Computer Simulation of Concerted Evolution of Patterns of Polygenes, Transposable Elements, and Origin Identity Labels: Negative Selection

Computer simulation of the population dynamics of the genomic patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of negative selection for an additive quantitative trait has been performed. It was demonstrated that active polygene alleles disappear very rapidly, whereas the patterns of TEs and OILs continue their evolution determined by strict selective inbreeding and gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. It was demonstrated that the final consensus pattern of OILs consists of the fragments of the original patterns, which contain neither active polygene alleles nor modifier or marker TEs. Neutral TE copies were present in the final pattern, as should be expected in the case of gene drift. Inbreeding coefficient increased steadily but by generation 100 reached values higher than 0.9. All other parameters and initial conditions being the same, the responses to negative and positive selections were asymmetric.     

Stabilizing selection and computer models of the joint evolution of patterns of polygenes,transposable elements,and origin identity labels

A computer model of the populations dynamics of the patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of stabilizing selection for an additive quantitative trait (with the target value being 0.4 of the maximum) was analyzed. It was demonstrated that the final plateaus of the trait value and the frequencies of the active values of polygenes are reached rapidly, namely, within five to seven generations (the effective selection period). The inbreeding coefficient during this period also grows rapidly and then gradually increases eventually reaching approximately 0.7. The inbreeding coefficient reaches plateau (at approximately 1.0) only in generations 300-350, which suggests the effect of gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. By generation 100 of selection, the final patterns of TEs and OILs were not formed completely. Fixations and losses, especially those of the OIL pattern, were delayed. In general, however, the population heterogeneity with respect to the patterns studied does not stabilize. This heterogeneity decreases the case of stabilizing selection, although more slowly than in the cases of positive and negative selections.     

Computer Simulation of the Joint Evolution of the Patterns of Polygenes, Transposable Elements, and Origin Identity Labels: Stabilizing Selection

A computer model of the populations dynamics of the patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of stabilizing selection for an additive quantitative trait (with the target value being 0.4 of the maximum) was analyzed. It was demonstrated that the final plateaus of the trait value and the frequencies of the active values of polygenes are reached rapidly, namely, within five to seven generations (the effective selection period). The inbreeding coefficient during this period also grows rapidly and then gradually increases eventually reaching 0.7. The inbreeding coefficient reaches plateau (at 1.0) only in generations 300–350, which suggests the effect of gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. By generation 100 of selection, the final patterns of TEs and OILs were not formed completely. Fixations and losses, especially those of the OIL pattern, were delayed. In general, however, the population heterogeneity with respect to the patterns studied does not stabilize. This heterogeneity decreases the case of stabilizing selection, although more slowly than in the cases of positive and negative selections.     

Computer modeling of joint selection response of MGE patterns and a polygenic system]

Using computer simulation, selection response of three genome patterns--polygenes, mobile genetic elements (MGEs), and labels of identity by origin (LIOs)--were studied. In each generation of selection, variability of each pattern type was described by on UPGMA tree. Stringent positive truncation selection on an additive polygenic trait and recombination between segments of the genetic map were considered. MGEs were classified into three groups: modifiers (enhancers) of the polygenic expression, markers, and independent copies. It was shown that at generations 30 to 40, 95-96% and 70-80% of respectively enforced and non-enforced active polygenic alleles were fixed (2-3% and 16-17% lost). In all generations, Hkn < or = Dkn of the length of the maximal route along the tree. At the same time, modifier MGEs were fixed for 85-88% (lost for 11-12%); marker MGEs, for 60-70 (lost for 21-25%); and independent copies, for 30-40 (lost for 50-60%). The behavior of independent MGE copies was generally consistent with the predictions of the genetic drift theory, modifier MGEs behaved similarly to the modified polygenes, and marker MGEs exhibited intermediate properties. The LIO patterns showed rapid homozygotization: their variability dropped dramatically between generations 10 and 30. In F50, the final consensus pattern of polygenes included 16 out of 18 enforced and 18 out of 21 non-enforced polygenic alleles. The fixation/loss ratios were 16:3 for modifier MGEs, 15:6 for marker MGEs, and 25:28 (with 7 polymorphic) for independent copies. The LIO consensus pattern contained 13 out of 100 original markers, which formed 26 fragments of one to ten map segments in size; 21 fragments contained active polygenic alleles, and 14 of them had also modifier MGEs. Recombinational shuffling of patterns was not completed. In the course of selection, active polygenic alleles take along adjacent segments, including those containing modifier MGEs and markers. These constitute the conservative part of all consensus patterns while the remaining segments are random.     

Computer system for simulating population dynamic patterns of polygenes and mobile genetic elements upon truncation selection for a quantitative trait

A computer system was developed for simulation of population dynamics of interacting polygene patterns and mobile genetic elements (MGEs) under selection for a quantitative trait. The system is stochastic (Monte Carlo) and takes into account the main sources of random change in the patterns (recombinations, transpositions, excisions), genetic drift, and determined trends of selection and other genetic processes in a finite population. Using this model, it is possible to analyze the dynamics of many population parameters that cannot be experimentally estimated: frequencies of polygenic alleles, proportions of adaptive and random fixations, average heterozygosities of polygenes and MGEs, coefficient of inbreeding, heritability, etc. In addition, the model can be used to test various hypotheses on polygene-MGE interaction.     

Computer Simulation of Joint Selection Response of MGE Patterns and a Polygenic System

Using computer simulation, selection response of three genome patterns—polygenes, mobile genetic elements (MGEs), and labels of identity by origin (LIOs)—were studied. In each generation of selection, variability of each pattern type was described by an UPGMA tree. Stringent positive truncation (+) selection on an additive polygenic trait and recombination between segments of the genetic map were considered. MGEs were classified into three groups: modifiers (enhancers) of the polygenic expression, markers, and independent copies. It was shown that at generations 30 to 40, 95–96% and 70–80% of respectively enforced and non-enforced active polygenic alleles were fixed (2–3% and 16–17% lost). In all generations, H ⁿ _k max D ⁿ _kof the length of the maximal route along the tree. At the same time, modifier MGEs were fixed for 85–88% (lost for 11–12%); marker MGEs, for 60–70% (lost for 21–25%); and independent copies, for 30–40 (lost for 50–60%). The behavior of independent MGE copies was generally consistent with the predictions of the genetic drift theory, modifier MGEs behaved similarly to the modified polygenes, and marker MGEs exhibited intermediate properties. The LIO patterns showed rapid homozygotization: their variability dropped dramatically between generations 10 and 30. In F50, the final consensus pattern of polygenes included 16 out of 18 enforced and 18 out of 21 non-enforced polygenic alleles. The fixation/loss ratios were 16 : 3 for modifier MGEs, 15 : 6 for marker MGEs, and 25 : 28 (with 7 polymorphic) for independent copies. The LIO consensus pattern contained 13 out of 100 original markers, which formed 26 fragments of one to ten map segments in size; 21 fragments contained active polygenic alleles, and 14 of them had also modifier MGEs. Recombinational shuffling of patterns was not completed. In the course of selection, active polygenic alleles take along adjacent segments, including those containing modifier MGEs and markers. These constitute the conservative part of all consensus patterns while the remaining segments are random.     

鲜食番茄果实中番茄红素含量的主基因－多基因混合遗传分析

选择2个番茄红素含量显著不同的鲜食番茄品系,通过P₁、P₂、F₁、F₂、B₁和B₂6世代联合分析法,研究分析了番茄红素的遗传规律。结果表明：番茄红素的遗传符合一个主基因和加性－显性－上位性多基因模型,主基因遗传力在B₁、B₂和F₂分别为6.85%、34.78％和58.33％,多基因遗传力在B₁、B₂和F₂分别为58.48％、30.69％和0。      

Effect of genotypic environment on phenotypic manifestation of radius incompletus mutation in Drosophila melanogaster

Genetic analysis of marked regions of Drosophila chromosome 3 was performed in order to localize the "effective factors" of the polygene system that controls the expression of the limiting mutation in radius incompletus, the major-effect gene. The marked homozygous strain with genotype th st ri sr ca was crossed with the "selection" riSN strain. Contributions of the marked regions of chromosome 3 to the expression of the proximal and distal fragments of the wing radial vein were estimated. It was demonstrated that the th-st region of the marked strain contained a polygene determining a large positive contribution to the lengths of both fragments, whereas the st-ri region contained a polygene determining a large negative contribution to the length of the distal fragment compared to the riSN strain. Crossings were performed between strains that contained Mendelian mutations of the ri, ve, and vn major-effect genes of the wing vein patterns. Unexpectedly, a strong, non-additive effect of the interaction between these mutations was found. This effect was expressed as a complete disarrangement of the wing vein pattern. Each participant gene may be regarded as a large-effect polygene relative to the other genes.     

烟草白粉病抗性基因的遗传分析

以烟草抗白粉病品种台烟7号为母本,感病品种NC89为父本,构建6个世代的群体,利用主基因 多基因混合遗传模型的分离分析方法,研究烟草白粉病的抗性遗传规律。结果表明,烟草白粉病抗性的遗传是由两对加性-显性-上位性主基因 加性-显性-上位性多基因（E-0模型）控制的。B1、B2和F2世代主基因的遗传率分别为88.05%、32.62%、84.43%,主基因遗传率很大,说明可以在抗病育种早期进行选择;B1、F2世代多基因遗传率均为0.00%,说明烟草白粉病的发生受一定环境影响。     

水稻种子抗老化遗传分析

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Transposable Element Regulation in Rice and Arabidopsis: Diverse Patterns of Active Expression and siRNA-mediated Silencing

Transposable elements (TEs) are DNA segments that can mediate or cause movement within genomes. We performed a comprehensive, whole-genome analysis of annotated TEs in rice (Oryza sativa L.) and Arabidopsis thaliana, focusing on their expression (mRNA data) and silencing (small RNA data), and we compared these data with annotated genes that are not annotated as transposons. TEs demonstrated higher levels of antisense mRNA expression in comparison to non-TE genes. The majority of the TEs were silenced, as demonstrated by higher levels of small RNAs and a lack of mRNA MPSS data. When TEs were expressed, their activity was usually limited to just one or a few of the mRNA libraries. When we examined TE expression at the whole-genome level and across the complete mRNA dataset, we observed that most activity was contributed by a few highly expressed transposable elements. These TEs were characterized by their low copy number and few matching small RNAs. Our results help define the relationship between gene expression and gene silencing for TEs, and indicate that TE silencing can impact neighboring genes, perhaps via a mechanism of heterochromatin formation and spreading. These data may be used to define active TEs and families of transposable elements that continue to shape plant genomes.     

Truncation family selection and nonsystematic inbreeding leads to a rapid fixation of a pattern of mobile genetic elements in a computer model

A computer simulation model of the population dynamics of a polygenic system and a pattern of mobile genetic elements (MGEs) under directional truncation selection for a quantitative trait was developed. Modifier MGEs were shown to be rapidly and adaptively fixed (or lost) together with the modified polygenes. Marker MGEs and independent MGE copies were fixed and lost just as rapidly but in a random manner. Using specific marking of initial haploid genomes and direct computing of the mean proportion of identical encounters at each locus in each generation, it was shown that the mean nonselective inbreeding coefficient F(n) dramatically increases in the course of selection, reaching values 0.7-0.9 in 15-20 generations. As a result, adaptive homozygotization of polygenes and modifier MGEs and random homozygotization of marker MGEs, independent MGE copies, and all other genes of the genome occurs. These results confirm the hypothesis on the "champion" polygene pattern advanced earlier to explain the data of selection experiments.     

植物数量性状遗传体系的分离分析方法研究

在传统的数量性状多基因遗传模型基础上提出主基因-多基因遗传模型具普遍性,纯主基因或纯多基因遗传模型只是其特例。由此初步建立了植物数量性状遗传体系分离分析方法。目前该方法可以检验2～3个主基因的个别遗传效应、多基因整体的遗传效应和两者的遗传率。本文介绍这种分离分析方法的研究经过、主要进展及应用效果,并以实例说明其分析步骤、方法和效果。     

水稻丽粳2号近等基因系杂种后代耐冷性遗传研究

在昆明低温冷害条件下,以十和田×(十和田和丽粳2号BC4F5)配制的杂种BC5F1、BC5F2、BC5F3和BC5F4及亲本为材料,用主基因-多基因混合遗传模型对丽粳2号作耐冷基因供体培育出的近等基因系进行孕穗期耐冷性遗传研究。结果表明:(1)杂种BC5F2、BC5F3和BC5F4分离群体在同一世代每穗实粒数与总粒数、结实率呈极显著的正相关;(2)以结实率为耐冷性鉴定指标,近等基因系孕穗期耐冷性受2对主基因和多基因共同控制,其主效基因的遗传率为90.97%,微效基因遗传率为3.83%,主基因和微效基因都存在加性-显性-上位性效应。     

甘蓝型油菜芥酸含量的主基因＋多基因遗传

应用植物数量性状主基因＋多基因混合遗传模型对甘蓝型油菜无芥酸品种HSTC     

Heavy heat shock induces genetic variation in a polygenic system of a quantitative trait in Drosophila

Results of two experiments dealing with positive and negative selection on the quantitative trait radius incompletus in an isogenic line of Drosophila melanogaster after heavy heat shock (HHS) are presented. Selection was not effective in the control without HHS. In experiment 1, in which offspring of HHS-exposed males lacked transposition induction, selection also was ineffective. By contrast, selection was highly effective in offspring of males that responded to HHS exposure by transposition induction. Thus, HHS, which is not mutagenic, generates genetic variation in a polygenic system of a quantitative trait via transpositions and excisions of mobile genetic elements. In experiment 2, positive and negative selection was conducted in three replicates, which showed concerted dynamics of the selected trait. This means that the trait dynamics is mainly related to the nearly deterministic process of accumulation of active polygenic alleles rather than to genetic drift. The induced variation of polygenic systems promotes rapid selection of "champion" genotypes. This variation is probably associated with "soft" modification of polygene expression by adjacent MGE copies.     

粳稻穗部性状遗传分析

从粳稻（Oryzasativassp.japonica）RIL群体中选取每穗颖花数极端少的品系丙堡3201和丙堡3205及每穗颖花数极端多的品系丙堡3145和丙堡3214,配制丙堡3201×丙堡3145和丙堡3214×丙堡3205两个组合的P1、P2、F1、B1、B2和F26个世代,调查每穗颖花数、每穗实粒数、穗长、一次枝梗数和二次枝梗数的表型分布,并运用主基因＋多基因混合遗传模型,对这5个性状进行了遗传分析。结果表明,每穗颖花数性状在2个组合的各分离世代均未出现超亲分离,而其它4个性状均有不同程度的超亲分离。一次枝梗数受1对主基因＋多基因控制;其余4个性状均受2对主基因＋多基因控制。每穗颖花数、每穗实粒数、穗长和二次枝梗数4个性状以主基因遗传为主,一次枝梗数性状以多基因遗传为主。     

Effect of genetic background on the ratios between different types of dermatoglyphic patterns: recessive genodermatoses

The ratios between dermatoglyphic patterns of different types were studied in males and females with and without hereditary diseases of the skin. It was found that ridge patterns of fingers are determined by special polygenes. Patients with monogenic dermatoses (X-linked ichthyosis and autosomal recessive ichthyosiform erythroderma) exhibited a suppressed formation of the loop pattern compared to control subjects.     

水稻籼型光温敏核雄性不育性遗传研究

1　引　　言水稻光温敏核雄性不育性是一种典型的生态遗传现象 ,其遗传行为既受内部基因控制 ,又受外部光、温等生态因子的调节 ,还与所处的遗传背景密切相关 .前人已对农垦 5 8Ｓ及其衍生系等粳型光温敏核不育性有过较系统地研究 ,并提出一对、二对、三对和重复基因突变等多种假说[3 ,5,7～ 9] ;但对籼型及非农垦 5 8Ｓ基因源的光温敏核不育性研究较少 .本文采用极大似然法 ,对不同来源的籼型光温敏核不育性进行系统研究 ,旨在揭示其遗传本质 ,为解决两系法杂交水稻推广过程中出现的不育起点温度“漂移”等问题提供理论依据 .2　材料与方法…