。我们利用全基因组关联研究(GWAS)的数据对原发性SS(1,290例和213,145例对照)和MS(4,888例和10,395例对照),仅限于欧洲血统。基于与原发性SS相关的遗传变异选择工具变量(IVs)。主要的MR方法是逆方差加权(IVW),由埃格先生补充,加权中位数,简单模式,和加权模式算法来评估MS和主要SS之间的双向因果关系。敏感性分析,包括MR-PRESSO和漏报分析,进行是为了确保我们研究结果的稳健性。排除具有多效性的SNP后,42和5个SNP被鉴定为原发性SS和MS的稳健IV,分别。我们的分析显示MS对原发性SS有显著的保护作用,IVW显示OR为0.896(95%CI:0.841-0.954,P=0.001)。没有检测到显著的异质性或水平多效性,支持结果的可靠性。我们的研究结果表明,MS对原发性SS具有潜在的保护作用,表明这两种自身免疫性疾病之间存在负因果关系。这为理解原发性SS和MS之间复杂的相互作用增加了有价值的遗传证据,为研究和治疗干预提供新的途径。
    This study aims to investigate the causal relationship between primary Sjögren\'s syndrome (SS) and multiple sclerosis (MS) using a two-sample Mendelian randomization (MR) analysis to provide insights into their common mechanisms and implications for therapeutic strategies. We utilized data from Genome-Wide Association Studies (GWAS) for primary SS (1,290 cases and 213,145 controls) and MS (4,888 cases and 10,395 controls), restricted to European ancestry. Instrumental variables (IVs) were selected based on genetic variants associated with primary SS. The primary MR method was Inverse Variance Weighted (IVW), supplemented by MR Egger, Weighted Median, Simple Mode, and Weighted Mode algorithms to assess the bidirectional causal relationships between MS and primary SS. Sensitivity analyses, including MR-PRESSO and leave-one-out analysis, were conducted to ensure the robustness of our findings. After excluding SNPs with pleiotropic effects, 42 and 5 SNPs were identified as robust IVs for primary SS and MS, respectively. Our analysis revealed a significant protective effect of MS on primary SS, with IVW showing an OR of 0.896 (95% CI: 0.841-0.954, P = 0.001). No significant heterogeneity or horizontal pleiotropy was detected, supporting the reliability of the results. Our findings suggest a potential protective effect of MS against primary SS, indicating a negative causal association between these two autoimmune diseases. This adds valuable genetic evidence to the understanding of the complex interplay between primary SS and MS, offering new avenues for research and therapeutic interventions.
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  • 文章类型: Journal Article
    这项研究探讨了循环炎症标志物与坐骨神经痛发展之间的因果关系,一种常见的衰弱状态。虽然以前的研究表明炎症可能是坐骨神经痛的一个因素,但是尚未进行彻底的遗传调查以确定因果关系。深入了解这些相互作用可能会发现新的治疗目标。
    我们使用了来自OpenGWAS数据库的数据,纳入了484,598人的大型欧洲队列,包括4549名坐骨神经痛患者。我们的研究集中于91种不同的循环炎症标志物。遗传变异被用作这些标记的工具变量(IVs)。分析采用方差倒数加权(IVW)作为主要方法,辅以加权中位数估计。通过敏感性研究对发现进行了验证,利用R软件进行统计计算。
    分析显示,在所研究的91种炎症标志物中,有52种与发生坐骨神经痛的风险存在显著的因果关系。关键标志物如CCL2、单核细胞趋化蛋白-4和蛋白S100-A12表现出正相关。此外,这些结果没有异质性或水平多效性.有趣的是,反向孟德尔随机分析还表明坐骨神经痛对某些炎症标志物的潜在致病作用,特别是Fms相关的酪氨酸激酶3配体。
    这项研究提供了强有力的证据,将特定的循环炎症标志物与坐骨神经痛的风险联系起来。强调炎症在其发病机制中的作用。这些发现可以为未来的靶向治疗研究提供信息,并增强我们对坐骨神经痛的生物学机制的理解。
    UNASSIGNED: This research explores the causal association between circulating inflammatory markers and the development of sciatica, a common and debilitating condition. While previous studies have indicated that inflammation may be a factor in sciatica, but a thorough genetic investigation to determine a cause-and-effect relationship has not yet been carried out. Gaining insight into these interactions may uncover novel treatment targets.
    UNASSIGNED: We utilized data from the OpenGWAS database, incorporating a large European cohort of 484,598 individuals, including 4,549 sciatica patients. Our study focused on 91 distinct circulating inflammatory markers. Genetic variations were employed as instrumental variables (IVs) for these markers. The analysis was conducted using inverse variance weighting (IVW) as the primary method, supplemented by weighted median-based estimation. Validation of the findings was conducted by sensitivity studies, utilizing the R software for statistical computations.
    UNASSIGNED: The analysis revealed that 52 out of the 91 inflammatory markers studied showed a significant causal association with the risk of developing sciatica. Key markers like CCL2, monocyte chemotactic protein-4, and protein S100-A12 demonstrated a positive correlation. In addition, there was no heterogeneity or horizontal pleiotropy in these results. Interestingly, a reverse Mendelian randomization analysis also indicated potential causative effects of sciatica on certain inflammatory markers, notably Fms-related tyrosine kinase 3 ligands.
    UNASSIGNED: The study provides robust evidence linking specific circulating inflammatory markers with the risk of sciatica, highlighting the role of inflammation in its pathogenesis. These findings could inform future research into targeted treatments and enhance our understanding of the biological mechanisms underlying sciatica.
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  • 文章类型: Journal Article
    使用IlluminaInfiniumSolCAPV212K马铃薯SNP阵列对来自全球的3,860种信任克隆马铃薯种质进行基因分型,以评估马铃薯种质收集中的遗传多样性和种群结构。二倍体,三倍体,四倍体,包括代表栽培马铃薯类群的五倍体种质。杂合性范围为9.7%至66.6%,随倍性水平增加,平均杂合性为33.5%。Identity,亲缘关系,和祖先使用层次聚类和基于模型的贝叶斯混合分析进行评估。在对体外克隆材料与原始母株的并排比较中,揭示了遗传身份错误,揭示了在数十年的加工和处理过程中可能发生的错误。构建了系统发育来评估种间和种内关系,该关系与结构分析一起支持马铃薯分类学的两种常用处理。加入通常基于分类学和倍性分类进行聚类,但有一些例外,但并非始终按地理来源进行聚类。结构分析确定了推定的杂种,并建议栽培马铃薯中的六个遗传簇,马铃薯种群之间发生了广泛的基因流,暗示大多数种群容易共享等位基因,并且渗入在马铃薯中很常见。马铃薯亚种。Andigena(ADG)和S.curtiloubum(CUR)显示出明显的混合。由于其广泛的地理分布,ADG可能具有广泛的混合物。Solanumphureja(PHU),茄子(CHA)/茄子亚种。stenotomum(STN),和马铃薯亚种。相对于所评估的物种,从登录名/种群的角度来看,马铃薯(TBR)种群的混合较少。还构建了来自genebank材料的核心和微型核心子集。SNP基因分型也进行了745种来自种子储户马铃薯收集,证实了两个马铃薯收集之间没有遗传重复,这表明这些藏品拥有不同的马铃薯遗传资源。InfiniumSNP马铃薯阵列是一个强大的工具,可以提供多样性评估,指纹基因库加入质量管理计划,用于研究和育种,并提供对马铃薯遗传资源集合中存在的多样性的复杂遗传结构和杂种起源的见解。
    A total of 3,860 accessions from the global in trust clonal potato germplasm collection w3ere genotyped with the Illumina Infinium SolCAP V2 12K potato SNP array to evaluate genetic diversity and population structure within the potato germplasm collection. Diploid, triploid, tetraploid, and pentaploid accessions were included representing the cultivated potato taxa. Heterozygosity ranged from 9.7% to 66.6% increasing with ploidy level with an average heterozygosity of 33.5%. Identity, relatedness, and ancestry were evaluated using hierarchal clustering and model-based Bayesian admixture analyses. Errors in genetic identity were revealed in a side-by-side comparison of in vitro clonal material with the original mother plants revealing mistakes putatively occurring during decades of processing and handling. A phylogeny was constructed to evaluate inter- and intraspecific relationships which together with a STRUCTURE analysis supported both commonly used treatments of potato taxonomy. Accessions generally clustered based on taxonomic and ploidy classifications with some exceptions but did not consistently cluster by geographic origin. STRUCTURE analysis identified putative hybrids and suggested six genetic clusters in the cultivated potato collection with extensive gene flow occurring among the potato populations, implying most populations readily shared alleles and that introgression is common in potato. Solanum tuberosum subsp. andigena (ADG) and S. curtilobum (CUR) displayed significant admixture. ADG likely has extensive admixture due to its broad geographic distribution. Solanum phureja (PHU), Solanum chaucha (CHA)/Solanum stenotomum subsp. stenotomum (STN), and Solanum tuberosum subsp. tuberosum (TBR) populations had less admixture from an accession/population perspective relative to the species evaluated. A core and mini core subset from the genebank material was also constructed. SNP genotyping was also carried out on 745 accessions from the Seed Savers potato collection which confirmed no genetic duplication between the two potato collections, suggesting that the collections hold very different genetic resources of potato. The Infinium SNP Potato Array is a powerful tool that can provide diversity assessments, fingerprint genebank accessions for quality management programs, use in research and breeding, and provide insights into the complex genetic structure and hybrid origin of the diversity present in potato genetic resource collections.
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