基于关联规则面向对象的海岸带海水养殖模式遥感识别

针对目前海水养殖模式遥感识别中的效率低,"同物异谱"、"异物同谱"和"椒盐"噪声等问题,该文研究了关联规则分类和面向对象相结合的养殖模式遥感识别方法,通过不同养殖模式的对象分割和关联规则的自动和智能获取,来构建海水养殖模式分类器。以高分一号PMS1卫星影像为数据源,把不同养殖模式对象的光谱、空间形态和纹理特征及其关联关系作为事务数据,使用Apriori算法挖掘类别作为后件的强规则,对粤东柘林湾养殖核心区内4种海水养殖模式(池塘养殖、网箱养殖、滩涂插养、浮筏吊养)水面信息进行提取。结果表明:基于关联规则面向对象的海水养殖模式分类精度能达到88.65%,比K-近邻法面向对象法精度提高了14.38个百分点,比关联规则挖掘分类法精度提高了12.16个百分点。关联规则分类和面向对象结合方法拓宽了传统逻辑推理分类方法中获取信息的途径,使分类更加自动化和智能化,且分类精度得到显著提高,可以成为海岸带海水养殖复杂模式识别的有效支持手段。     

Genome‐wide association analysis of salmon lice (Lepeophtheirus salmonis) resistance in a North American Atlantic salmon population

Our objective was to detect single nucleotide polymorphisms (SNPs) associated with resistance to the salmon louse in the Saint John River aquacultural population of North American Atlantic salmon using estimated breeding values (EBVs) and 6K genotypes from the parent‐generation and lice count phenotypes from the challenged, but ungenotyped, offspring‐generation. In 2011 and 2012, we challenged recent smolts with approximately 100 copepodids each. Fish were euthanized once the lice reached the chalimus stages and lice count, sex, tank and salt water weight were recorded. We used a multiple trait model to estimate breeding values for the parent‐generation using their own fresh water weights and the salt water weights and lice counts of the offspring‐generation. Salmon lice count heritability for untransformed and transformed data was 0.17 and 0.29 respectively. Two different genome‐wide association study methods were compared: (i) forward multiple linear regression and (ii) a mixed linear model using principal components to correct for population stratification as implemented in the egscore function of GenABEL. The two methods detected different SNPs located on different chromosomes. The multiple regression method incorporated 70 SNPs found on chromosomes 2, 7, 9, 12, 14, 15, 21, 22, 1p/23, 24. Many SNPs entered into the forward multiple regression are likely to be false positives from not correcting for the observed population stratification and cryptic relatedness. In contrast, the mixed linear model identified only two SNPs, one on chromosome 1p/23 (6.9%) and one on chromosome 1q (6.1%) consistent with louse‐resistance being a quantitative trait.     

我国生态农业历史中利用植物辅助效应的实践

我国有着悠久的生态农业历史,农、林生态系统中的植物种间关系被关注最多。种间关系主要有3种,即竞争、辅助和中性。过去,竞争关系是被研究最多的一种。近20年来,辅助关系逐渐受到重视并被引入主流生态学理论中。本文分析了这些经验记载的生态学机理,其中描述最多的是植物幼苗的遮阴以及土壤养分的改良(豆科植物固氮作用)。此外,在缓冲极端温度(夏季高温以及冬季低温)、减少杂草竞争、防止动物捕食、减少水分胁迫等方面也有少量记录。我国古代不仅有利用两种植物种间辅助效应的丰富记载,还有利用多种植物综合和复合的种间辅助关系,以及植物与动物之间的复杂关系构建生态系统的记载。特别是华南地区具有利用多种植物与动物间关系来构建基塘生态系统、复合果园生态系统、茶园生态系统等方面传统经验的记载。深入挖掘我国传统植物间辅助效应的记载,并对其进行科学研究,是生态学中非常有价值的课题。因此,本文从社会-生态记忆的角度,对古代文献中关于植物间辅助效应的记载进行梳理与分析,希望引起学界同仁对这些传统经验的重视,并在此基础上通过现代生态学的实验方法验证这些记载的真实性与适用性,为生态恢复、生态农业、现代林业及生态系统管理等提供有益的借鉴。     

Association mapping identifies markers related to major early‐maturating traits in upland cotton (Gossypium hirsutum L.)

Association mapping is a promising tool to identify genes for quantitative traits. A total of 172 upland cotton (Gossypium hirsutum L.) accessions were assessed. The panel was phenotyped for four major early‐maturating traits across multiple environments and genotyped using 331 polymorphic simple sequence repeat (SSR) markers. The gene diversity of the 331 markers averaged 0.40 (range: 0.04–0.78), and the polymorphism information content (PIC) averaged 0.34 (range: 0.04–0.75). Thirty‐nine significant markers related to early‐maturating traits were simultaneously detected in at least two environments. Among the 39 markers, 11 for seed period (SP), seven for bud period (BP), six for flower and boll period (FBP), and 15 for growth period (GP). These markers were stable and could be used for marker‐assisted selection (MAS). Favourable alleles for SP, BP, FBP and GP were explored. These alleles can be directly used in MAS to improve cotton early maturity. This study lays the foundation for analysing the genetic mechanisms underlying early maturity, as well as the use of MAS to target traits in cotton.     

AQP7基因内含子4多态性与郏县红牛生长性状的关联分析

本试验旨在研究郏县红牛AQP7基因内含子4的遗传变异,分析其遗传多态性对生长性状的影响。采用PCR-SSCP、DNA序列分析及生物信息学技术探讨郏县红牛AQP7基因内含子4的多态性及其与生长性状的关联情况。结果发现,郏县红牛AQP7基因内含子4存在A、B、C 3个等位基因,其基因频率依次为0.838、0.076、0.086;郏县红牛AQP7基因4种不同基因型与其体重和胸围有显著相关(P< 0.05),与其他指标不存在相关性(P> 0.05),且BC基因型个体的体重和胸围均显著大于其他3种基因型(P< 0.05)。暗示BC基因型是提高郏县红牛生长性状的有利基因型,AQP7基因内含子4的遗传多态性与郏县红牛的生长性状存在相关,因此可作为该品种生长性状分子标记辅助选择的候选基因。     

瓦氏雅罗鱼耐碱性状相关分子标记的筛选

本研究以来自达里湖(碱水)和松花江(淡水)的瓦氏雅罗鱼(Leuciscus waleckii)杂交F2为实验材料,通过碱度耐受实验进行性状测定,以39对多态的EST-SSR和SSR为标记,对77个F2个体进行基因分型,根据Fisher确切概率法对F2基因型和耐碱性状进行关联分析。结果发现,有2个标记与耐碱性状显著相关(P0.05),其中1个标记为EST-SSR,从瓦氏雅罗鱼转录组数据库中调取该EST序列,基因注释结果显示该序列与团头鲂(Megalobrama amblycephala)低氧诱导因子HIF-3?基因、草鱼的低氧诱导因子HIF-4?基因具有很高的同源性。该基因的主要功能是参与鱼类的耐低氧反应过程,加强鱼类的耐低氧能力。本研究对于今后深入研究此功能基因的作用机制及培育适于盐碱水域养殖的鱼类新品种具有重要的意义。     

苏皖交界河网区后生浮游动物群落结构及其影响因子分析

鉴于长江中下游河网水流条件复杂,河流生境变化导致的浮游动物群落结构特异性,于2012年10月(平水期)和12月(枯水期)在长江下游江苏和安徽交界处的河网区布设6个采样点,进行轮虫和甲壳动物采样调查,并检测NH+4-N、NO-2-N、TN、TP、CODMn和Chl.a含量等水环境指标。结果表明,河网区共检出轮虫31种,优势种包括螺旋龟甲轮虫(Keratella cochlearis)和疣毛轮虫(Synchaeta sp.)等;枝角类14种,优势种为象鼻溞(Bosmina sp.);桡足类20种,优势种为跨立小剑水蚤(Microcyclops varicans)、中华窄腹剑水蚤(Limnoithona sinensis)和温剑水蚤(Thermocyclops sp.)。轮虫密度最高,平均为350.69个/L,其次为桡足类3.44个/L,枝角类最少,仅0.15个/L。轮虫和甲壳动物的季节变化规律不同,平水期的轮虫种类多于枯水期,枝角类和桡足类则相反,浮游动物的密度变化规律也类似。CCA分析表明,氮、磷、CODMn和Chl.a共同影响了浮游动物的群落结构与分布,枯水期轮虫密度与枝角类和桡足类密度均显著正相关(P0.01),叶绿素a与3类浮游动物密度也显著正相关(P0.05)。受长江汛后水文条件的影响,河网区浮游动物群落组成及优势种变化有其特定规律,轮虫与甲壳动物的种间关系也对其种类和密度的季节变化造成影响,而食物限制则是枯水期种群竞争的重要因素。     

Novel SNP in 5' flanking region of EDG1 associated with marbling in Japanese Black beef cattle

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The endothelial differentiation , sphingolipid G-protein-coupled receptor , 1 ( EDG1 ) gene has been considered as a positional functional candidate for the gene responsible for marbling. We have recently reported that 2 single nucleotide polymorphisms (SNPs), c.-312A > G in the 5' untranslated region (UTR) and c.*446G > A in the 3' UTR in EDG1 were associated with marbling in Japanese Black beef cattle, but this was not functional and a causal mutation for marbling. In the present study, we detected 2 novel SNPs, referred to as g.1475435G > A and g.1471620G > T , in the 5' flanking region of the EDG1 between low-marbled and high-marbled steer groups, which were previously shown to have EDG1 expression differences in musculus longissimus muscle. The g.1475435G > A SNP seemed not to segregate in Japanese Black beef cattle. The g.1471620G > T SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. Based on these findings, we hypothesized that the g.1471620G > T SNP might have an impact on EDG1 expression and also marbling.     

Estimation of phenotypic divergence in a collection of <Emphasis Type="Italic">Capsicum</Emphasis> species for yield-related traits

Phenotypic divergence among the 24 accessions belonging to a collection of six species of Capsicum from different geoclimatic regions available in field gene bank of CIMAP, Lucknow, India, was quantified by multivariate analysis for 12 quantitative and qualitative traits. Based on their values, all 24 accessions were grouped into six clusters such that the genetic stocks within cluster had smaller D ² values among themselves than those belonging to different clusters. The accessions of Capsicum annuum were distributed in different clusters in morphotyping representing different species, suggesting that taxonomic characteristics are not always related to agronomic traits. No parallelism/association was found between geographical and phenotypic diversity. Accessions 15 and 23 (clusters V and VI, respectively) had distinct identity. The three characteristics that played the greatest role in differentiation were fruit diameter, number of fruits per plant, and leaf diameter, which can be utilized as conventional/morphological markers for the improvement of chilli yield and obtaining good segregants in chilli breeding programs.     

紫花苜蓿秋眠性的SSR标记关联分析

【目的】发掘紫花苜蓿秋眠性关联位点,为揭示紫花苜蓿秋眠性状的遗传规律和分子机制提供理论依据。【方法】紫花苜蓿关联群体由75份321个四倍体紫花苜蓿基因型构成,其中中国紫花苜蓿品种每份材料选取6-8个基因型;其余材料每份选取3-4个基因型。利用紫花苜蓿基因组均匀分布的85对SSR（Simple sequence repeats）标记,对321个紫花苜蓿基因型进行扫描。于2014-2015年连续两年对紫花苜蓿秋眠性开展调查,并利用一般线性模型（GLM）及混合线性模型（MLM）2种方法,开展秋眠性与SSR分子标记的关联分析。【结果】紫花苜蓿秋眠性表现出极显著的基因型、年际及基因型×年际互作效应。2014年,表型变异幅度为5.1-55.1 cm,平均值为22.4 cm,变异系数为45.5%。2015年,变异幅度在3.5-44.9 cm,平均为15.2 cm,变异系数为43.7%。秋季株高两年均呈现接近正态分布特征。广义遗传力为0.71。MLM模型很好的控制了紫花苜蓿秋眠性的假阳性关联。基于MLM模型,在2014年共找到12个显著关联的SSR位点,表型贡献率为2.42%-6.73%。2015年共找到11个,表型贡献率为2.45%-4.81%。在这些关联位点中,分布于Chr 2的m83_157、Chr 3的m525_230和m525_231、及Chr 4的m429_245,在两种模型及两年内均被重复检测到。【结论】通过两种模型发掘到4个与紫花苜蓿秋眠性显著相关的位点,经过验证后可以用于紫花苜蓿秋眠性分子标记辅助选择育种。