Sources of Wilhelm Johannsen’s Genotype Theory

This paper describes the historical background and early formation of Wilhelm Johannsen’s distinction between genotype and phenotype. It is argued that contrary to a widely accepted interpretation (For instance, W. Provine, 1971. The Origins of Theoretical Population Genetics. Chicago: The University of Chicago Press; Mayr, 1973; F. B. Churchill, 1974. Journal of the History of Biology 7: 5–30; E. Mayr, 1982. The Growth of Biological Thought, Cambridge: Harvard University Press; J. Sapp, 2003. Genesis. The Evolution of Biology. New York: Oxford University Press) his concepts referred primarily to properties of individual organisms and not to statistical averages. Johannsen’s concept of genotype was derived from the idea of species in the tradition of biological systematics from Linnaeus to de Vries: An individual belonged to a group – species, subspecies, elementary species – by representing a certain underlying type (S. Müller-Wille and V. Orel, 2007. Annals of Science 64: 171–215). Johannsen sharpened this idea theoretically in the light of recent biological discoveries, not least those of cytology. He tested and confirmed it experimentally combining the methods of biometry, as developed by Francis Galton, with the individual selection method and pedigree analysis, as developed for instance by Louis Vilmorin. The term “genotype” was introduced in W. Johannsen’s 1909 (Elemente der Exakten Erblichkeitslehre. Jena: Gustav Fischer) treatise, but the idea of a stable underlying biological “type” distinct from observable properties was the core idea of his classical bean selection experiment published 6 years earlier (W. Johannsen, 1903. Ueber Erblichkeit in Populationen und reinen Linien. Eine Beitrag zur Beleuchtung schwebender Selektionsfragen, Jena: Gustav Fischer, pp. 58–59). The individual ontological foundation of population analysis was a self-evident presupposition in Johannsen’s studies of heredity in populations from their start in the early 1890s till his death in 1927. The claim that there was a “substantial but cautious modification of Johannsen’s phenotype–genotype distinction” (Churchill, 1974, p. 24) from a statistical to an individual ontological perspective derives from a misreading of the 1903 and 1909 texts. The immediate purpose of this paper is to correct this reading of the 1903 monograph by showing how its problems and results grow out of Johannsen’s earlier work in heredity and plant breeding. Johannsen presented his famous selection experiment as the culmination of a line of criticism of orthodox Darwinism by William Bateson, Hugo de Vries, and others (Johannsen, 1903). They had argued that evolution is based on stepwise rather than continuous change in heredity. Johannsen’s paradigmatic experiment showed how stepwise variation in heredity could be operationally distinguished from the observable, continuous morphological variation. To test Galton’s law of partial regression, Johannsen deliberately chose pure lines of self-fertilizing plants, a pure line being the descendants in successive generations of one single individual. Such a population could be assumed to be highly homogeneous with respect to hereditary type, and Johannsen found that selection produced no change in this type. Galton, he explained, had experimented with populations composed of a number of stable hereditary types. The partial regression which Galton found was simply an effect of selection between types, increasing the proportion of some types at the expense of others.     

Genotype–phenotype correlations in Leber hereditary optic neuropathy

Leber hereditary optic neuropathy (LHON), acute or subacute vision loss due to retinal ganglion cell death which in the long run leads to optic nerve atrophy is one of the most widely studied maternally inherited diseases caused by mutations in mitochondrial DNA. Although three common mutations, 11778G>A, 14484T>C or 3460G>A are responsible for over 90% of cases and affect genes encoding complex I subunits of the respiratory chain, their influence on bioenergetic properties of the cell is marginal and cannot fully explain the pathology of the disease. The following chain of events was proposed, based on biochemical and anatomical properties of retinal ganglion cells whose axons form the optic nerve: mitochondrial DNA mutations increase reactive oxygen species production in these sensitive cells, leading to caspase-independent apoptosis. As LHON is characterized by low penetrance and sex bias (men are affected about 5 times more frequently than women) the participation of the other factors—genetic and environmental—beside mtDNA mutations was studied. Mitochondrial haplogroups and smoking are some of the factors involved in the complex etiology of this disease.     

Genotype–phenotype correlation in long QT syndrome families

Heterogeneity in clinical manifestations is a well-known feature in Long QT Syndrome (LQTS). The extent of this phenomenon became evident in families wherein both symptomatic and asymptomatic family members are reported. The study hence warrants genetic testing and/or screening of family members of LQTS probands for risk stratification and prediction.Of the 46 families screened, 18 probands revealed novel variations/compound heterozygosity in the gene/s screened. Families 1–4 revealed probands carrying novel variations in KCNQ1 gene along with compound heterozygosity of risk genotypes of the SCN5A, KCNE1 and NPPA gene/s polymorphisms screened. It was also observed that families- 5, 6 and 7 were typical cases of “anticipation” in which both mother and child were diagnosed with congenital LQTS (cLQTS). Families- 16 and 17 represented aLQTS probands with variations in IKs and INa encoding genes. First degree relatives (FDRs) carrying the same haplotype as the proband were also identified which may help in predictive testing and management of LQTS. Most of the probands exhibiting a family history were found to be genetic compounds which clearly points to the role of cardiac genes and their modifiers in a recessive fashion in LQTS manifestation.     

Genotype — environment interaction in tissue cultures of birch

Summary In vitro culture experiments were carried out with three birch genotypes characterized by certain genealogical relationships which serve as indicators of genetic similarity or dissimilarity. Each genotype was grown in each of six different environments (medium types), and callus growth and colour were observed. The aim was to improve our understanding of the operation of genetic and environmental effects at the early stages of regeneration in vitro. For this purpose we tried to answer the question as to whether genetic differences exert effects that are consistently distinguishable under different environments or whether environmental differences exert effects that are consistently distinguishable between different genotypes. Since conventional analytical methods, such as the analysis of variance, are inappropriate for providing satisfactory answers to this question, we applied a new concept of interpretation. With the help of this concept we obtained the following results which appear to be unique among their kind. 1) For both characters, callus growth and callus colour, genetic differences are masked only slightly by the environments while environmental differences are almost completely masked by the genotypes. Thus, in the present experiment, interaction is one-sided in the sense that environmental effects interact strongly with genotypic effects but genotypic effects interact only slightly with the environmental ones. 2) Nuclear effects seem to be responsible for the differences observed in callus growth, while the differences in callus colour can be explained by the joint action of nuclear and extranuclear effects.     

From Genotype �� Environment Interaction to Gene �� Environment Interaction

Historically in plant breeding a large number of statistical models has been developed and used for studying genotype × environment interaction. These models have helped plant breeders to assess the stability of economically important traits and to predict the performance of newly developed genotypes evaluated under varying environmental conditions. In the last decade, the use of relatively low numbers of markers has facilitated the mapping of chromosome regions associated with phenotypic variability (e.g., QTL mapping) and, to a lesser extent, revealed the differetial response of these chromosome regions across environments (i.e., QTL × environment interaction). QTL technology has been useful for marker-assisted selection of simple traits; however, it has not been efficient for predicting complex traits affected by a large number of loci. Recently the appearance of cheap, abundant markers has made it possible to saturate the genome with high density markers and use marker information to predict genomic breeding values, thus increasing the precision of genetic value prediction over that achieved with the traditional use of pedigree information. Genomic data also allow assessing chromosome regions through marker effects and studying the pattern of covariablity of marker effects across differential environmental conditions. In this review, we outline the most important models for assessing genotype × environment interaction, QTL × environment interaction, and marker effect (gene) × environment interaction. Since analyzing genetic and genomic data is one of the most challenging statistical problems researchers currently face, different models from different areas of statistical research must be attempted in order to make significant progress in understanding genetic effects and their interaction with environment.     

Genotype × environment interaction, environmental heterogeneity and the lek paradox

Substantial additive genetic variance (V(A)) often exists for male signalling traits in spite of the directional selection that female choice imposes. One solution to this problem, a conundrum generally termed the 'lek paradox', is that genotype × environment interaction (GEI) occurs and generates a 'crossover' of reaction norms in which no one genotype performs in a superior manner in all environments. Theoretical work indicates that such crossover can sustain genetic variance provided that either (i) spatial heterogeneity in environmental conditions combined with limited migration among populations or (ii) temporal heterogeneity in environmental conditions combined with occasional generation overlap is present. Whereas some recent studies have revealed the intersection of reaction norms for sexually selected traits in laboratory and in natural populations, associated information on environmental heterogeneity, migration and generation overlap has not been investigated. We studied this question in an acoustic pyralid moth, Achroia grisella, in which previous work indicated GEI and crossover of reaction norms for several parameters of the male song evaluated by females. We measured reaction norms for male song as expressed when development was completed under different environmental conditions in four neighbouring, yet isolated, populations during 1 year and in one of these populations during consecutive years. Crossover occurred for the various song parameters in the several populations, but we did not observe a higher incidence of crossover between genotypes taken from two different populations than from the same population. However, for several key song parameters, crossover between genotypes taken from two different years was higher than that between genotypes from the same year. We suggest that temporal heterogeneity in the form of varying selection could potentially conserve V(A) in A. grisella, but we also note other factors that might contribute.     

Mutation spectrum of phenylketonuria in Syrian population: Genotype–phenotype correlation

Characterization of the molecular basis of phenylketonuria (PKU) in Syria has been accomplished through the analysis of 78 unrelated chromosomes from 39 Syrian patients with PKU. Phenylalanine hydroxylase (PAH) gene mutations have been analyzed by using molecular detection methods based on the restriction fragment length polymorphism (RFLP), artificial constructed restriction sites (ACRS) PCR and direct DNA sequencing. 56.4% of the patients had cPKU. A mutation detection rate of 79.49% was achieved and sixteen different mutations were found: missense 56.25%, splice site 37.5%, and frameshift 6.25%. The predominant mutation in this population sample was p.R261Q G>A, p.F55>Lfs and p.R243Q G>A. No mutation in six PKU patients was observed. In 57.9% of patient genotypes, the metabolic phenotype could be predicted. The identification of the mutations in the PAH gene and the genotype–phenotype correlation should facilitate the evaluation of metabolic phenotypes, diagnosis, implementation of optimal dietary therapy, and determination of prognosis in the patients and genetic counseling for the patient's relatives.     

Association between Alcohol, Smoking and HLA-DQAI＊0201 Genotype in Psoriasis

Psoriasis is a chronic skin disease triggered by genetic, environment or other risk factors such as infection, drugs, stress, moisture, alcohol, and smoking. A major psoriasis susceptibility locus at 6p21.3 has been identified. Further studies found that HLA-DQA1*0201 allele was associated with psoriasis. However, there were few data exploring an association between the environmental factors and susceptibility genes. In this study, the samples of 189 patients with psoriasis and 333 healthy controls were collected with their consent and were carried on analysis through polymerase chain reaction sequence-specific primer (PCR-SSP) method. The proportion of male psoriasis patients engaging in the smoking and alcohol was much higher than that of the control group (P<0.005). The HLA-DQA1*0201 allele was present at significantly higher frequency in the patients with psoriasis (OR=4.25, P<1.0 x 10(-6)). Association was found between smoking, alcohol and HLA-DQA1*0201 in male patients with psoriasis (OR>6.91, P<1.0 x 10(-4)).     

Phenotype–Genotype Analysis of Chinese Patients with Early-Onset LMNA-Related Muscular Dystrophy

This study aimed to analyze the correlation between the phenotype and genotype of Chinese patients with early-onset lamin A (LMNA)-related muscular dystrophy (MD). The clinical and myopathological data of 21 Chinese pediatric patients with early-onset LMNA-related MD were collected and analyzed. LMNA gene mutation analysis was performed by direct sequencing of genomic DNA. Sublocalization of wild-type and mutant proteins were observed by immunofluorescence using cultured fibroblasts and human embryonic kidney 293 (HEK 293) cell. Seven patients were diagnosed with Emery-Dreifuss muscular dystrophy (EDMD) and 14 were diagnosed with LMNA-associated congenital muscular dystrophy (L-CMD). Four biopsy specimens from the L-CMD cases exhibited inflammatory changes. Abnormal nuclear morphology was observed with both transmission electron microscopy and lamin A/C staining. We identified 10 novel and nine known LMNA gene mutations in the 21 patients. Some mutations (c.91G>A, c.94_96delAAG, c.116A>G, c.745C>T, c.746G>A, and c.1580G>C) were well correlated with EDMD or L-CMD. LMNA-related MD has a common symptom triad of muscle weakness, joint contractures, and cardiac involvement, but the severity of symptoms and disease progression differ greatly. Inflammatory change in biopsied muscle is a characteristic of early-stage L-CMD. Phenotype–genotype analysis determines that some mutations are well correlated with LMNA-related MD.     

Genotype and extra-pair paternity in the house wren: a rare-male effect?

Females in socially monogamous species may select extra-pair (EP) mates to increase the heterozygosity, and hence fitness, of their offspring. We tested this hypothesis in the house wren (Troglodytes aedon), a largely monogamous songbird in which EP young are common. We typed paired males and females, nestlings, and males on neighbouring territories, at five to seven microsatellite loci over 2 years in a Wyoming, USA, population. We identified EP sires at 20 nests with EP young. In pairwise comparisons, we found no significant differences between cuckolded within-pair (WP) males and EP sires in three measures of heterozygosity (mean d2, standardized heterozygosity and internal relatedness). However, EP sires had fewer alleles that were common within the population than did the WP males they cuckolded. Nearby males who were EP sires also had fewer common alleles than did nearby males who did not sire EP young. Females in our population may be more prone to accept copulations from males with rare genotypes than from males with common genotypes. Alternatively, selection of rare-male sperm may occur within the female reproductive tract. Because mating with rare males is likely to increase offspring heterozygosity, our data suggest that EP mating may provide genetic benefits to females.     

Amyloid-β Pathology and APOE Genotype Modulate Retinoid X Receptor Agonist Activity in Vivo

Previous data demonstrate that bexarotene (Bex), retinoid X receptor (RXR) agonist, reduces soluble and insoluble amyloid-β (Aβ) in Alzheimer disease (AD)-transgenic mice either by increasing the levels of mouse apolipoprotein E (apoE) or increasing ABCA1/ABCG1-induced apoE lipoprotein association/lipidation. However, although the mechanism of action of RXR agonists remains unclear, a major concern for their use is human (h)-APOE4, the greatest AD genetic risk factor. If APOE4 imparts a toxic gain-of-function, then increasing apoE4 may increase soluble Aβ, likely the proximal AD neurotoxin. If the APOE4 loss-of-function is lipidation of apoE4, then induction of ABCA1/ABCG1 may be beneficial. In novel EFAD-Tg mice (overexpressing h-Aβ42 with h-APOE), levels of soluble Aβ (Aβ42 and oligomeric Aβ) are highest in E4FAD hippocampus (HP) > E3FAD-HP > E4FAD cortex (CX) > E3FAD-CX, whereas levels of lipoprotein-associated/lipidated apoE have the opposite pattern (6 months). In E4FAD-HP, short-term RXR agonist treatment (Bex or {"type":"entrez-nucleotide","attrs":{"text":"LG100268","term_id":"1041422930","term_text":"LG100268"}}LG100268; 5.75–6 months) increased ABCA1, apoE4 lipoprotein-association/lipidation, and apoE4/Aβ complex, decreased soluble Aβ, and increased PSD95. In addition, hydrogel delivery, which mimics low sustained release, was equally effective as gavage for Bex and {"type":"entrez-nucleotide","attrs":{"text":"LG100268","term_id":"1041422930","term_text":"LG100268"}}LG100268. RXR agonists induced no beneficial effects in the E4FAD-HP in a prevention protocol (5–6 months) and actually increased soluble Aβ levels in E3FAD-CX and E4FAD-CX with the short-term protocol, possibly the result of systemic hepatomegaly. Thus, RXR agonists address the loss-of-function associated with APOE4 and exacerbated by Aβ pathology, i.e. low levels of apoE4 lipoprotein association/lipidation. Further studies are vital to address whether RXR agonists are an APOE4-specific AD therapeutic and the systemic side effects that limit translational application.     

ABO Genotype, ‘Blood-Type’ Diet and Cardiometabolic Risk Factors

Background

The ‘Blood-Type’ diet advises individuals to eat according to their ABO blood group to improve their health and decrease risk of chronic diseases such as cardiovascular disease. However, the association between blood type-based dietary patterns and health outcomes has not been examined. The objective of this study was to determine the association between ‘blood-type’ diets and biomarkers of cardiometabolic health and whether an individual''s ABO genotype modifies any associations.

Methods

Subjects (n = 1,455) were participants of the Toronto Nutrigenomics and Health study. Dietary intake was assessed using a one-month, 196-item food frequency questionnaire and a diet score was calculated to determine relative adherence to each of the four ‘Blood-Type’ diets. ABO blood group was determined by genotyping rs8176719 and rs8176746 in the ABO gene. ANCOVA, with age, sex, ethnicity, and energy intake as covariates, was used to compare cardiometabolic biomarkers across tertiles of each ‘Blood-Type’ diet score.

Results

Adherence to the Type-A diet was associated with lower BMI, waist circumference, blood pressure, serum cholesterol, triglycerides, insulin, HOMA-IR and HOMA-Beta (P<0.05). Adherence to the Type-AB diet was also associated with lower levels of these biomarkers (P<0.05), except for BMI and waist circumference. Adherence to the Type-O diet was associated with lower triglycerides (P<0.0001). Matching the ‘Blood-Type’ diets with the corresponding blood group did not change the effect size of any of these associations. No significant association was found for the Type-B diet.

Conclusions

Adherence to certain ‘Blood-Type’ diets is associated with favorable effects on some cardiometabolic risk factors, but these associations were independent of an individual''s ABO genotype, so the findings do not support the ‘Blood-Type’ diet hypothesis.     

Molecular and Phylogenetic Analyses Suggest an Additional Hepatitis B Virus Genotype “I”

A novel hepatitis B virus (HBV) strain (W29) was isolated from serum samples in the northwest of China. Phylogenetic and distance analyses indicate that this strain is grouped with a series of distinct strains discovered in Vietnam and Laos that have been proposed to be a new genotype I. TreeOrderScan and GroupScan methods were used to study the intergenotype recombination of this special group. Recombination plots and tree maps of W29 and these putative genotype I strains exhibit distinct characteristics that are unexpected in typical genotype C strains of HBV. The amino acids of P gene, S gene, X gene, and C gene of all genotypes (including subtypes) were compared, and eight unique sites were found in genotype I. In vitro and in vivo experiments were also conducted to determine phenotypic characteristics between W29 and other representative strains of different genotypes obtained from China. Secretion of HBsAg in Huh7 cells is uniformly abundant among genotypes A, B, C, and I (W29), but not genotype D. HBeAg secretion is low in genotype I (W29), whose level is close to genotype A and much lower than genotypes B, C, and D. Results from the acute hydrodynamic injection mouse model also exhibit a similar pattern. From an overview of the results, the viral markers of W29 (I1) in Huh7 cells and mice had a more similar level to genotype A than genotype C, although the latter was closer to W29 in distance analysis. All evidence suggests that W29, together with other related strains found in Vietnam and Laos, should be classified into a new genotype.     

Biomass and Genotype × Environment Interactions of Populus Energy Crops in the Midwestern United States

Using Populus feedstocks for biofuels, bioenergy, and bioproducts is becoming economically feasible as global fossil fuel prices increase. Maximizing Populus biomass production across regional landscapes largely depends on understanding genotype × environment interactions, given broad genetic variation at strategic (genomic group) and operational (clone) levels. A regional network of Populus field tests was established in the Midwest USA in 1995, 1997, and 2000 to assess relative productivity of 187 clones grown at Westport, Minnesota (45.7° N, 95.2° W); Waseca, Minnesota (only 2000; 44.1° N, 93.5° W); Arlington, Wisconsin (43.3° N, 89.4° W); and Ames, Iowa (42.0° N, 93.6° W). We evaluated biomass potential throughout plantation development and identified clones with yield substantially greater than commercial controls (Eugenei, NM6). For each site, biomass ranges (Mg ha^?1 year^?1) of the best six clones were: Westport: 2.3 to 3.9 (5 years), 8.0 to 10.1 (8 years), and 8.9 to 11.3 (10 years); Waseca: 10.4 to 13.4 (7 years); Arlington: 5.1 to 7.1 (3 years), 14.8 to 20.9 (6 years), and 16.1 to 21.1 (8 years); and Ames: 4.3 to 5.3 (4 years), 11.1 to 20.9 (7 years), and 14.3 to 24.5 (9 years). Mean biomass of the best three clones was 1.4 to 2.7 times greater than controls as trees developed at Westport (1995, 1997) and Waseca 2000. Genotype × environment interactions governed biomass production, with clone–mean rank correlations across sites ranging from 0.29 to 0.81. We identified generalist genotypes (e.g. Crandon, NC14105, NM2) with elevated biomass across the region and specialists (e.g. 7300501, 80X01015, and NC14103) with exceptional biomass at specific locations.     

Genotype–phenotype mapping and the end of the ‘genes as blueprint’ metaphor

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G→P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch''s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened the need for a different conceptual treatment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G→P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G→P maps. These include RNA folding, protein function and the study of evolvable software. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G→P mapping problem.