A Non segregation F2 Population Derived from the Cross of Triploid×Diploid in Rice

A non-segregating F2 population was obtained from the cross of tfiploid × diploid in rice ( Oryza sativa L. ). The maternal parent used in cross was SAR-3 which is an autotriploid occurring in the field, and the paternal was a restored line Sheng 47. The F2 population from the same F1 plant appears uniform, and so does F3. Results from coefficients of variation (CV) of F2, Ducan’s test of F3 and SSRs marker analysis showed that the F2 of SAR-3 × Sheng 47 was non-segregating. Markers for either parent could be present in F2 progenies. In some cases, both markers for each parent could be found on one chromosome. The authors presume that after crossing there might be recombination of chromosome followed by homozygotization. Stability of early generation could be utilized in breeding, as it is a new approach to shorten the breeding procedures.     

Quantitative trait locus mapping of pyrethroid resistance in Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera: Chrysomelidae)

Quantitative trait locus (QTL) mapping is a valuable new tool for locating genomic regions that underlie variation in important traits such as insecticide resistance. Because QTL mapping complements a candidate gene strategy for understanding the genetic architecture of important traits, it may also facilitate the identification of genes causing important variation. After mapping the QTL locations, markers closely linked to QTL can be used for genetic analysis of population structure and to measure the spread and increase of resistance-causing QTL alleles. In this study, QTL influencing resistance to the pyrethroid insecticide esfenvalerate were mapped in the Colorado potato beetle Leptinotarsa decemlineata (Say) (CPB). Three QTL contributing to esfenvalerate resistance were identified from a mapping population of 79 individuals analyzed at 90 marker loci. One QTL had a large effect and two QTL had smaller effects. The major QTL occurs on the X chromosome, overlapping the position of a candidate gene (Leptinotarsa decemlineata Voltage sensitive sodium channel [LdVssc1]) previously implicated in pyrethroid resistance. Resistance-increasing alleles at the two minor-effect QTL originated with the susceptible parent, suggesting that alleles of small effect may be segregating in susceptible populations. Comparison of the New York population from which the susceptible parent originated with a more-susceptible population from North Carolina suggests that the minor-effect loci identified here may explain some of the variation in tolerance observed among susceptible populations. DNA sequencing of a portion of LdVssc1 shows that the resistance-conferring allele from the resistant parent does not contain the kdr mutation previously found in CPB and typically observed in other insects that are resistant to pyrethroid insecticides because of changes in this gene.     

The relationship between single parent and parent pair genetic likelihoods in genealogy reconstruction

In the present paper, techniques of genealogy reconstruction based on genetic likelihoods of parent-offspring relationships are explored. Previous applications of such techniques have involved human populations, with emphasis placed on identification of parent pairs followed by reconstruction of families. In natural populations, this approach is neither practical nor necessarily a realistic representation of population structure. It is proposed that for natural populations emphasis should be placed first on locating the most likely mothers and fathers for a given individual, then seeking the most likely pair among that subset of genetically possible parents. Thus the genealogy is ultimately represented as a set of genotype triplets consisting of each individual coupled with its mother and father. Mathematical analyses show a strong positive correlation between single parent and parent pair likelihoods within triplets; this result is corroborated by statistical investigation of data from a natural plant population. Therefore the practice of constructing parent pairs using only likely single parents is justifiable on statistical grounds.     

Major gene detection for fusiform rust resistance using Bayesian complex segregation analysis in loblolly pine

The presence of major genes affecting rust resistance of loblolly pine was investigated in a progeny population that was generated with a half-diallel mating of six parents. A Bayesian complex segregation analysis was used to make inference about a mixed inheritance model (MIM) that included polygenic effects and a single major gene effect. Marginalizations were achieved by using Gibbs sampler. A parent block sampling by which genotypes of a parent and its offspring were sampled jointly was implemented to improve mixing. The MIM was compared with a pure polygenic model (PM) using Bayes factor. Results showed that the MIM was a better model to explain the inheritance of rust resistance than the pure PM in the diallel population. A large major gene variance component estimate (> 50% of total variance), indicated the existence of major genes for rust resistance in the studied loblolly pine population. Based on estimations of parental genotypes, it appears that there may be two or more major genes affecting disease phenotypes in this diallel population.     

Association between Sscp Haplotypes at the Bovine Growth Hormone Gene and Milk Protein Percentage

The bovine Growth Hormone gene (bGH) is an attractive candidate gene for milk production in cattle. Single-strand conformation polymorphisms at bGH were identified and used to define haplotype configurations at this gene in the Israeli Holstein dairy cattle population (Bos taurus) and in the parent animals of the International Bovine Reference Family Panel (a collection of B. taurus and B. indicus crosses). B. taurus and B. indicus haplotypes at the bGH gene differed qualitatively, confirming the previously proposed long evolutionary separation of these cattle subraces. Only a small number of bGH haplotypes were present in the Israel Holstein population. One of the haplotypes, apparently of B. indicus origin, was found to have a highly significant positive effect on milk protein percentage. This illustrates the utility of the haplotype approach for uncovering candidate gene involvement in quantitative genetic variation in agricultural populations. The strong effect of an indicine haplotype in a taurine background raises the possibility that indicine alleles at other candidate genes may comprise a genetic resource for improvement of taurine populations. It is proposed that haplotype analysis may be a useful adjunct to measures of genetic distance for evaluating rare breeds with respect to gene conservation.     

Simultaneous determination of fluctuating age structure and mortality from field data

The use of a Leslie matrix for analysis of a population normally implies that the age structure of the population is known. However, this restriction can be overcome if the population can be partitioned into recognisably different stages, and some information on stage duration and fecundity is available, in which case the age structure may be determined by the analysis itself. As an example of this approach we consider the estimation of the mortality rate applying to a population from a sequence of observed stage frequency vectors. The technique does not require that the population has attained a stable age structure nor that distinct cohorts can be recognised.     

Dermatoglyphic changes during the population admixture between Kam and Han Chinese

Genetic studies and gene localization for human dermatoglyphs are currently ongoing. However, the inheritance modes of various genetic traits are not well understood because of the complexity of dermatoglyph genetics. The study of admixed populations can contribute to the understanding of population genetic traits of dermatoglyphs. Here, we present the dermatoglyphic characteristics of Kam and Liujia Han, and the admixed population consisting of these two parent populations.The characteristics of the admixed population do not always fall in the same ranges as the parent population characters but do seem to be biased to Kam or Liujia parent populations, depending on sex and ethnicity of parents. The total frequencies of different fingerprint types do not differ among these populations, but several of the quantitative traits and the palm true pattern frequencies do significantly differ between admixed and parent populations. The simple arch fingerprint frequency decreases significantly in the admixed population in comparison with parent populations while both simple whorl fingerprint frequency and finger ridge counts increase significantly. True pattern frequency of the span area of interdigital III and IV areas on right hands and the radial-loop frequency of the right index fingers in the admixed populations are consistent with their matrilineal population. These dermatoglyphic changes may result from increased heterozygosity in the admixed population. The genetic modes of these changes may be relatively simple and will be useful for future dermatoglyph genetic studies.      

A Bayesian approach to ordering gene markers

A technique is presented whereby a marker map can be constructed using resource family data with an entire class of missing data. The focus is on a half-sib design where there is only information on a single parent and its progeny. A Bayesian approach is utilised with solutions obtained via a Markov chain Monte Carlo algorithm. Features of the approach include the capacity to determine parameters for the ungenotyped dam population, the ability to incorporate published information and its reliability, and the production of posterior densities and the consequent deduction of a wide range of inferences. These features are demonstrated through the analysis of simulated and experimental data.     

A methodology for evaluation of parent-mutant competition using a generalized non-linear ecosystem model

A generalized, non-linear population dynamics model of an ecosystem is used to investigate the direction of selective pressures upon a mutant by studying the competition between parent and mutant populations. The model has the advantages of considering selection as operating on the phenotype, of retaining the interaction of the mutant population with the ecosystem as a whole, and of setting a reasonable balance between theoretical manageability and quantitative testability.The model is used to make generalizations about several aspects of evolution in a terminal consumer (e.g. top carnivore). Mutations which avoid over exploitation of the prey species or introduce intra-specific population regulators will be selected against.Application of the method is limited primarily by the assumptions of a non-fluctuating environment, an asymptotically stable steady state before the mutation, absence of genetic drift, and uniformity of selective pressure on the mutant population.The method described in this paper is well suited for handling the high degree of complexity experienced in most ecosystems. Thus the methodology present may become a powerful tool in the approach to certain evolutionary questions.     

Quantitative statistical analysis of standard and human blood proteins from liquid chromatography, electrospray ionization, and tandem mass spectrometry

It will be important to determine if the parent and fragment ion intensity results of liquid chromatography, electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) experiments have been randomly and independently sampled from a normal population for the purpose of statistical analysis by general linear models and ANOVA. The tryptic parent peptide and fragment ion m/z and intensity data in the mascot generic files from LC-ESI-MS/MS of purified standard proteins, and human blood protein fractionated by partition chromatography, were parsed into a Structured Query Language (SQL) database and were matched with protein and peptide sequences provided by the X!TANDEM algorithm. The many parent and/or fragment ion intensity values were log transformed, tested for normality, and analyzed using the generic Statistical Analysis System (SAS). Transformation of both parent and fragment intensity values by logarithmic functions yielded intensity distributions that closely approximate the log-normal distribution. ANOVA models of the transformed parent and fragment intensity values showed significant effects of treatments, proteins, and peptides, as well as parent versus fragment ion types, with a low probability of false positive results. Transformed parent and fragment intensity values were compared over all sample treatments, proteins or peptides by the Tukey-Kramer Honestly Significant Difference (HSD) test. The approach provided a complete and quantitative statistical analysis of LC-ESI-MS/MS data from human blood.     

Mapping quantitative trait loci using multiple families of line crosses.

To avoid a loss in statistical power as a result of homozygous individuals being selected as parents of a mapping population, one can use multiple families of line crosses for quantitative trait genetic linkage analysis. Two strategies of combining data are investigated: the fixed-model and the random-model strategies. The fixed-model approach estimates and tests the average effect of gene substitution for each parent, while the random-model approach treats each effect of gene substitution as a random variable and directly estimates and tests the variance of gene substitution. Extensive Monte Carlo simulations verify that the two strategies perform equally well, although the random model is preferable in combining data from a large number of families. Simulations also show that there may be an optimal sampling strategy (number of families vs. number of individuals per family) in which QTL mapping reaches its maximum power and minimum estimation error. Deviation from the optimal strategy reduces the efficiency of the method.     

Balancing population size and genetic information in parentage analysis studies

In parentage analysis studies, the parameters of interest typically are not the parent assignments themselves, but population parameters such as variance in fertility, self-pollination rate, or average dispersal distances. The precision of parameter estimates is affected by two factors: the number of offspring under consideration, and the precision with which the offspring can be assigned to parents. When assignment of parents is based on genetic information, the confidence in assignments is affected by the number and polymorphism of the loci considered, and by the number of potential parents in the population. Studying larger populations may yield higher numbers of offspring, but since larger populations contain more potential parents, more (or more highly polymorphic) loci are necessary to attain a given level of confidence in the parent assignments. This article addresses how to relate the size of the population and the number of loci when designing a study. It is shown that the number of loci needed to assign all offspring unambiguously is proportional to the logarithm of the population size. In some cases, the constant of proportionality can be determined, eliminating the need for simulation-based projections. Population-wide measures of uncertainty in parent assignments are also introduced, and it is shown that holding uncertainty "steady" as the population size increases also requires increasing the number of loci proportional to the logarithm of the population size. Data from a study of self-pollination are used to illustrate the techniques suggested.     

Pollen dispersal patterns and population persistence in a small isolated population of <Emphasis Type="Italic">Fagus crenata</Emphasis>

The potential of long-distance pollen dispersal and the effects of small population size and population isolation on persistence of Fagus crenata populations were investigated in a small, severely isolated population (the Gofuku-ji population) and two other populations located within 7 km of this population (including 87 adult trees in total). Parentage analysis using 13 microsatellite loci showed that 94 of 100 seedlings derived from seeds collected from the Gofuku-ji population had parent pairs within this population, six had one parent within the population, and four of the six seedlings had alleles that were not detected in any of the three populations, indicating that some pollen is dispersed over distances exceeding 7 km. The estimated expected heterozygosity and effective population size were lower in the Gofuku-ji population than in previously examined large continuous populations. Therefore, levels of genetic diversity within the population may have been reduced by strong genetic drift and limitations of pollen- and seed-mediated gene flow associated with the small size and severe isolation. The contemporary mating pattern estimated at the seedling stage was biased toward outbreeding, which may be explained by possible processes: the level of inbreeding in the adult trees is increased; then, inbreeding frequently occurs but is rarely successful, while outbreeding successfully produces offspring. Additionally, high levels of significant linkage disequilibrium and higher numbers of alleles than expected under mutation–drift equilibrium from analyses of the populations’ evolutionary history suggest that the Gofuku-ji population may have experienced admixture before its severe isolation. Therefore, the persistence of the Gofuku-ji population is being adversely affected by the decrease in population size and severe isolation. Further studies of gene flow via pollen in other populations with various degrees of isolation could enhance our understanding of the effects of population isolation and long-distance pollen dispersal in F. crenata and similar species.     

Increased genetic variance after a population bottleneck

A conventional view holds that population bottlenecks cause massive losses of genetic variability, thus endangering the viability of the derived population. Although some alleles that were infrequent in the parent population may be lost new empirical evidence from Drosophila and housefly populations has demonstrated that genetic variance available to selection may actually increase following a single severe bottleneck. Several theoretical models support this view, and suggest that the increase may result from conversion of balanced epistatic variance to additive variance that becomes immediately available to selection. These effects appear to be greatest on the inheritance of quantitative characters, releasing new variance through the disruption of covariance matrices that underlie and interrelate quantitative traits. Thus, character change in adaptation and speciation may, in some instances, be promoted by founder events.     

Comparing parentage inference software: reanalysis of a red deer pedigree

Knowledge of the parentage of individuals is required to address a variety of questions concerning the evolutionary dynamics of wild populations. A major advance in parentage inference in natural populations has been the use of molecular markers and the development of statistical methods to analyse these data. Cervus, one of the most widely used parentage inference programs, uses molecular data to determine parent–offspring relationships. However, Cervus does not make use of all available information: additional phenotypic information may exist predicting parent–offspring relationships, and additional genetic information may be exploited by simultaneously considering multiple types of relationships rather than just pairwise or just parent–offspring relationships. Here we reanalyse data from a wild red deer population using two programs capable of using this additional information, MasterBayes and COLONY2, and quantify the impact of these alternative approaches by comparison with a ‘known pedigree’ estimated using a larger suite of microsatellite makers for a subset of the population. The use of phenotypic information and multiple relationships increased the number of correct assignments. We highlight the differences between programs, particularly the use of population‐ rather than individual‐level statistical confidence in Cervus. We conclude that the use of additional information allows MasterBayes and COLONY2 to assign more correct paternities, whereas their use of individual‐ rather than population‐level confidence generates fewer erroneous assignments. We suggest that maximal information may be gained by combining outputs from different programs. Higher accuracy and completeness of pedigree information will improve parameters estimated from pedigree information in studies of natural populations.     

一种有效的复杂疾病基因定位的检测法

连锁不平衡（LD）应用于某些复杂疾病基因的定位,近年来发展了许多LD定位方法,除TDT外,大多数LD定位方法须先假定无人群混和,人群混合可增大在疾病基因定位时犯Ⅰ类错误的机率,产生无效结果。此方法利用LD来检测标记位点和疾病敏感位点（DSL）的连锁（有连锁不平衡）相关（有连锁）。分析时采用不相关样本,已知其父母基因型和至少父母之一为杂合子,再将随机样本依基因型不同分类,然后对来自不同类的数据应用有力的统计方法进行单独和联合分析。此LD定位法不仅适用于患病和正常个体,而且有效消除据父母基因分类的样本定位时人群混合的影响,分析结果和模拟结果也表明此方法解决了在检测标记位点和疾病敏感位点之间的连锁和相关时人群混和的问题,但与TDT比,此法在检测的位点为DSL时丙能有效和充分地利用矫正数据,检测位点不是DSL时,此法和TDT法可相互补充更有效地检测连锁的DSL。     

Parent/offspring Relations for a Fitness Related Character

Some parent/offspring relations of a quantitative character are discussed, in particular in relation to the mean change from one generation to the next. It is shown that the prediction of this “progress” as the heritability multiplied by the selection differential takes only the slope of the parent/offspring relation into account and holds if, and only if, the population mean is a fixpoint of the mid-parent/offspring regression in the case of a character that is unrelated to sex. In particular, two examples show that this may not be the case if the character is related to fitness by pleiotropic effects of single genes.     

姜花属SRAP分子标记连锁图谱构建

采用拟测交作图策略,利用白姜花×圆瓣姜花的F1群体87个单株,分别构建了父母本的基于SRAP标记的连锁图谱。通过筛选,414对引物中,92对引物可以检测到拟测交位点。在检测到的398个拟测交位点中,237个来自于父本圆瓣姜花,161个来自于母本。经过卡方（x^2）测验及连锁分析,父本中,203个标记进入23个连锁群,覆盖了1386．8cm;母本中,139个标记进入18个连锁群,覆盖了917．1cm。     

Something Old and Something New: Wedding Recombinant Inbred Lines with Traditional Line Cross Analysis Increases Power to Describe Gene Interactions

In this paper we present a novel approach to quantifying genetic architecture that combines recombinant inbred lines (RIL) with line cross analysis (LCA). LCA is a method of quantifying directional genetic effects (i.e. summed effects of all loci) that differentiate two parental lines. Directional genetic effects are thought to be critical components of genetic architecture for the long term response to selection and as a cause of inbreeding depression. LCA typically begins with two inbred parental lines that are crossed to produce several generations such as F1, F2, and backcrosses to each parent. When a RIL population (founded from the same P1 and P2 as was used to found the line cross population) is added to the LCA, the sampling variance of several nonadditive genetic effect estimates is greatly reduced. Specifically, estimates of directional dominance, additive x additive, and dominance x dominance epistatic effects are reduced by 92%, 94%, and 56% respectively. The RIL population can be simultaneously used for QTL identification, thus uncovering the effects of specific loci or genomic regions as elements of genetic architecture. LCA and QTL mapping with RIL provide two qualitatively different measures of genetic architecture with the potential to overcome weaknesses of each approach alone. This approach provides cross-validation of the estimates of additive and additive x additive effects, much smaller confidence intervals on dominance, additive x additive and dominance x dominance estimates, qualitatively different measures of genetic architecture, and the potential when used together to balance the weaknesses of LCA or RIL QTL analyses when used alone.     

Isolation of facultatively aerobic actinomycetes from the gut, parent soil and mound materials of the termites Procubitermesaburiensis and Cubitermes severus

Abstract Isolates of the genus Streptomyces were readily obtained from the intestines of two African species of soil-feeding termites by an aerobic explant technique using starch casein medium, and from their parent soil and mound materials by dilution plating. Discriminant analysis of the isolates, based on 44 representative characters, showed that the population derived directly from the termites was significantly different from that of the feed soil or the mound. The termite gut was considered to be a good source of unusual actinomycetes, but strains isolated under aerobic conditions are likely to be allochthons selected by the intestinal environment, which is highly alkaline and anaerobic. An anaerobic, filamentous isolate was obtained which may be a component of the prokaryotic symbiont population mediating termite digestion.