GENSTAT programs for performing Muir's alternative partitioning of genotype-by-environment interaction

Genotype-by-environment (GE) interaction exists when different cultivars or strains have different phenotypic responses to environmental variation (Merila and Fry 1998). The phenomenon is of major concern in plant breeding, as it can limit gains in selecting superior cultivars. In animal breeding, the problem is also an important issue because breeding stocks are developed by a few companies but are used worldwide (Lin and Togashi 2002).     

Interpreting genotype-by-environment interaction using redundancy analysis

Summary Methods for the interpretation of genotype-by-environment interaction in the presense of explicitly measured environmental variables can be divided into two groups. Firstly, methods that extract environmental characterizations from the data itself, which are subsequently related to measured environmental variables, e.g., regression on the mean or singular value decomposition of the matrix of residuals from additivity, followed by correlation, or regression, methods. Secondly, methods that incorporate measured environmental variables directly into the model, e.g., multiple regression of individual genotypical responses on environmental variables, or factorial regression in which a genotype-by-environment matrix is modelled in terms of concomitant variables for the environmental factor. In this paper a redundancy analysis is presented, which can be derived from the singular-value decomposition of the residuals from additivity by imposing the restriction on the environmental scores of having to be linear combinations of environmental variables. At the same time, redundancy analysis is derivable from factorial regression by rotation of the axes in the space spanned by the fitted values of the factorial regression, followed by a reduction of dimensionality through discarding the least explanatory axes. Redundancy analysis is a member of the second group of methods, and can be an important tool in the interpretation of genotype-by-environment interaction, especially with reference to concomitant environmental information. A theoretical treatise of the method is given, followed by a practical example in which the results of the method are compared to the results of the other methods mentioned.     

Epistasis and genotype-by-environment interaction of grain protein content in durum wheat

Parental, F(1) , F (2) , BC (1) and BC (2) generations of four crosses involving four cultivars of durum wheat (Triticum durum Desf.) were evaluated at two sites in Tunisia. A three-parameter model was found inadequate for all cases except crosses Chili x Cocorit 71 at site Sidi Thabet and Inrat 69 x Karim at both sites. In most cases a digenic epistatic model was sufficient to explain variation in generation means. Dominance effects (h) and additive x additive epistasis (i) (when significant) were more important than additive (d) effects and other epistatic components. Considering the genotype-by-environment interaction, the non-interactive model (m, d, h, e) was found adequate. Additive variance was higher than environmental variance in three crosses at both sites. The estimated values of narrow-sense heritability were dependent upon the cross and the sites and were 0%-85%. The results indicate that appropriate choice of environment and selection in later generations would increase grain protein content in durum wheat.     

Effects of pH on the kinetics of the interaction between anthracyclines and lipid bilayers

In the present study we have analyzed the kinetics of the initial steps (first 10 seconds) of the interaction between the anthracycline daunomycin (DNM) and artificial lipid vesicles bearing opposite surface charge. The process can be monitored by measuring the fluorescence increase of the drug accompanying its association with the lipid bilayers. The results indicated that DNM consistently interacts to a larger extent with the liposomes having negative surface charge than with those having positive surface charge, suggesting the involvement of electrostatic components in the interaction. In contrast, DNM associates with the vesicles bearing positive surface charge 2 – 3 times faster (in terms of the apparent rate constants describing the process of interaction) than with those having negative surface charge, an observation probably related to the more fluid physical state of the former. Regarding the rate of access of DNM to the vesicles, rather than depending on the surface charge of the vesicles, this is critically affected by the ionization state of the drug, i. e. by the pH. Thus, the rate at which the interaction proceeds is increased nearly 15-fold when the pH of the medium increases from 7.0 to 8.3, regardless of the surface charge of the liposomes. On this basis, and taking into account the fact that the anthracyclines enter the cells by passive diffusion, possible effects of pH on the transport of these drugs through the membranes of tumor cells are discussed. Received: 3 December 1996 / Accepted: 4 July 1997     

NBA1/MERIT40 and BRE interaction is required for the integrity of two distinct deubiquitinating enzyme BRCC36-containing complexes

BRCC36-deubiquitinating enzyme (DUB) forms two different complexes through interactions with two different adaptor proteins Abraxas and ABRO1 in cells. Abraxas mainly localizes in the nucleus, mediating the interaction of BRCC36 with BRCA1. ABRO1 is mainly localized in the cytoplasm. Because it lacks the BRCA1-interacting motif, the ABRO1 complex does not interact with BRCA1. Both BRCC36-containing complexes contain common components including BRE and NBA1/MERIT40. Here, we found that the two complexes are assembled in a similar manner and NBA1 and BRE interaction is critical for maintaining the integrity of both of the complexes. Knockdown of NBA1 or BRE leads to decreased levels of components of the two BRCC36-containing complexes. We provided evidence that NBA1 interacts with BRE through a C-terminal conserved motif of the NBA1 protein and a C-terminal UEV domain of the BRE protein. Furthermore, the NBA1-BRE interaction is required for cellular resistance to ionizing irradiation and NBA1's role in recruiting BRCA1 to DNA damage sites. Together, these studies reveal critical interactions required for the formation and function of BRCC36-containing DUB complexes.     

Signal reliability compromised by genotype-by-environment interaction and potential mechanisms for its preservation

Sexual selection based on signaling requires that signals used by females in mate choice are reliable indicators of a male's heritable total fitness. A signal and the preference for it are expected to be heritable, resulting in the maintenance of genetic covariance between these two traits. However, a recent article has proposed that signals may quickly become unreliable in the presence of both environmental variation and genotype-by-environment interaction (G x E) with crossing reaction norms, potentially compromising the mechanisms of sexual selection. Here we examine the heritability and plasticity of a male dominance advertisement in the bank vole, Clethrionomys glareolus, in stable and changing rearing environments from father to son. The bank vole is naturally exposed to considerable sources of spatial and temporal environmental variation and male reproductive success is determined by both intra- (male-male competition) and inter- (females prefer to mate with dominant males) sexual selection. Significant G x E for male dominance was found with crossing reaction norms. Plasma testosterone level (T), rather than condition, determined a male's dominance and T also showed a significant G x E. Dominance showed a considerable plasticity across environments, but was only heritable under stable conditions. We document a negative between-environments correlation of male dominance, suggesting that when the environment changes between father and son, the dominance signal is unreliable to females and sexual selection may be compromised. We discuss how G x E and environmental variation interacting with other mechanisms may preserve the reliability of signals and thus the mechanism of sexual selection itself.     

Heritability of and correlations among genotype-by-environment stability statistics for grain yield in bread wheat

Several genotype-by-environment stability measures are in use, but little information exists about their inheritance or genetic inter-relationships. Among those measures in common use are the linear regression coefficient (b), deviations from regression (s_b), coefficient of determination (R²), coefficient of phenotypic variation (CPV) and, more recently, interaction principal components (IPCA) of the additive-main-effect-and-multiplicative-interaction (AMMI) model. Because of the factorial structure of the data, the diallel cross is well suited to study these parameters and their relationship to quantitative traits. For this study a complete diallel cross, derived by mating eight lines from a broad based bread wheat breeding population, was grown for several growing seasons at two Ugandan locations, one of which was prone to yellow rust. Stability parameters and grain yield were measured for each cross. CPV had the highest narrow-sense heritability (h²=0.522) followed by IPCA1 of the AMMI (h²=0.461). Lowest narrow-sense heritabilities were calculated for b and R² (h²=0.150 and 0.100 respectively). There were high additive genetic correlations (r_A) between grain yield and CPV (r_A=−0.933), grain yield and IPCA1 (r_A=0.707), and grain yield and IPCA2 (r_A=0.751). The genetic association between CPV and IPCA1 was also high and negative (r_A= −0.934). These results suggest that it may be possible to select simultaneously for high and stable grain yield in this broad-based bread wheat breeding pool by selecting outyielders that exhibit a low CPV. Received: 25 July 2000 / Accepted: 7 December 2000     

Heterogeneity ratio: a measure of beta-diversity and its use in community classification

Fifteen previously proposed similarity indices are examined for the effects of sample size and/or group size (the number of samples included in a cluster). The three indices ofCλ,NESS, andC′λ are free from effects, but the former two are unsuitable for arithmetic averaging unless all of the sample sizes are equal. Thus clustering usingC′λ is found to be superior to the combination of any other similarity index and the group-average strategy. Unfortunately none of these measures have the desirable property of measuring the difference in component species among samples independent of the alpha-diversity. A new index of similarity (HR) is developed based on the assumption that community from which samples are taken is described by a logseries distribution. This new index measures the beta-diversity among samples without the influence of sample size and group size, and has the advantage that the significance of fusing samples can statistically be tested. An example clustering withHR is shown and compared with those obtained by other clustering strategies.     

Glycosaminoglycan interaction networks and databases

Glycosaminoglycans are complex polysaccharides exhibiting a large structural and conformational diversity. These key biological players organize the extracellular matrix, contribute to cell–matrix interactions, and regulate cell signaling. Natural and synthetic libraries of glycosaminoglycans have been spotted on microarrays to find glycosaminoglycan partners and determine the size and the chemical groups promoting protein binding. Advances in glycosaminoglycan sequencing allow the characterization of glycosaminoglycan sequences interacting with proteins, and glycosaminoglycan-mediated pull-down proteomics can identify glycosaminoglycan-binding proteins at a proteome scale in various biological samples. The analysis of the glycosaminoglycan interaction networks generated using these data gives insights into the molecular and cellular mechanisms underlying glycosaminoglycan functions. These interactomes can also be used to design inhibitors targeting specific GAG interactions for therapeutic purpose.     

Patterns of additive genotype-by-environment interaction in tree height of Norway spruce in southern and central Sweden

Genotype-by-environment (G × E) interaction for tree height measured at ages 7 to 13 was investigated in 20 large open-pollinated progeny trials for Norway spruce (Picea abies (L.) H. Karst.) in southern and central Sweden. Factor analytic method using spatially adjusted data and a reduced animal model was used to explore the pattern of G × E interaction. Extended factor analyses captured 93.0% of additive G × E interaction variances using three factors. The mean daily temperature less than 3.2 °C in May and June explained 27.8% G × E interaction, and it was moderately correlated with the first factor, indicating that spring or autumn frost weather condition could be a main driver for G × E interaction in Norway spruce. Cluster analysis has divided 20 trials into either 6 clusters or 3 clusters. Both sets of clusters reflected the geography of the trials (climates) and the genetic connectedness among testing series, indicating that more trials with better connectedness are required to examine whether current delineation of breeding or seed zones is optimal. Parental stability using latent regression could be used to locate best parents that have the highest breeding values and are highly stable across trials.     

Stabilization of phosphatidylinositol 4-kinase type IIbeta by interaction with Hsp90

Mammalian cells express two isoforms of type II phosphatidylinositol 4-kinase: PI4KIIα and PI4KIIβ. PI4KIIα exists almost exclusively as a constitutively active integral membrane protein because of its palmitoylation (Barylko, B., Gerber, S. H., Binns, D. D., Grichine, N., Khvotchev, M., Südhof, T. C., and Albanesi, J. P. (2001) J. Biol. Chem. 276, 7705-7708). In contrast, PI4KIIβ is distributed almost evenly between membranes and cytosol. Whereas the palmitoylated membrane-bound pool is catalytically active, the cytosolic kinase is inactive (Wei, Y. J., Sun, H. Q., Yamamoto, M., Wlodarski, P., Kunii, K., Martinez, M., Barylko, B., Albanesi, J. P., and Yin, H. L. (2002) J. Biol. Chem. 277, 46586-46593; Jung, G., Wang, J., Wlodarski, P., Barylko, B., Binns, D. D., Shu, H., Yin, H. L., and Albanesi, J. P. (2008) Biochem. J. 409, 501-509). In this study, we identify the molecular chaperone Hsp90 as a binding partner of PI4KIIβ, but not of PI4KIIα. Geldanamycin (GA), a specific Hsp90 inhibitor, disrupts the Hsp90-PI4KIIβ interaction and destabilizes PI4KIIβ, reducing its half-life by 40% and increasing its susceptibility to ubiquitylation and proteasomal degradation. Cytosolic PI4KIIβ is much more sensitive to GA treatment than is the integrally membrane-associated species. Exposure to GA induces a partial redistribution of PI4KIIβ from the cytosol to membranes and, with brief GA treatments, a corresponding increase in cellular phosphatidylinositol 4-kinase activity. Stimuli such as PDGF receptor activation that also induce recruitment of the kinase to membranes disrupt the Hsp90-PI4KIIβ interaction to a similar extent as GA treatment. These results support a model wherein Hsp90 interacts predominantly with the cytosolic, inactive pool of PI4KIIβ, shielding it from proteolytic degradation but also sequestering it to the cytosol until an extracellular stimulus triggers its translocation to the Golgi or plasma membrane and subsequent activation.     

Condition-dependence,genotype-by-environment interactions and the lek paradox

The lek paradox states that maintaining genetic variation necessary for 'indirect benefit' models of female choice is difficult, and two interrelated solutions have been proposed. 'Genic capture' assumes condition-dependence of sexual traits, while genotype-by-environment interactions (GEIs) offer an additional way to maintain diversity. However, condition-dependence, particularly with GEIs, implies that environmental variation can blur the relationship between male displays and offspring fitness. These issues have been treated separately in the past. Here we combine them in a population genetic model, and show that predictions change not only in magnitude but also in direction when the timing of dispersal between environments relative to the life cycle is changed. GEIs can dramatically improve the evolution of costly female preferences, but also hamper it if much dispersal occurs between the life history stage where condition is determined and mating. This situation also arises if selection or mutation rates are too high. In general, our results highlight that when evaluating any mechanism promoted as a potential resolution of the lek paradox, it is not sufficient to focus on its effects on genetic variation. It also has to be assessed to what extent the proposed mechanism blurs the association between male attractiveness and offspring fitness; the net balance of these two effects can be positive or negative, and often strongly context-dependent.     

Condition-dependence, genotype-by-environment interactions and the lek paradox

The lek paradox states that maintaining genetic variation necessary for ‘indirect benefit’ models of female choice is difficult, and two interrelated solutions have been proposed. ‘Genic capture’ assumes condition-dependence of sexual traits, while genotype-by-environment interactions (GEIs) offer an additional way to maintain diversity. However, condition-dependence, particularly with GEIs, implies that environmental variation can blur the relationship between male displays and offspring fitness. These issues have been treated separately in the past. Here we combine them in a population genetic model, and show that predictions change not only in magnitude but also in direction when the timing of dispersal between environments relative to the life cycle is changed. GEIs can dramatically improve the evolution of costly female preferences, but also hamper it if much dispersal occurs between the life history stage where condition is determined and mating. This situation also arises if selection or mutation rates are too high. In general, our results highlight that when evaluating any mechanism promoted as a potential resolution of the lek paradox, it is not sufficient to focus on its effects on genetic variation. It also has to be assessed to what extent the proposed mechanism blurs the association between male attractiveness and offspring fitness; the net balance of these two effects can be positive or negative, and often strongly context-dependent.     

Interaction of an anionic surfactant with a recombinant cutinase from Fusarium solani pisi: a spectroscopic study

Structural effects resulting from the interaction of the anionic surfactant sodium bis[2-ethylhexyl]ester sulfosuccinic acid (AOT) with a recombinant cutinase are studied and characterised by means of spectroscopic techniques. Levels of interaction are described in terms of surfactant to protein molar ratio (MR). Three major regions may be identified: MR=0–10, MR=10–30 and MR>30. The latter corresponds to co-operative binding of the surfactant to protein leading to overall denaturation as observed by far-UV circular dichroism (CD) and 8-anilino-1-naphtalene-sulfonic acid (1,8-ANS) fluorescence. For MR=10–30, steady-state fluorescence suggests slight conformational changes while near-UV CD shows almost complete loss of signal for the chromophore residues. Finally, the first level, MR=0–10, reveals two distinct effects of interaction. For very low MR (0–5), the protein seems to remain structurally intact. However, at MR=10, both near-UV CD and unfolding kinetics reveal a structurally disturbed protein contrary to steady-state fluorescence spectra. This suggests that AOT interacts specifically with cutinase at this level, through electrostatic interactions mostly. By promoting localised disruption or destabilisation of crucial native electrostatic interactions, the surfactant initiates conformational loss of tertiary structure, leading to higher denaturation as MR increases.     

Yield stability and population diversity in oats (Avena sp.)

Summary The relationship between yield stability and populations containing various numbers and combinations of diverse homozygous and homogeneous lines was examined in an environment in which considerable variability occurs among and within growing seasons. Two groups (1,2), each containing 15 populations (4 pure lines grown singly and 11 multilines consisting of mechanical mixtures of all possible 2,3 and 4 way combinations of these 4 pure lines) were tested in each of 5 consecutive years. The pure lines in group 1 and 2 were selected on the basis of previous yield and yield variability respectively. In group 1, no significant differences were found among the 5 year means or the deviation mean squares of the 15 populations but highly significant differences among regression coefficients were present. The regression coefficients of the 4 pure lines differed considerably, indicating that this stability parameter was genetically influenced. The regression coefficients of the multilines tended towards unity regardless of the regression coefficients of the pure lines involved. In group 2, highly significant differences were found among the 5 year means, regression coefficients and deviation mean squares of the 15 populations. No consistent, predictable pattern was apparent between the mean and stability values of the pure lines and the multilines in which they were included. Differences between the 2 groups suggest that higher yield and greater stability result in the multilines if relatively high yielding pure lines are selected for inclusion. In general, the results indicated that multilines containing a number of diverse homozygous and homogeneous pure lines have satisfactory yields and enhanced yield stability. However, adequate testing of the pure lines and potential multilines over a broad range of environments is essential to determine desirable combinations.     

Interdomain Hydrophobic Interactions Modulate the Thermostability of Microbial Esterases from the Hormone-Sensitive Lipase Family

Microbial hormone-sensitive lipases (HSLs) contain a CAP domain and a catalytic domain. However, it remains unclear how the CAP domain interacts with the catalytic domain to maintain the stability of microbial HSLs. Here, we isolated an HSL esterase, E40, from a marine sedimental metagenomic library. E40 exhibited the maximal activity at 45 °C and was quite thermolabile, with a half-life of only 2 min at 40 °C, which may be an adaptation of E40 to the permanently cold sediment environment. The structure of E40 was solved to study its thermolability. Structural analysis showed that E40 lacks the interdomain hydrophobic interactions between loop 1 of the CAP domain and α7 of the catalytic domain compared with its thermostable homologs. Mutational analysis showed that the introduction of hydrophobic residues Trp²⁰² and Phe²⁰³ in α7 significantly improved E40 stability and that a further introduction of hydrophobic residues in loop 1 made E40 more thermostable because of the formation of interdomain hydrophobic interactions. Altogether, the results indicate that the absence of interdomain hydrophobic interactions between loop 1 and α7 leads to the thermolability of E40. In addition, a comparative analysis of the structures of E40 and other thermolabile and thermostable HSLs suggests that the interdomain hydrophobic interactions between loop 1 and α7 are a key element for the thermostability of microbial HSLs. Therefore, this study not only illustrates the structural element leading to the thermolability of E40 but also reveals a structural determinant for HSL thermostability.     

Investigations on the role of π–π interactions and π–π networks in eNOS and nNOS proteins

π–π Interactions play an important role in the stability of protein structures. In the present study, we have analyzed the influence of π–π interactions in eNOS and nNOS proteins. The contribution of these π–π interacting residues in sequential separation, secondary structure involvement, solvent accessibility and stabilization centers has been evaluated. π–π interactions stabilize the core regions within eNOS and nNOS proteins. π–π interacting residues are evolutionary conserved. There is a significant number of π–π interactions in spite of the lesser natural occurrences of π-residues in eNOS and nNOS proteins. In addition to π–π interactions, π residues also form π–π networks in both eNOS and nNOS proteins which might play an important role in the structural stability of these protein structures.     

中国种子植物区系定量化研究 V．区系相似性

本文总结了应用相似系数即关联系数进行植物区系相似性分析的现状,指出了存在的问题．然后,从集合论角度讨论了区系相似性、相似关系及其相似系数的实质．作者以为在区系相似性分析中应用Ｒ．Ｒ．Ｓｏｋａｌ和Ｃ．Ｄ．Ｍｉｃｈｅｎｅｒ（１９５８）提出的简单匹配系数比较适宜,同时亦能避免以往区系相似性分析中缺乏可比性及某些“表相”相似等问题．最后,还提出了总体相似系数和类型相似系数二个新概念,以便按照吴征镒教授关于中国植物区系研究的学术思想统一研究各个不同地区植物区系的相似性．对此,作者用了６个区系实例进行了演算说明．     

广东南岭自然保护区堇菜属植物垂直分布格局的研究

在南岭自然保护区核心区选择海拔高度为500—600m、600—800m、800—1000m、1000—1200m、1200—1400m、1400—1600m、1600—1800m、1800—1902m共8个连续的海拔梯度,分别对植物群落中的堇菜属植物进行普查。结果表明,随着海拔升高,各海拔段有堇菜属植物5、8、9、10、9、7、3、1种,以中海拔段的物种多样性较高。两海拔段间距离越近,物种相似性系数越大;距离越远,相似性系数越小。在中海拔段,堇菜属植物种类的多度最大,两端较小。南岭自然保护区堇菜属植物的垂直分布格局呈“中间膨胀型”或“单峰型”,与普遍的木本植物一致,这种格局可能是与沿海拔水热梯度的变化相关。