贵阳花溪古茶树遗传进化的SNP分析

试验采用SNP(单核苷酸多态性)技术对贵阳花溪古茶树资源的遗传多样性、群体结构和遗传进化进行了分析.结果表明,利用生物信息学分析古茶树样品的重测序数据,获得了1 656 258个SLAF标签,古茶树样品平均测序深度为24.21x,其中多态性的SLAF标签有462 897个,共得到283 376个高一致性的群体SNP标记.从基于SNP标记获得的进化树可以看出,来自相近地方的古茶树在进化树上基本上处于相近位置,但是花溪古茶树存在着广泛的遗传变异,主成分分析(PCA)获得了与进化树一致的结果.群体结构分析可清晰地把古茶树资源分为乔木型和灌木型2个类群.乔木型古茶树位于进化树下部,而灌木型古茶树处于进化树上部,表明茶树是由乔木型向灌木型进化的.     

Cultivation effects on soil texture and fertility in an arid desert region of northwestern China

In arid desert regions of northwestern China, reclamation and subsequent irrigated cultivation have become effective ways to prevent desertification, expand arable croplands, and develop sustainable agricultural production. Improvement in soil texture and fertility is crucial to high soil quality and stable crop yield. However, knowledge on the long-term effects of the conversion of desert lands into arable croplands is very limited. To address this problem, we conducted this study in an arid desert region of northwestern China to understand the changes in soil physical-chemical properties after 0, 2, 5, 10, 17, and 24 years of cultivation. Our results showed that silt and clay contents at the 17-year-old sites increased 17.5 and 152.3 folds, respectively, compared with that at the 0-year-old sites. The soil aggregate size fraction and its stability exhibited an exponential growth trend with increasing cultivation ages, but no significant change was found for the proportion of soil macroaggregates (>5.00 mm) during the 17 years of cultivation. The soil organic carbon (SOC) content at the 24-year-old sites was 6.86 g/kg and increased 8.8 folds compared with that at the 0-year-old sites. The total (or available) nitrogen, phosphorus, and potassium contents showed significant increasing trends and reached higher values after 17 (or 24) years of cultivation. Changes in soil physical-chemical properties successively experienced slow, rapid, and stable development stages, but some key properties (such as soil aggregate stability and SOC) were still too low to meet the sustainable agricultural production. The results of this long-term study indicated that reasonable agricultural management, such as expanding no-tillage land area, returning straw to the fields, applying organic fertilizer, reducing chemical fertilizer application, and carrying out soil testing for formula fertilization, is urgently needed in arid desert regions.     

Relationship of Icelandic cattle with Northern and Western European cattle breeds,admixture and population structure

ABSTRACT

Icelandic cattle is believed to have been brought from Norway during the settlement of Iceland around AD 870-930. Previous research on genetic relationships has indicated that Icelandic cattle is most related to northern Nordic indigenous breeds. Using single nucleotide polymorphism genotype data from Icelandic cattle and 29 Northern and Western European cattle breeds, we studied relationships and admixture among these breeds, and assessed population structure in Icelandic cattle. Population structure analysis through principal component analysis, estimation of ancestry, and analysis of patterns of population splitting and mixing revealed that Icelandic cattle are most related to three Finncattle breeds (Eastern, Northern and Western Finncattle), and Swedish Mountain cattle. Icelandic cattle has very low levels of admixture. We observed very limited population structure in Icelandic cattle. The observed structure was due to variable sire contributions. Over 1000 years of almost complete isolation has made Icelandic cattle highly genetically distinct from other cattle breeds.     

Soil Quality for Rice Productivity and Yield Sustainability under Long-term Fertilizer and Manure Application

Productivity and sustainability of rice-rice cropping system depend upon the soil quality which is primarily governed by application of fertilizers and manures. However, such information is limited and hence, the present investigation was carried out in a 9-year-old long-term fertilizer experiment at Bhubaneswar, India. There were seven treatments (control, application of 100% NPK, 150% NPK, 100% NPK + Zn, 100% NPK + FYM, 100% NPK + Zn + B, and 100% NPK + Zn + S) laid out in randomized block design with four replications. Indicators of soil quality (physical, chemical, and biological) were diagnosed from 30 numbers of soil properties measured on the post-wet season soil and soil quality was assessed taking productivity and sustainability of dry season rice as goal functions. Results revealed that the highest productivity and sustainability of dry season rice was found with application of 100% NPK + FYM. This treatment, in general, showed better physical, chemical, and biological properties than rest of the treatments. The highest soil quality index (SQI) was recorded in 100% NPK + FYM (0.941) treatment followed by 150% NPK (0.826) with CEC diagnosed as the only key indicator for rice productivity. For yield sustainability in dry season, reserve K and total N were important contributing 89% and 11%, respectively to the SQI. Therefore, these soil properties could be used to monitor soil quality in wet season. Application of FYM along with 100% NPK could sustain the productivity of dry season rice by improving soil properties under subtropical rice-rice system.     

基于近红外漫反射光谱的规模化奶牛场粪水氮磷定量分析及模型构建

为建立规模化奶牛场粪水中氮磷含量现场快速检测方法,以实现准确预测的同时替代常规监测程序,选取23家天津市典型种养结合模式的规模化奶牛场,围绕粪水处理全过程环节依次开展样品采集、实验室常规化学检测、近红外漫反射光谱采集,并进行主成分分析和偏最小二乘分析,建立多种动态复合影响因素条件下的全局、全程快速检测定量分析模型。结果表明:主成分分析不仅反映出同一奶牛场粪水有机组分随处理环节的变化,而且也反映出不同奶牛场粪水样品的差异性,以及在粪水处理过程中各因素对后续模型的影响程度。建立的全过程环节定量分析模型对总氮含量预测结果与实际含量的线性拟合相关系数R为0.96,预测均方根误差RMSEP为187.80;对总磷含量预测结果与实际含量的线性拟合相关系数R为0.91,预测均方根误差RMSEP为3.59。建立的全局定量分析模型对总氮含量预测结果与实际含量的线性拟合相关系数R为0.96,预测均方根误差RMSEP为238.59;总磷含量预测结果与实际含量的线性拟合相关系数R为0.91,预测均方根误差RMSEP为6.56。研究表明,基于近红外漫反射光谱和偏最小二乘法对规模化奶牛场粪水处理全过程环节粪水样品中氮、磷含量进行定量分析是可行的;纵向模型比横向模型能提供更好的预测结果;近红外漫反射光谱技术可实时、快速、高效地对规模化奶牛场粪水处理全过程总氮和总磷进行跟踪和监控。     

Sargassum horneri as a Functional Food Ameliorated IgE/BSA-Induced Mast Cell Activation and Passive Cutaneous Anaphylaxis in Mice

Sargassum horneri (S. horneri), an edible brown alga, has been proposed as a functional food with an improvement effect on abnormal skin immune responses. The present study investigates the anti-allergic effect of an ethanol extract from S. horneri (SHE) on immunoglobulin E (IgE)/bovine serum albumin (BSA)-mediated activation in bone marrow-derived cultured-mast cells (BMCMCs) and passive cutaneous anaphylaxis (PCA) reaction in mice. SHE markedly and dose-dependently suppressed the degranulation of BMCMCs by reducing the β-hexosaminidase and histamine release without cytotoxicity. In addition, SHE significantly decreased the FcεRI expression on the surface of BMCMCs and its IgE binding. Moreover, SHE reduced the mRNA expression and the production of allergic cytokines; interleukin (IL)-1β, IL-4, IL-5, IL-6, IL-10, IL-13; interferon (IFN)-γ and/or tumor necrosis factor (TNF)-α; and a chemokine, thymus and activation-regulated chemokine (TARC), by suppressing the activation of Src-family kinases and nuclear factor (NF)-κB signaling. In further study, the application of SHE reduced the PCA reaction in an IgE/BSA-induced type I allergic mice model. Taken together, we suggest that SHE has an anti-allergic effect in type I allergic responses.     

应用PCR-DGGE技术比较绵羊瘤胃、网胃、瓣胃和皱胃菌群的多样性

本研究采用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)技术结合DGGE图谱条带的克隆和测序比较了绵羊瘤胃、网胃、瓣胃和皱胃菌群的多样性,同时对菌群进行了聚类分析和主成分分析。结果表明:绵羊瘤胃、网胃、瓣胃和皱胃内容物DGGE图谱的平均条带数分别为18、13、16和15条;瘤胃和瓣胃内菌群的多样性指数、均匀度和丰富度均较高,分别为2.83、0.79、17.00和2.82、0.79、16.80,而网胃和皱胃内容物较低,分别为2.52、0.70、12.60和2.73、0.76、15.40;聚类分析结果显示不同胃的内容物菌群具有一定差异,但不同动物个体相同胃的内容物相似性系数均高于0.63;PCR-DGGE图谱中测序的条带大多数归为拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes),优势菌群为厚壁菌门(Firmicutes)细菌、拟杆菌门(Bacteroidetes)细菌、未培养瘤胃细菌(uncultured rumen bacterium)、未培养细菌(uncultured bacterium)和韦荣球菌科(Veillonellaceae)细菌,特异性细菌为不动杆菌属(Acinetobacter sp.)细菌和瘤胃球菌属(Ruminococcaceae)细菌。结果提示,绵羊4个胃中均含有种类丰富和数量巨大的细菌,且随着消化道部位由前往后的顺序,菌群的多样性呈现先高后降低再升高的趋势。     

An in vivo analysis of the therapeutic and synergistic properties of Chinese medicinal formula Yin-Chen-Hao-Tang based on its active constituents

6,7-Dimethylesculetin (D), geniposide (G) and rhein (R) are the three major active ingredients of Yin-Chen-Hao-Tang (YCHT), a famous Chinese herbal formula, which has been shown to be clinically effective for treating hepatic injury (HI) syndrome. The present study was conducted to investigate the therapeutic and synergistic effects of COC (combination of D, G and R) on HI rats by combining pharmacokinetic with biochemical analysis strategy. Plasma was analyzed by using reversed-phase high performance liquid chromatography (RP-HPLC). Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) models were built to evaluate the therapeutic and synergistic effects of COC at the biochemical level. Here, we report that the COC combination could increase the plasma level, slow elimination rate, exert a more robust therapeutic effect than any one or two of the three individual compounds by hitting multiple targets in a rat model of HI. Overall, this beneficially accounts for the popular view that traditional Chinese medicine (TCM) formula usually takes multi-component to exert their therapeutic effects. We suggest that dissecting the mode of action of clinically effective formula to be capable of producing a sufficient effect at low doses.     

Soil quality assessment under shifting cultivation and forests in Northeastern Himalaya of India

The study aimed to evaluate the impact of shifting cultivation on soil quality, in Wokha district of Nagaland, using weighted soil quality index (SQIw). Four forest sites and three sites under shifting cultivation were selected and physical (texture and bulk density) and chemical (pH, electrical conductivity, cation exchange capacity, organic carbon, available N, P, K, exchangeable cations) parameters were analyzed. The SQIw was calculated on a minimum data set selected by principal component analysis, followed by varimax rotation algorithm and through subsequent normalization of the parameters using the linear scoring function. Significant (P < 0.05) variations in SQIw were found across the depth of the soil and land use according to severity of factors associated with land use. Three different classes of soil quality were also identified: high quality (SQIw > 0.70) for two forest soils (FS1 and FS2) and land under shifting cultivation (JH1), low quality (SQIw < 0.50), only to FS3, and intermediate quality (0.50 < SQI < 0.70) in all other soils. The approach used in this study proved to be sensitive to evaluate the soil quality, however further research is required to better understand the sustainability of shifting cultivation by including more physical, biological and chemical indicators.     

山西普通菜豆初级核心种质农艺性状遗传多样性研究

旨在明确山西省普通菜豆种质资源的主要类型,各类型的主要农艺性状特征及多样性特点。以152份山西省普通菜豆初级核心种质为试材,在田间进行农艺性状鉴定,对152份资源的24个性状进行聚类分析、多样性分析和主成分分析法。结果表明:山西普通菜豆初级核心种质可划分为5种类型。从各分组多样性来看,半蔓+蔓生-紫茎紫花型和蔓生-籽粒斑纹型多样性指数I最高,而直立型资源多样性指数I最低;从各性状多样性来看,质量性状多样性总体低于数量性状,但粒色则表现出明显丰富的多样性。通过主成分分析,将普通菜豆23个农艺性状归属为7个主成分,初步明确了各主成分代表的农艺性状。通过上述研究,明确了山西普通菜豆主要类型、多样性特征和各主成分代表的主要农艺性状,可为资源鉴定评价提供综合性状指标。