Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression

Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation

The total protein of the mouse brain was fractionated into three fractions, supernatant, pellet extract and rest pellet suspension, by a procedure that avoids any loss of groups or classes of proteins. The supernatant proteins were resolved to a maximum by large-gel two-dimensional electrophoresis. Two-dimensional patterns from ten individual mice of the commonly used inbred strain C57BL/6 (species: Mus musculus) were prepared. The master pattern was subjected to densitometry, computer-assisted image analysis and treatment with our spot detection program. The resulting two-dimensional pattern, a standard pattern for mouse brain supernatant proteins, was divided into 40 squares, calibrated, and specified by providing each spot with a number. The complete pattern and each of the 40 squares are shown in our homepage (http://www.charite.de/ humangenetik). The standard pattern comprises 8767 protein spots. To identify the proteins known so far in the brain fraction investigated, a first set of 200 spots was analyzed by matrix-assisted laser desorption/ionization - mass spectrometry (MALDI-MS) after in-gel digestion. By screening protein databases 115 spots were identified; by extending the analysis to selected, genetically variant protein spots, 166 spots (including some spot series) were identified in total. This number was increased to 331 by adding protein spots identified indirectly by a genetic approach. By comparing the two-dimensional patterns from C57BL/6 mice with those of another mouse species (Mus spretus), more than 1000 genetically variant spots were detected. The genetic analysis allowed us to recognize spot families, i.e., protein spots that represent the same protein but that are post-translationally modified. If some members of the family were identified, the whole family was considered as being identified. Spot families were investigated in more detail, and interpreted as the result of protein modification or degradation. Genetic analysis led to the interesting finding that the size of spot families, i.e., the extent of modification or degradation of a protein, can be genetically determined. The investigation presented is a first step towards a systematic analysis of the proteome of the mouse. Proteome analysis was shown to become more efficient, and, at the same time, linked to the genome, by combining protein analytical and genetic methods.

Water-deficit-responsive proteins in maritime pine

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) was used to identify drought-responsive proteins during progressive water deprivation of two-year old maritime pine seedlings. Stress was applied by withholding water during vegetative growth. Needles were sampled before, during and after the stress. Out of about 1000 spots that were quantified by computer analysis, 38 responded during stress. Some proteins were accumulated while others were suppressed. One to three internal microsequences were obtained for 11 proteins, 10 of which were identified on the basis of sequence homologies. These proteins are quite diverse and are involved in photosynthesis, cell elongation, antioxidant metabolism and lignification.

Interactions among dosage-dependent trans-acting modifiers of gene expression and position-effect variegation in Drosophila

We have investigated the effect of dosage-dependent trans-acting regulators of the white eye color gene in combinations to understand their interaction properties. The consequences of the interactions will aid in an understanding of aneuploid syndromes, position-effect variegation (PEV), quantitative traits, and dosage compensation, all of which are affected by dosage-dependent modifiers. Various combinations modulate two functionally related transcripts, white and scarlet, differently. The overall trend is that multiple modifiers are noncumulative or epistatic to each other. In some combinations, developmental transitions from larvae to pupae to adults act as a switch for whether the effect is positive or negative. With position-effect variegation, similar responses were found as with gene expression. The highly multigenic nature of dosage-sensitive modulation of both gene expression and PEV suggests that dosage effects can be progressively transduced through a series of steps in a hierarchical manner.

Proteome and proteomics: new technologies, new concepts, and new words

The goal of proteomics is a comprehensive, quantitative description of protein expression and its changes under the influence of biological perturbations such as disease or drug treatment. Quantitative analysis of protein expression data obtained by high-throughput methods has led us to define the concept of "regulatory homology" and use it to begin to elucidate the basic structure of gene expression control in vivo. Such investigations lay the groundwork for construction of comprehensive databases of mechanisms (cataloguing possible biological outcomes), the next logical step after the soon to be completed cataloguing of genes and gene products. Mechanism databases provide a roadmap towards effective therapeutic intervention that is more direct than that offered by conventional genomics approaches.

Protein changes in response to progressive water deficit in maize . Quantitative variation and polypeptide identification

Three-week-old plants of two unrelated lines of maize (Zea mays L.) and their hybrid were submitted to progressive water stress for 10 d. Changes induced in leaf proteins were studied by two-dimensional electrophoresis and quantitatively analyzed using image analysis. Seventy-eight proteins out of a total of 413 showed a significant quantitative variation (increase or decrease), with 38 of them exhibiting a different expression in the two genotypes. Eleven proteins that increased by a factor of 1.3 to 5 in stressed plants and 8 proteins detected only in stressed plants were selected for internal amino acid microsequencing, and by similarity search 16 were found to be closely related to previously reported proteins. In addition to proteins already known to be involved in the response to water stress (e.g. RAB17 [Responsive to ABA]), several enzymes involved in basic metabolic cellular pathways such as glycolysis and the Krebs cycle (e.g. enolase and triose phosphate isomerase) were identified, as well as several others, including caffeate O-methyltransferase, the induction of which could be related to lignification.

Genetics of complex disease: approaches, problems, and solutions

Complex or multifactorial diseases are defined as diseases that are ultimately determined by a number of genetic and environmental factors. Although there are many technologies and strategies that can be used to detect genetic factors influencing complex diseases, these technologies and strategies have inherent limitations. In fact, the very name "complex disease" suggests that the results from relevant studies will not be simple to decipher. Ultimately, both the detection and precise characterization of a factor's contribution to a complex disease are difficult undertakings, because the effect of any one factor may be obscured or confounded by other factors. However, the genetic dissection of complex diseases can be greatly facilitated by paying heed to two very basic distinctions. The first distinction is between complexity at the level of individuals and complexity at the level of populations. The second distinction is between the two sequentially pursued components of gene discovery paradigms: gene identification and gene effect characterization. Although genetic epidemiology, as a research field, is oriented to both components of gene discovery for complex diseases, it is suited to gene effect characterization at the population level more than anything else. This paper reviews the origins of the genetic basis of complex traits, as well as the problems plaguing genetic epidemiologic analysis strategies, with the hope of showing how greater attention to these distinctions, as well as a greater integration of relevant knowledge, can alleviate confusion and shape future investigations. In addition, a new discipline, "phenomics" or "phenometrics," could be initiated that would complement genomic research as presently performed.

Polymorphism and locus-specific effects on polymorphism at microsatellite loci in natural Drosophila melanogaster populations

We have studied the natural variation at microsatellite loci in two African and five non-African populations of Drosophila melanogaster. Ten dinucleotide simple sequence loci were cloned from chromosomally mapped P1 clones and typed for single individuals from isofemale lines of the respective populations. We find that the African populations harbor the largest degree of diversity, while the non-African populations show a lower diversity. This supports previous results that D. melanogaster originated in Africa and spread across the rest of the world in historic times. Using genetic distance measures, we find also a distinct population subdivision between the non-African populations. Most interestingly, we find for some loci in some populations a strongly reduced variability, which cannot be explained by bottleneck effects. Employing a conservative test based on the variance in repeat number, we find that at least one locus in one population deviates significantly from the expectations of mutation-drift equilibrium. We suggest that this may be due to a recent selective sweep in this chromosomal region that may have been caused by a linked locus that was involved in local adaptation of the population.

Fixation, segregation and linkage of allozyme loci in inbred families of the Pacific oyster Crassostrea gigas (Thunberg): implications for the causes of inbreeding depression

The effect that inbreeding has on the fixation and segregation of genes has rarely been confirmed by direct observation. Here, fixation, segregation, and linkage of allozymes is investigated in the progeny of self-fertilized hermaphrodites of the normally outcrossing Pacific oyster Crassostrea gigas. The estimate of fixation pooled over loci, individuals, and families, F = 0.462, is significantly lower than the expected value of 0.5. Log-likelihood ratios reveal significant heterogeneity in fixation among individuals, among families, and among loci. In addition, the grand pooled segregation ratio, 127:243:54, deviates significantly from 1:2:1, with a bias against homozygotes for alleles of lesser frequency in the natural population. Segregation ratios for 11 of 14 loci are significantly heterogeneous among families, and exact tests for segregation within families reveal 16 significant results out of 51 tests. Thus, fixation and segregation of allozyme markers in inbred oyster families deviates from the expectations of neutral inbreeding theory. Di-genic disequilibria are significant for four of 74 di-locus pairs revealing two linkage groups. Strong viability selection is apparently conditional on the genotype of the hermaphrodite-founders and is largely focused on these two linkage groups. These genetic effects are explained by interaction between cis-linked factors and polymorphic regulatory backgrounds.

Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila

In Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster, codon bias may be maintained by a balance among mutation pressure, genetic drift, and natural selection favoring translationally superior codons. Under such an evolutionary model, silent mutations fall into two fitness categories: preferred mutations that increase codon bias and unpreferred changes in the opposite direction. This prediction can be tested by comparing the frequency spectra of synonymous changes segregating within populations; natural selection will elevate the frequencies of advantageous mutations relative to that of deleterious changes. The frequency distributions of preferred and unpreferred mutations differ in the predicted direction among 99 alleles of two D. pseudoobscura genes and five alleles of eight D. simulans genes. This result confirms the existence of fitness classes of silent mutations. Maximum likelihood estimates suggest that selection intensity at silent sites is, on average, very weak in both D. pseudoobscura and D. simulans (magnitude of NS approximately 1). Inference of evolutionary processes from within-species sequence variation is often hindered by the assumption of a stationary frequency distribution. This assumption can be avoided when identifying the action of selection and tested when estimating selection intensity.

Potential of two-dimensional electrophoresis in routine identification of closely related durum wheat lines

Four closely related durum wheat varieties were compared by computer-assisted analysis of two-dimensional electrophoretic maps of leaf proteins. A low inter-varietal polymorphism was revealed and seven reliable qualitatively varying proteins allowed rapid visual identification of genotypes. For numerous spots, presence/absence or quantitative variations were greatly affected by a batch effect. Several criteria that should be used to discard unreliable spots or gels a priori were reviewed. Nevertheless, it was shown that, provided that the experimental design allows the integration of the batch effect, screening for discriminant markers as well as computing distances based on protein quantity variations are possible and allow variety identification. Euclidean and Mahalanobis distances allowed variety discrimination and single gel classification with a minimum risk of error, not only by taking into account the quantitative variations in discriminant proteins selected by analysis of variance, but also by taking into account all reproducible spots. The possible applications of two-dimensional electrophoresis in variety identification are discussed.

Genetic dissection of height in maritime pine seedlings raised under accelerated growth conditions

Random Amplified Polymorphic DNAs (RAPDs) were used to investigate quantitative trait loci (QTL) for traits related to height growth on 126 F2 seedlings of maritime pine (Pinuspinaster Ait). The haploid megagametophyte was used to determine the maternal genotype of each F2 individual. The seedlings were raised for 2 years in a greenhouse under accelerated growth conditions consisting of intense fertilization combined with continuous light treatments. Total height was measured at different developmental stages, and height growth components were measured after the second growth period. QTLs were identified for each trait. For total height, QTLs of different developmental stages were located on distinct linkage groups. However, rather than a complete temporal change in QTL expression, our results showed that maturation may induce a progressive shift of the genetic control of height growth. This may provide an explanation for a low juvenile-mature phenotypic correlation previously reported for height. Height growth components related to the initiation (controlled by the apical meristem) and elongation of shoot cycles (controlled by the subapical meristem) were mapped to different chromosomes, suggesting that the activity of these meristems is controlled by separate genetic mechanisms.

The maize two-dimensional gel protein database: towards an integrated genome analysis program

This paper describes the first maize database of proteins separated by two-dimensional electrophoresis. Fifty-six coleoptile proteins and 18 leaf proteins from two maize lines were partially microsequenced. Thirty-six proteins (49%) displayed high similarity with database proteins. Nine of these proteins, representing five different functions, had never been described in maize. No conclusive function could be found for 45 polypeptides (61% of the microsequenced proteins). In addition, an alternative identification method, based on amino acid analysis, allowed candidates to be proposed for 17 proteins out of 44 additional proteins analyzed in the coleoptiles. These results are stored in a database which also includes, when available, genetic information about the chromosomal location of structural genes and regulatory factors of proteins. This database is being used in the context of a project on the genetic mapping of the expressed genome in maize.

Detecting epistatic genetic variance with a clonally replicated design: models for lowvs high-order nonallelic interaction

A quantitative genetic model, that uses known family structure with clonal replicates to separate genetic variance into its additive, dominance and epistatic components, is available in the current literature. Making use of offspring testing, this model is based on the theory that components of variance from the linear model of an experimental design may be expressed in terms of expected covariances among relatives. However, if interactions between a pair of quantitative trait loci (QTLs) explain a large proportion of the total epistasis, it will seriously overestimate the additive and dominance variances but underestimate the epistatic variance. In the present paper, a new model is developed to manipulate this problem by combining parental and offspring material into the same test. Under the condition described above, the new model can provide an accurate estimate for additive x additive variances. Also, its accuracy in estimating dominance and total epistatic variances is much greater than the accuracy of the previous model. However, if there is obvious evidence showing the major contribution of high-order interactions, especially among ≥ 4QTLs, to the total epistasis, the previous model is more appropriate to partition the genetic variance for a quantitative trait. The re-analysis of an example from a factorial mating design in poplar shows large differences in estimating variance components between the new and previous models when two different assumptions (lowvs high-order epistatic interactions) are used. The new model will be an alternative to estimating the mode of quantitative inheritance for species, especially for longlived, predominantly outcrossing forest trees, that can be clonally replicated.

Distance indices in a comparison between the A, D, I and R genomes of the Triticeae tribe

Two-dimensional gel electrophoresis of shoot proteins was used to study the relationships between Triticum, Secale, and Hordeum. A high level of polymorphism was found among the 1275 spots scored: only 198 spots were found common to all. But, under the hypothesis that only allelic variations were observed, the mean number of alleles per locus was only two. Phenograms were built from different distance indices. All of them showed Triticum genomes A and D close to each other, Hordeum far from the Triticum cluster, and Secale at an intermediate position. A discussion on the use of various distance indices is presented.

Characterizing allelic proteins for genome mapping in maize

Mapping cDNA probes in order to construct genetic linkage maps is becoming a widespread strategy for genome analysis and gene isolation, particularly in cultivated plant species. Nevertheless, almost all cDNAs reveal two or more unlinked loci, making it difficult to identify the gene(s) actually expressed. In a highly polymorphic species, such as maize, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) of proteins may circumvent this limitation. With the analysis of various segregating populations, we previously showed that the apparent position shifts of proteins on the 2-D gels are monogenic and codominant. In this paper we compared allelic proteins on the basis of their high performance liquid chromatography (HPLC) profile and partial amino acid sequences. In a sample of 20 position shifts, the allelic proteins appeared to be similar in all but one case, strongly suggesting that polymorphism of structural genes is involved. Thus 2-D PAGE could prove to be a useful tool for genome mapping: when a cDNA probe detects several loci, a position shift of the encoded protein will allow the identification of the gene translated in the organ considered.

Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome

The two-dimensional electrophoresis (2-DE) technique developed by Klose in 1975 (Humangenetik 1975, 26, 211-234), independently of the technique developed by O'Farrell (J. Biol. Chem. 1975, 250, 4007-4021), has been revised in our laboratory and an updated protocol is presented. This protocol is the result of our experience in using this method since its introduction. Many modifications and suggestions found in the literature were also tested and then integrated into our original method if advantageous. Gel and buffer composition, size of gels, use of stacking gels or not, necessity of isoelectric focusing (IEF) gel incubation, freezing of IEF gels or immediate use, carrier ampholytes versus Immobilines, regulation of electric current, conditions for staining and drying the gels - these and other problems were the subject of our concern. Among the technical details and special equipment which constitute our 2-DE method presented here, a few features are of particular significance: (i) sample loading onto the acid side of the IEF gel with the result that both acidic and basic proteins are well resolved in the same gel; (ii) use of large (46 x 30 cm) gels to achieve high resolution, but without the need of unusually large, flat gel equipment; (iii) preparation of ready-made gel solutions which can be stored frozen, a prerequisite, among others, for high reproducibility. Using the 2-DE method described we demonstrate that protein patterns revealing more than 10 000 polypeptide spots can be obtained from mouse tissues. This is by far the highest resolution so far reported in the literature for 2-DE of complex protein mixtures. The 2-DE patterns were of high quality with regard to spot shape and background. The reproducibility of the protein patterns is demonstrated and shown to be thoroughly satisfactory. An example is given to show how effectively 2-DE of high resolution and reproducibility can be used to study the genetic variability of proteins in an interspecific mouse backcross (Mus musculus x Mus spretus) established by the European Backcross Collaborative Group for mapping the mouse genome. We outline our opinion that the structural analysis of the human genome, currently pursued most intensively on a worldwide scale, should be accompanied by a functional analysis of the genome that starts from the proteins of the organism.

Mapping in plants: progress and prospects

Comprehensive genetic maps are now available for all of the world's important crop species. Data show a remarkable conservation of order of markers over family-wide taxonomic groupings and illuminate species relationships and mechanisms of genome evolution. Comparison of genetic and physical maps has revealed differences in genetic distance throughout genomes with implications for genome organization, gene isolation and transformation.

Molecular markers and protein quantities as genetic descriptors in maize. I. Genetic diversity among 21 inbred lines

Twenty-one maize (Zea mays L.) inbred lines were analysed using isozyme electrophoresis, restriction fragment length polymorphism (RFLP), and two-dimensional electrophoresis of denatured proteins (2-D PAGE). Our goal was (1) to assess the genetic variability among these lines which are potential progenitors for the development of forage maize hybrids in Europe, and (2) to compare the relationship pattern revealed by the polymorphism at marker loci with the one derived from the amount of protein variability assessed by computer-assisted analysis of the 2-D electrophoregrams. Fourteen markers were obtained from isozyme polymorphism, 84 from the restriction fragment length polymorphism, and 70 from protein shifts revealed by 2-D PAGE. The Rogers' distance computed on the set of molecular markers was the most efficient to describe the pedigree relationships between lines. Quantitative protein data gave a picture of relationships between lines clearly different from the monogenic markers. When unrelated pairs of lines were considered, the Rogers' distance was weakly correlated to distances based on quantitative variations in the amount of protein which may be consistent with their polygenic control and the occurrence of gene interactions.