植物数量性状遗传体系检测中回交或自交家系重复试验数据的分析方法

为提高主基因+多基因混合遗传分析的精度,降低试验误差,采用重复内分组随机区组设计,对低遗传力性状的B1:2和B2:2或F2:3家系平均数资料进行遗传分析.通过AIC准则和适合性检验比较无主基因(A-0)、1对主基因(A)、2对主基因(B)、多基因(C)、1对主基因+多基因(D)和2对主基因+多基因(E)模型以鉴定其遗传模式.采用IECM算法估计混合模型参数.通过油菜HSTC14×宁油7号初花期F2:3家系平均数资料阐明该方法。 abstract:To improve the precision in the genetic analysis of quantitative traits,the B1:2 and 132:2,or F2:3 families in a randomized blocks design were used to identify the mixed major gene plus polygene inheritance model while error variance was estimated from the analysis of variance.Five kinds of genetic models were established,including:one-major-gene model,two-major-gene model,polygene model,mixed one-major-gene plus polygene model,and mixed two-major-gene plus polygene model.The AIC value and a set of tests of goodness-of-fit were used to identify the most fitted model among the possible ones.The iterated ECM (IECM) algorithm was used to obtain maximum likelihood estimates of the parameters in sample likelihood function.An example of the genetic analysis of days from planting to flowering of a rape cross was used to illuminate the above procedure.     

小麦异交群体选择分化的RAPD分析

用RAPD分子标记技术及数量遗传分析手段对小麦异交群体趋异选择4代得到的各子群体的遗传关系进行了分析,并对两种结果进行了相关分析。采用11个引物扩增出134个位点,RAPD分析结果表明,群体具有丰富的遗传变异,整个群体的多态位点百分率达0.8134,杂合度达0.3006;子群体间遗传分化较小,相对基因分化系数Gst为0.2310,固定指数平均0.2120,标准遗传距离为0.1044±0.048,表明遗传变异多数来自群体之内。而数量遗传分析发现,选择性状进展都与预期方向相符,主成分遗传距离大部分达显著水平,说明选择使群体发生了相当程度的分化。对两种遗传距离进行聚类分析表明,二种信息间关系各类群成员多不一致。其原因可能在于：数量性状是人工选择的目标,RAPD是基因组随机序列的扩增,二者之间的相关与引物选择有关。 Abstract：The genetic relations of some subpopulations in the fourth generation of selection in outbreeding population of winter wheat were examined by RAPD techniques and quantitative analysis. The correlations of the two results were examined.For RAPD analysis, 11 primers were adopted, and 134 sites were amplified. The results showed that abundant genetic variations existed in the populations. In the whole population, the percentage of polymorphic sites (P) is 0.8134, and the averaged heterozygosity is 0.3006. However,genetic differentiation among subpopulations is small. The relative gene differentiation (Gst) is 0.2310,fixed index averages 0.2120, and the standard genetic distance between subpopulations is 0.1044±0.048.All above shows that most of the genetic variations existed within populations.The cluster results from RAPD analysis and principal component distances showed that similarity relations were only found in small part of the subpopulations. The reason for the results may be that the genes concerned for quantitative traits are selected directly,while the genes involved in RAPD analysis are only random samples of the whole genomes.     

数量性状发育遗传模型及其分析方法的研究进展

发育遗传模型是同时反映性状遗传和发育本质、提供影响遗传变异及调整发育进程的有关因素的信息的模型。建立在群体遗传学基础上的直接效应模型适用于单一基因控制的简单性状。渐成模型将遗传变异分解成直接分量和渐成分量(母体效应和互作效应),能更好地反映有机体遗传和发育的生物学机制。生长轨迹模型有效地综合了复杂性状各分量的发育动态,可获得连续的、综合的、详细的、动态的发育信息。条件遗传分析方法不仅可以估算特定时间段的净效应,且可将净效应分解为不同遗传分量,了解各效应分量的相对贡献。 Abstract：Developmental genetic models and analysis methods for quantitative traits are presented.Developmental genetic models should reflect the genetic and developmental essence,and provide the information of the factors influencing the genetic variation and the developmental process.Direct effect models,which based on the population genetics,may be suitable to analyze simple traits with single gene.Epigenetic models can decompose the whole genetic variation into direct and epigenetic components (maternal effects and epigenetic interaction effects),so that biological mechanism can be better understood.Growth trace models effectively synthesize the developmental dynamics of components of complex traits.With them,continuous,compositive,detailed,and dynamic information of development is available.Conditional analysis method can not only estimate the net effects in a specific time interval,but also depose them into genetic components and help to appreciate the contributions of different effects.     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei （Primulaceae）： implications for its conservation

Omphalogramma souliei Franch. is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. souliei in NW Yunnan, China. The genetic diversity at the species level is low with P=42.5% （percentage of polymorphic bands） and Hsp=0.1762 （total genetic diversity）. However, a high level of genetic differentiation among populations was detected based on different measures （Nei＇s genetic diversity analysis： Gst=0.6038; AMOVA analysis： Fst=0.6797）. Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenogamy predominated and autogamy played an assistant role in O. souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis)

The Chinese tree shrew (Tupaia belangeri chinensis) is a small experimental animal with a close affinity to primates. This species has long been proposed to be an alternative experimental animal to primates in biomedical research. Despite decades of study, there is no pure breed for this animal, and the overall genetic diversity of wild tree shrews remains largely unknown. In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations, we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew. An analysis of a wild population of 117 individuals collected from the suburb of Kunming, China, showed that these loci exhibited a highly expected heterozygosity (0.616). These 12 microsatellites were sufficient for individual identification and parentage analysis. The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.     

Use of Random Amplified Polymorphic DNA Analysis for Economically Important Food Crops

The objective of this review is to summarize numerous studies on the use of the random amplified polymorphic DNA （RAPD） technique on rice, corn, wheat, sorghum, barley, rye, and oats to examine its feasibility and validity for assessment of genetic variation, population genetics, mapping, linkage and marker assisted selection, phylogenetic analysis, and the detection of somaclonal variation. Also we discuss the advantages and limitations of RAPD. Molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The simplicity of the RAPD technique made it ideal for genetic mapping, plant and animal breeding programs, and DNA fingerprinting, with particular utility in the field of population genetics.     

Simple Sequence Repeat Analysis of Genetic Diversity in Primary Core Collection of Peach （Prunus persica）

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach （Prunus persica （L.） Batsch） was evaluated by using simple sequence repeats （SSRs）. The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach 〉 Crisp peach 〉 Flat peach 〉 Nectarine 〉 Honey Peach 〉 Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging （UPGMA） placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.     

High Genetic Diversity in a Rare, Narrowly Endemic Primrose Species： Primula interjacens by ISSR Analysis

Prirnula interjacens Chen (Primulaceae) is a rare and narrow endemic species of centralsouth of Yunnan Province in China. This species consists of two varieties: P.interjacens var. interjacens known with only one population, and P.interjacens var. epilosa with two populations. Intersimple sequence repeat (ISSR) marker was used to detect the genetic diversity of the three extant populations. We expected a low genetic diversity level, but our results revealed a high level of intraspecific genetic diversity (at population level: P=59.75%, HE=0.2368, and Hpop=0.3459; at species level: P=75.47%, HT= 0.320 5, and Hsp = 0.4618), probably resulting from floral heteromorphism and preferring outcrossing. A moderate level of genetic differentiation among populations was detected based on Nei‘s genetic diversity analysis (26.13%) and Shannon‘s diversity index (25.09%). Although P./ntedacens var. intedacens and P. interjacens var. epilosa were morphologically distinct, UPGMA cluster analysis showed that the two varieties had no distinct genetic differentiation and may be treated as a single taxon. Conservation measures are suggested, including in situ and ex situ strategies, based on the observed population genetic information.     

Identification and genetic mapping of four novel genes that regulate leaf development in Arabidopsis

Molecular and genetic characterizations of mutants have led to a better understanding of many developmental processes in the model system Arabidopsis thaliana.However,the leaf development that is specific to plants has been little studies.With the aim of contributing to the genetic dissection of leaf development,we have performed a large-scare screening for mutants with abnormal leaves.Among a great number of leaf mutants we have generated by T-DNA and transposon tagging and ethylmethae sulfonate (EMS) mutagenesis,four independent mutant lines have been identified and studied genetically.Phenotypes of these mutant lines represent the defects of four novel muclear genes designated LL1(LOTUS LEAF 1),LL2(LOTUS LEAF2),URO(UPRIGHT ROSETTE),and EIL(ENVIRONMENT CONDITION INDUCED LESION).The phenotypic analysis indicates that these genes play important roles during leaf development.For the further genetic analysis of these genes and the map-based cloning of LL1 and LL2,we have mapped these genes to chromosome regions with an efficient and rapid mapping method.     

Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data(11,087 newly-sequenced whole genomes) and culture-based resistance profiles(10,991 out of the11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.     

遗传多样性概述

遗传多样性作为生物多样性的重要组成部分,是物种多样性、生态系统多样性和景观多样性的基础。随着研究方法和实验技术的发展,遗传多样性研究从形态学水平、细胞学（染色体）水平、生理生化水平逐渐发展到分子水平。形态标记、细胞学标记、等位酶分析、DNA多态性分析等方法,为我们研究遗传多样性提供了有效的工具。特别是DNA多态性分析是一种更为直接而有效的方法。     

非等试验设计胚乳品质性状的遗传分析方法

根据朱军(1996)提出的包括基因型×环境互作的胚乳品质性状三倍体遗传模型,运用蒙特卡罗模拟证明,以混合线性模型统计分析的MINQUE法,对非等试验设计获得的实验数据进行数量遗传分析是可行的.蒙特卡罗模拟结果表明在样本群体大小基本一致的条件下,采用相等试验设计或非等试验设计所估算的遗传参数的偏差(Blas)和功效值(Power)没有明显差异,表明以非等试验设计获得的非平衡数据也可用来进行遗传分析,估算上述遗传模型中的各项遗传方差分量和协方差分量,并且可以采用朱军(1993)提出的AUP法来预测遗传模型中的各项遗传效应值.     

Genetic Analysis of Invasive Plant Populations at Different Spatial Scales

Measuring genetic diversity requires selection of a spatial scale of analysis. Different levels of genetic structuring are revealed at different spatial scales, however, and the relative importance of factors driving genetic structuring varies along the spatial scale continuum. Unequal gene flow is a major factor determining genetic structure in plant populations at the local level, while the effect of selection imposed by environmental heterogeneity increases with the spatial scale of analysis. At a continental and global scale genetic structure of invasive plant populations is significantly affected by founder effect and propagule transport via human vectors. Although genetic analysis at one spatial scale provides only partial information about the invasion process, little published research reports such data for the same species at multiple scales. A multi-faceted approach to investigating the genetic structure of invasive plant species that incorporates sampling at different spatial and temporal scales would provide a more complete picture of the role of genetic forces in invasion.     

短葶飞蓬云南三个种群的核型与等位酶分析

通过核型和等位酶分析,对短葶飞蓬（Erigeron breviscapus)种群遗传结构进行了较全面的研究。研究材料来自丽江,昆明,邱北,核型分析表明,这3个种群都为二倍体种群（2n=2x=18),以丽江种群为例,短葶飞蓬核型为2n=2x=18=6m 10sm(2SAT) 2st,10种酶的等位酶分析表明,短葶飞蓬的遗传变异存在于种群内,种群间遗传一致度高（I=0.9172),遗传距离小（D=0.0876),遗传距离与空间距离大致成正相关。     

Genetic dissection of gene regulation in multiple mouse tissues

The analysis of the influence of genetic variation on regulation of gene expression at a near-genome-wide level has become the focus of much recent interest. It is widely appreciated that many genes are expressed in a tissue-specific manner and that others are more ubiquitously expressed but relatively little is known about how genetic variation might influence these tissue patterns of gene expression. In this review we discuss what is known about the tissue specificity of the influence of genetic variation and review the challenges that we face in combining hugely parallel, microarray-based gene analysis with equally expensive genetic analysis. We conclude that the available data suggest that genetic variation is essentially tissue specific in its effects upon gene expression and this has important implications for experimental analysis.     

Constructing of system of genetic analysis in Pseudomonas mendocina

A Tn10-containing variant of the pRK2013 plasmid, pRK2013-7, was used in the genetic analysis of Pseudomonas mendocina as chromosome-mobilizing inheritable factor that is able to integrate into the bacterial chromosome and transfer genetic markers with a frequency ranging from 3.2 x 10(-7) to 3.5 x 10(-3). The results of interrupted matings allowed localization of 10 genetic markers. This system of genetic analysis is suitable for P. mendocina mapping.     

植物居群遗传变异的空间自相关分析

本文介绍了植物遗传变异空间自相关分析的理论、方法与应用,包括将基因型作为绝对型数据与等位基因频率作为连续型数据进行自相关分析的基本方法等。并对影响植物居群遗传变异空间结构的因素以及研究居群内遗传结构的重要意义作了评述。     

Dependence of the results of a genetic analysis of self-pollinating cereal species on the specificity of the mapping population

The available in literature information as for results of genetic analysis of several self-pollinating cereal species involving the use of plant lines with alien genetic material as the object of analysis is summarized. The restrictions caused by specificity of the investigated material as for the possible explanation of the obtained results are emphasized. Several suggestions concerning the preliminary study of introgressive plant lines before their including into experimental programs on genetic analysis are made.     

多重耐药肺炎克雷伯菌获得性耐药相关基因和可移动遗传元件检测与指标聚类分析

目的 探讨一组多重耐药肺炎克雷伯菌(MDR-KPN)中获得性耐药相关基因和可移动遗传元件遗传标记的存在状况以及二者的相关性.方法 收集2008年8月至2010年5月浙江省杭州市和湖州市6所医院共47株MDR-KPN,采用聚合酶链反应(PCR)的方法分析74种获得性耐药基因和24种可移动遗传元件遗传标记,并用指标聚类分析(SPSS法)分析获得性耐药相关基因和可移动遗传元件遗传标记的相关性.结果 47株MDR-KPN共检出5种β-内酰胺类获得性耐药基因、6种氨基糖苷类获得性耐药基因、3种喹诺酮类获得性耐药基因、6种其他获得性耐药基因、1种整合子遗传标记、2种转座子遗传标记、4种插入序列遗传标记、2种接合性质粒遗传标记和1种噬菌体原标记;指标聚类分析(SPSS法)将上述阳性检出基因分成A、B两大簇.结论 指标聚类分析提示获得性耐药相关基因和可移动遗传元件密切相关;由Ⅰ类整合子( intI1)、插入序列(IS26、ISEcp1、ISKpn6)、耐药质粒(trbC)介导的TEM-1和KPC是本组菌株的特征.在肺炎克雷伯菌中做指标聚类分析为国内首次报道.     

Global genetic analysis

The introduction of molecular markers in genetic analysis has revolutionized medicine. These molecular markers are genetic variations associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification, pharmacogenetics and population-based studies. Among variations being analyzed, single nucleotide polymorphisms seem to be most useful in large-scale genetic analysis. This review discusses approaches for genetic analysis, use of different markers, and emerging technologies for large-scale genetic analysis where millions of genotyping need to be performed.