Population-genetic variation in Scots pine <Emphasis Type="Italic">Pinus sylvestris</Emphasis> L. from the main forest regions of Ukraine

Using electrophoretic analysis of 22 isozyme loci controlling ten enzyme systems, we studied intrapopulation and interpopulation variation of Scots pine Pinus sylvestris L. in the main forest regions of Ukraine. In 15 of the populations examined, 76.5% of genes were polymorphic, and an average plant was shown to be heterozygous at 23.2% of the genes. The lowest and highest values of major polymorphism parameters were characteristic of respectively the relic populations of Ukrainian Carpathians and the populations from the steppe and forest-steppe zones. Neis genetic distances between the populations varied from 0.006 to 0.031 (on average 0.016). Cluster analysis failed to show clear trends in the population distribution relative to their geographical position.Translated from Genetika, Vol. 41, No. 2, 2005, pp. 216–228.Original Russian Text Copyright © 2005 by Korshikov, Kalafat, Pirko, Velicoridko.     

Genetic variation and differentiation of Abies alba Mill. populations from Ukrainian Carpathians

Using electrophoretic analysis of 11 enzyme systems, we studied the genetic structure and differentiation of eight natural populations of silver fir Abies alba Mill. in the Ukrainian Carpathians. Of 24 isozyme loci identified, 66.8% proved to be polymorphic. The mean numbers of alleles and genotypes per locus in the populations were respectively 3.1 and 4.5. Each A. alba tree was on average heterozygous at 15.9% of genes. In six populations, the genotypic distribution for all of the loci examined corresponded to Hardy-Weinberg proportions. The populations studied had low levels of subdivision (F(ST) = 0.018; GST = 0.019) and differentiation. Nei's genetic distances between the A. alba populations in the region ranged from 0.002 to 0.009, being on average 0.006.     

Genetic variation and differentiation of peat-bog and dry-meadow populations of the dwarf mountain pine Pinus mugo Turra in the highlands of the Ukrainian Carpathians

Based on electrophoretic analysis of 21 isozyme loci controlling 10 enzyme systems, the intra- and inter-population variation was studied in two peat-bog and three dry-meadow populations of the dwarf mountain pine Pinus mugo Turra from the highlands of the Ukrainian Carpathians. In the studied samples (a total of 164 trees), on average 62% of the studied genes were polymorphic; the mean heterozygosity was 21.3%. The dry-meadow populations differed from the peat-bog populations by allele and genotype diversity and by heterozygosity although the indices characterizing population heterogeneity (Fst and Gst) were small (0.027 and 0.032, respectively). Nei's genetic distances between the populations ranged of 0.011 to 0.032 with the mean of 0.018.     

Genetic structure of populations of Norway spruce (Picea abies (L.) Karst.) from Ukrainian Carpathians

The genetic diversity, subdivision, and differentiation of nine populations of Norway spruce (Picea abies (L.) Karst.) in Ukrainian Carpathians were studied using electrophoretic analysis of variability of enzyme systems in 346 trees aged from 80 to 150 years. Based on electrophoretic fractionation of enzymes extracted from seed endosperms in vertical slabs of 7.5% polyacrylamide gel, 20 loci of nine enzyme systems (ADH, ACP, DIA, GDH, GOT, MDH, LAP, FDH, SOD) were identified, and 71 allele variant were revealed. Each tree was heterozygous on average in 15.8% of its genes. The populations were characterized by low subdivision (F(ST) = 0.017) and differentiation (D(N)=0.005). The main contribution to heterogeneity of population genetic structure was made by loci Dia-3, Lap-1, and Sod-3. Clustering and multivariate analysis revealed no observed trends in geographical or altitudinal position of the populations.     

Patterns of ribosomal gene variation in elite commercial chicken pure line populations

The nucleolus organizer region (NOR) encodes the tandemly repeated 18S, 5.8S and 28S ribosomal (r) RNA genes. The NORs of broiler and layer commercial chicken pure lines were studied to establish the type and extent of genetic variation at this important locus. The parameters studied were gene copy number, repeat size, and diversity of NOR-types. The populations were organized into three groups for analysis including brown-egg broiler (13 lines), brown-egg layer (six lines), and white-egg layer (eight lines). The ribosomal gene copy number average of the white-egg layer populations was significantly lower (329 genes) than that of the brown-egg layers (372 genes); the brown-egg broiler ribosomal gene average was intermediate (350 genes). The white-egg layer populations exhibited a ribosomal repeat unit average size of 36 kb, significantly different from the brown-egg layer and brown-egg broiler average repeat unit size of 32.5 and 33.9 kb, respectively. NOR array size was similar among the three groups (6 mb). The brown-egg broiler populations exhibited polymorphic NOR patterns, intra- and interline, whereas the white-egg layer populations were essentially monomorphic for NOR-type; brown-egg layers exhibited an intermediate level of NOR diversity. Some NOR array characteristics may be a function of breed origin as brown-egg commercial populations, both broilers and layers, have similar breed origins and exhibited similarities for predominant repeat unit size as compared with white-egg layer populations. However, the finding that brown-egg broiler lines typically exhibit a greater number of segregating NOR-types than brown-egg layer lines suggests that the selection schemes of broiler vs. layer pure line populations may also have influenced the degree of variation at this gene complex.     

Genetic Variation and Differentiation of Peat-Bog and Dry-Meadow Populations of the Dwarf Mountain Pine Pinus mugo Turra in the Highlands of the Ukrainian Carpathians

Based on electrophoretic analysis of 21 isozyme loci controlling 10 enzyme systems, the intra- and interpopulation variation was studied in two peat-bog and three dry-meadow populations of the dwarf mountain pine Pinus mugoTurra from the highlands of the Ukrainian Carpathians. In the studied samples (a total of 164 trees), on average 62% of the studied genes were polymorphic; the mean heterozygosity was 21.3%. The dry-meadow populations differed from the peat-bog populations by allele and genotype diversity and by heterozygosity although the indices characterizing population heterogeneity (F _st and G _st) were small (0.027 and 0.032, respectively). Nei's genetic distances between the populations ranged of 0.011 to 0.032 with the mean of 0.018.     

Genetic diversity and differentiation of Gmelin larch Larix gmelinii populations from Evenkia (Central Siberia)

Within- and among-population diversity of Gmelin larch Larix gmelinii (Rupr.) Rupr. from Evenkia was inferred from data on 17 genes determining allozyme diversity of ten enzymes. More than 50% of the genes proved to be polymorphic. On average, each tree was heterozygous at 9.2% genes. Heterozygosity expected from the Hardy-Weinberg proportions was higher, 12.5%. A deficit of heterozygous genotypes was observed in all populations under study and attributed to inbreeding. With Wright's F statistics, average individual inbreeding was estimated at 26.6% relative to the population (F(IS)) and at 27.8% relative to the species (F(IT)). The greatest deficit of heterozygosity was observed for the youngest population. Within-population variation accounted for more than 98% of the total variation, while the contribution of among-population variation was 1.66%. Genetic distance between populations varied from 0.0025 to 0.0042, averaging 0.0035.     

Chlorophyll-deficient gene and morphological variations in Korean populations of maize (Zea mays)

We studied cultivated and naturalized Korean maize populations to determine the extent to which the chlorophylldeficient mutation and the phenotypic variations of two morphological characters (i.e., red coleoptiles and epicotyls, and the number of the first root hairs) are maintained. The frequency of the chlorophyll-deficient mutant gene (2.73% on average) was highly variable. Frequencies of red coleoptiles and epicotyls also were higher than expected from a mutation-selection balance. The average number of hairy phenotypes within populations was 1.8, ranging from 0.0 to 4.0. Naturalized populations were closely related to with cultivated communities. Most striking, however, was the more significant difference among populations than within populations with regard to both the frequency of chlorophyll-deficient mutant genes and the phenotypic variations of our two morphological characters. On a per-gene basis, the majority of the phenotypic variation (mean of 73.3%) resided among populations.     

Efficiency of genome-wide association studies in random cross populations

Genome-wide association studies (GWAS) with plant species have employed inbred lines panels. We evaluated the efficiency of GWAS in non-inbred and inbred populations and assessed factors affecting GWAS. Fifty samples of 800 individuals from populations with linkage disequilibrium were simulated. Individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits controlled by ten quantitative trait loci (QTLs) and 90 minor genes, assuming different degrees of dominance and broad sense heritabilities of 40 and 80%. The average SNP density was 0.1 centiMorgan (cM) and the QTL heritabilities ranged from 3.2 to 11.8%. The results for random cross populations evidenced that to increase the QTL detection power, the additive-dominance model must be fitted for traits controlled by dominance effects but must not be fitted for traits showing no dominance. The power of detection was maximized by increasing the sample size to 400 and the false discovery rate (FDR) to 5%. The average power of detection for the low, intermediate, and high heritability QTLs achieved 52.4, 87.0, and 100.0%, respectively. Assuming sample sizes of 400 and 800, the observed FDR was equal to or lower than the specified level of significance. The association mapping was highly precise, since at least 97% of the declared QTLs were detected by the SNP inside it (average bias of 0.4 cM). Besides controlling the FDR, relatedness (and identity by state) efficiently controls the number of significant associations outside the QTL interval (not all false positive associations). The analysis of the inbred random cross population provided essentially the same results as the non-inbred populations.     

Natural transfer of nuclear genes in hybrid populations of green frogs Rana esculenta L., 1758 complex: space-time analysis of the phenomenon

Spatial and temporal analysis of frequency distribution patterns of the Rana esculenta (=lessonae)-specific allele, Ldh-B71, in the populations and individuals of R. ridibunda from the Middle Dnieper region was performed. It was established that the allele was accumulated in the populations of Kiev, where on average 15 to 25% of individuals steadily preserved this allele through at least three to four generations. Furthermore, the allele frequency in juveniles and adults was similar. These findings suggest that the frogs carrying foreign genetic material were not eliminated from the populations, and hence, the observed introduction of foreign genes was adaptively neutral. The transfer of the genetic material from one species to another may be considered as a possible mechanism of the formation of an additional source for population genetic variation, which, however, do not seems to be evolutionary progressive.     

High gene flow promotes the genetic homogeneity of arable weed populations at the landscape level

To determine whether weed populations growing in neighbouring fields were genetically isolated, we investigated the genetic contamination of Alopecurus myosuroides populations in organic fields by populations in conventional fields. Herbicide resistance was used as a marker for gene flow to organic populations, which are not under herbicide selective pressure. Organic fields contained on average 74.5% herbicide-resistant plants (80.1% in conventional fields). Identical resistance alleles were found in neighbouring organic and conventional fields. AFLP analysis revealed that populations from organic and conventional fields had similar neutral genetic diversity. Massive pollen flow from conventional fields is likely chiefly responsible for the genetic makeup of A. myosuroides populations from organic fields. Using a demo-genetic model, we propose that demographic collapses of populations due to effective weed control enhance gene flow towards these populations. Fields with a low weed density could act as ‘genetic sinks’ that would facilitate the diffusion of genes from neighbouring, dense weed populations. Populations of allogamous wind-pollinated weed species like A. myosuroides occurring in neighbouring fields are therefore clearly not independent units. Adaptive evolution and management of such weeds should thus be considered on a scale broader than the field.     

湖南新田野生大豆自然居群遗传多样性分析

利用SSR分子标记技术对8个来自湖南新田的野生大豆自然居群遗传多样性进行了分析.结果表明:(1)所分析的材料中73对SSR引物共检测到397个等位变异,等位变异数范围为2～10个,平均为5.4个;期望杂合度(He)的变化范围从0.16～0.82,平均为0.64.(2)分子方差分析发现,居群间存在着严重的遗传分化,群体69%的变异存在于居群间,31%的遗传变异存在于居群内.(3)新田的8个居群中桑梓路边(SZLB)和桑梓(SZ)两个居群的遗传多样性比其他群体的高,而新田1 km处(XT1)、新田2 km处(XT2)和新田6 km处(XT6)野生大豆居群的遗传多样性较低.(4)根据遗传距离可将8居群分为3类:新田1 km处和新田2 km处为一类;新田6 km处单独为一类;大冠岭上龙秀、龙秀后山、桑梓、桑梓路边和青龙等处为一类.(5)居群遗传距离和地理距离之间存在线性相关,相关系数为0.837(P<0.01);海拔与期望杂合度呈显著正相关,相关系数为0.92(P=0.001).研究结果表明,湖南新田野生大豆具有较高的遗传多样性,但不同居群的遗传多样性差异很大;位于该县高海拔山区大冠岭一带的野生大豆居群是湖南新田地区的一个多样性中心.     

Genetic Diversity and Differentiation of Gmelin Larch Larix gmelinii Populations from Evenkia (Central Siberia)

Within- and among-population diversity of Gmelin larch Larix gmelinii (Rupr.) Rupr. from Evenkia was inferred from data on 17 genes determining allozyme diversity of ten enzymes. More than 50% of the genes proved to be polymorphic. On average, each tree was heterozygous at 9.2% genes. Heterozygosity expected from the Hardy–Weinberg proportions was higher, 12.5%. A deficit of heterozygous genotypes was observed in all populations under study and attributed to inbreeding. With Wright's F statistics, average individual inbreeding was estimated at 26.6% relative to the population (F _IS) and at 27.8% relative to the species (F _IT). The greatest deficit of heterozygosity was observed for the youngest population II. Within-population variation accounted for more than 98% of the total variation, while the contribution of among-population variation was 1.66%. Genetic distance between populations varied from 0.0025 to 0.0042, averaging 0.0035.     

Analysis of the mitochondrial DNA variation in pond smelt Hypomesus olidus (Osmeridae)

Pond smelt Hypomesus olidus (Pallas, 1814), one of the five species of the genus Hypomesus, family Osmeridae, was examined for intraspecific variation of the mitochondrial DNA cytb (1062 bp) and COI (567 bp) genes. Among the ten single substitutions discovered, only one, leading to the substitution of isoleucine by valine, was nonsynonymous, while the remaining substitutions were synonymous. The degree of genetic divergence among pooled nucleotide sequences in H. olidus populations examined constituted 0.4% on average, ranging from 0.2 to 0.6%. These values were not higher than the levels of divergence between the individuals within the populations. Phylogenetic analysis of the populations examined did not reveal their subdivision depending of their geographic location, and pointed to the absence of intraspecific differentiation of the species.     

基于线粒体COⅠ基因序列的东南沿海可口革囊星虫遗传多样性分析

为了解我国东南沿海可口革囊星虫自然群体的遗传多样性及遗传结构, 以线粒体COⅠ基因为分子标记, 对浙江象山(XS)与温岭(WL)、福建宁德(ND)、广东湛江(ZJ)4个可口革囊星虫自然群体的80个样本的COⅠ基因片段进行PCR扩增、序列测定和分析。结果表明, 在815 bp长度的核苷酸片段中, A、T、C、G碱基的平均含量分别为29.8%、31.0%、22.6%和16.6%, A+T含量(60.8%)高于C+G含量(49.2%), 表现出较强的AT偏好性。共检测到29个核苷酸变异位点, 定义了29种单倍型, 总群体单倍型多样性指数(H_d)、核甘酸多样性指数(P_i)及平均核苷酸差异数(K)分别为0.932、0.0036及2.8902, 表现出高的H_d和低的P_i。单倍型邻接关系树的拓扑结构简单, 未呈现明显的地理谱系结构。群体内的遗传距离为0.0027—0.0040, 群体间的遗传距离为0.0032—0.0040。两两群体间的遗传分化系数(F_st)和分子方差分析(AMOVA)表明, 可口革囊星虫的遗传变异主要来自于群体内, 而群体间无显著分化。中性检验和核苷酸不配对分布结果揭示, 可口革囊星虫经历了群体历史扩张事件, 大致发生在4.6万年前的更新世晚期。     

基因转录介导同质园条件下拟南芥不同地理种群的光合能力分化

不同环境条件决定着植物光合能力的多态性,但在相同环境条件下同种植物不同种群间表现出光合能力分化的内在机制仍不清楚,本文旨在揭示同质园条件下欧洲拟南芥(Arabidopsis thaliana)不同地理种群光合能力的分化以及其基因转录调控机制。在同质园条件下,测定来自欧洲不同气候区的23个拟南芥的地理种群的气体交换参数、叶绿素荧光参数及SPAD值综合比较其光合能力差异。另外,根据测定结果选取光合能力差异的典型种群,利用实时定量PCR技术对光合相关基因表达水平进行验证。比较研究发现欧洲不同气候区拟南芥的地理种群间的气体交换参数差异较大,其中净光合速率的变化范围为2～11μmol·m^-2·s^-1;而叶绿素荧光参数变异幅度较小,变异幅度几乎不超过10%。聚类分析表明23个拟南芥种群被分为强光合能力和弱光合能力2组,强光合种群主要分布在中欧和西欧地区,净光合速率平均为7.37μmol·m^-2·s^-1;而弱光合种群则主要分布在东欧和南欧,净光合速率平均为4.46μmol·m^-2·s     

白皮松的保育遗传学研究I．基因保护分析

在白皮松主要分布区抽取了10个天然群体进行酶电泳分析,共测定了16种酶系统,得到31个清晰酶位点和53个等位基因。按照基因频率进行分类,53个基因中有32个全局基因、14个广域基因、6个局域基因和1个特异基因。通过计算机模拟建立基因捕获曲线的结果表明,随机抽取5个群体可平均捕获99．9％的基因。群体的等位基因频率与地理生态因子的相关分析表明,Idh与Pgi—2两个位点的基因频率呈现明显的梯度变异。该项研究为有效保护白皮松天然群体的基因资源提供了依据。     

白皮松的保育遗传学研究Ⅰ.基因保护分析

在白皮松主要分布区抽取了10个天然群体进行酶电泳分析,共测定了16种酶系统,得到31个清晰酶位点和53个等位基因。按照基因频率进行分类,53个基因中有32个全局基因、14个广域基因、6个局域基因和1个特异基因。通过计算机模拟建立基因捕获曲线的结果表明,随机抽取5个群体可平均捕获99.9%的基因。群体的等位基因频率与地理生态因子的相关分析表明,Idh与Pgi^-2两个位点的基因频率呈现明显的梯度变异。该项研究为有效保护白皮松天然群体的基因资源提供了依据。     

扎龙芦苇遗传多样性ISSR分析

采用ISSR分子标记技术对扎龙湿地的5个野生芦苇居群进行了遗传多样性研究.从75条ISSR引物中筛选出10个特异性强、稳定性好的引物进行ISSR分析.共获得96个位点,其中多态位点94个,多态位点百分率为97.92％.PopGene分析结果表明:居群的平均多态位点百分率为56.46％,Shannon's多样性指数(J)...