Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes

Organisms producing resting stages provide unique opportunities for reconstructing the genetic history of natural populations. Diapausing seeds and eggs often are preserved in large numbers, representing entire populations captured in an evolutionary inert state for decades and even centuries. Starting from a natural resting egg bank of the waterflea Daphnia, we compare the evolutionary rates of change in an adaptive quantitative trait with those in selectively neutral DNA markers, thus effectively testing whether the observed genetic changes in the quantitative trait are driven by natural selection. The population studied experienced variable and well documented levels of fish predation over the past 30 years and shows correlated genetic changes in phototactic behavior, a predator-avoidance trait that is related to diel vertical migration. The changes mainly involve an increased plasticity response upon exposure to predator kairomone, the direction of the changes being in agreement with the hypothesis of adaptive evolution. Genetic differentiation through time was an order of magnitude higher for the studied behavioral trait than for neutral markers (DNA microsatellites), providing strong evidence that natural selection was the driving force behind the observed, rapid, evolutionary changes.

Genetic effects of kangaroo harvesting

There is concern that the commercial harvest of kangaroos (Macropus spp.) is affecting species fitness and evolutionary potential because the harvest selects for larger individuals, particularly males. This paper reviews the likely effect of selective harvesting on specific traits associated with fitness, including size, and on adaptive genotypes through generalised loss of gene diversity. Heritability for traits associated with fitness is low generally. The intensity of selection imposed by harvesting is low for several reasons: the geographic size of genetic populations is much larger than the harvest localities, which are therefore not closed but open with immigration acting to correct any change in allele frequencies through harvesting; the harvest targets kangaroos above a threshold weight that includes all adult males, not the largest males specifically; larger, older males may not confer significant fitness benefits on offspring; fitness traits are inherited through both sexes while males are targeted predominantly; populations are not at a selective equilibrium because food availability fluctuates, and the fittest is unlikely to be the largest. Comparisons of harvested and unharvested populations do not show any loss of gene diversity as a result of harvesting. The likelihood of a long-term genetic impact of kangaroo harvesting as currently practiced is negligible.

On systems thinking, systems biology and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

The potential of microarrays to assist shrimp breeding and production: a review

The shrimp aquaculture industry is a relatively new livestock industry, having developed over the past 30 years. Thus, it is poised to take advantage of new technologies from the outset of selective breeding programs. This contrasts with long established livestock industries, where there are already highly specialised breeds. This review focuses specifically on the potential application of microarrays to shrimp breeding. Potential applications of microarrays in selective breeding programs are summarised. Microarrays can be used as a rapid means to generate molecular markers for genetic linkage mapping, and genetic maps have been constructed for yeast, Arabidopsis and barley using microarray technology. Microarrays can also be used in the hunt for candidate genes affecting particular traits, leading to development of perfect markers for these traits (i.e. causative mutations). However, this requires that microarray analysis be combined with genetic linkage mapping, and that substantial genomic information is available for the species in question. A novel application of microarrays is to treat gene expression as a quantitative trait in itself and to combine this with linkage mapping to identify quantitative trait loci controlling the levels of gene expression; this approach may identify higher level regulatory genes in specific pathways. Finally, patterns of gene expression observed using microarrays may themselves be treated as phenotypic traits in selection programs (e.g. a particular pattern of gene expression might be indicative of a disease tolerant individual). Microarrays are now being developed for a number of shrimp species in laboratories around the world, primarily with a focus on identifying genes involved in the immune response. However, at present, there is no central repository of shrimp genomic information, which limits the rate at which shrimp genomic research can be progressed. The application of microarrays to shrimp breeding will be extremely limited until there is a shared repository of genomic information for shrimp, and the collective will and resources to develop comprehensive genomic tools for shrimp.

Assumption-free estimation of heritability from genome-wide identity-by-descent sharing between full siblings

The study of continuously varying, quantitative traits is important in evolutionary biology, agriculture, and medicine. Variation in such traits is attributable to many, possibly interacting, genes whose expression may be sensitive to the environment, which makes their dissection into underlying causative factors difficult. An important population parameter for quantitative traits is heritability, the proportion of total variance that is due to genetic factors. Response to artificial and natural selection and the degree of resemblance between relatives are all a function of this parameter. Following the classic paper by R. A. Fisher in 1918, the estimation of additive and dominance genetic variance and heritability in populations is based upon the expected proportion of genes shared between different types of relatives, and explicit, often controversial and untestable models of genetic and non-genetic causes of family resemblance. With genome-wide coverage of genetic markers it is now possible to estimate such parameters solely within families using the actual degree of identity-by-descent sharing between relatives. Using genome scans on 4,401 quasi-independent sib pairs of which 3,375 pairs had phenotypes, we estimated the heritability of height from empirical genome-wide identity-by-descent sharing, which varied from 0.374 to 0.617 (mean 0.498, standard deviation 0.036). The variance in identity-by-descent sharing per chromosome and per genome was consistent with theory. The maximum likelihood estimate of the heritability for height was 0.80 with no evidence for non-genetic causes of sib resemblance, consistent with results from independent twin and family studies but using an entirely separate source of information. Our application shows that it is feasible to estimate genetic variance solely from within- family segregation and provides an independent validation of previously untestable assumptions. Given sufficient data, our new paradigm will allow the estimation of genetic variation for disease susceptibility and quantitative traits that is free from confounding with non-genetic factors and will allow partitioning of genetic variation into additive and non-additive components.

A linkage study of academic skills defined by the Queensland Core Skills Test

This study used genome-wide linkage analysis to detect Quantitative Trait Loci (QTLs) implicated in variation in general academic achievement as measured by the Queensland Core Skills Test (QCST) (Queensland Studies Authority, 2004). Data from 210 families were analysed. While no empirically derived significant or suggestive peaks for general academic achievement were indicated a peak on chromosome 2 was observed in a region where Posthuma et al. (2005) reported significant linkage for Performance IQ (PIQ) and suggestive linkage for Full Scale IQ (FSIQ), and Luciano et al. (this issue) observed significant linkage for PIQ and word reading. A peak on chromosome 18 was also observed approximately 20 cM removed from a region recently implicated in reading achievement. In addition, on chromosomes 2 and 18 peaks for a number of specific academic skills, two of which were suggestive, coincided with the general academic achievement peaks. The findings suggest that variation in general academic achievement is influenced by genes on chromosome 2 which have broad influence on a variety of cognitive abilities.

Analysing diversity in sugarcane resistance gene analogues

As resistance genes have been shown to contain conserved motifs and cluster in many plant genomes, the identification of resistance gene analogues can be used as a strategy for both the discovery of DNA markers linked to disease resistance loci and the map-based cloning of disease resistance genes. Sugarcane suffers from many important diseases and an analysis of resistance gene analogues offers a means to identify DNA markers linked to resistance loci. However, sugarcane has the most complex genome of any crop plant and initially it is important to understand the extent of resistance gene analogue diversity in the sugarcane genome before genetic analysis. We review herein how more than 100 expressed sequence tags with homology to different resistance genes have been identified in sugarcane with many mapped as single-dose restriction fragment length polymorphism markers. Importantly, some of these resistance gene analogues have been shown to be linked to disease resistance genes or disease quantitative trait loci. In an attempt to more efficiently analyse additional resistance gene analogues in sugarcane, we report on experiments aimed at investigating the molecular diversity of several resistance gene analogue families using a modified form of a technique termed Ecotilling. Using Ecotilling, we were able to rapidly detect single nucleotide polymorphisms in fragments amplified by PCR from four different resistance gene analogue families, SoRP1D, SoPTO, SoXa21 and SoHs1pro-1. An analysis of a diverse set of sugarcane varieties, including modern sugarcane cultivars and several S. officinarum and S. spontaneum clones, indicated that all amplicons, apart from SoHs1pro-1, contained significant polymorphism within the gene region studied. However, a comparison among these sugarcane clones, including between the parents of two sugarcane mapping populations, indicated that most polymorphisms were multi-dose, not single-dose, preventing their genetic map location or association with disease susceptibility or resistance from being determined.

Dissecting the complex genetic basis of mate choice

The genetic analysis of mate choice is fraught with difficulties. Males produce complex signals and displays that can consist of a combination of acoustic, visual, chemical and behavioural phenotypes. Furthermore, female preferences for these male traits are notoriously difficult to quantify. During mate choice, genes not only affect the phenotypes of the individual they are in, but can influence the expression of traits in other individuals. How can genetic analyses be conducted to encompass this complexity? Tighter integration of classical quantitative genetic approaches with modern genomic technologies promises to advance our understanding of the complex genetic basis of mate choice.

Genome-wide linkage scan for loci influencing plasma triglycerides

Background: Plasma triglyceride concentration is known to be a significant risk factor for cardiovascular disease (CVD). Previous studies have found that the level of triglycerides is strongly influenced by genetic factors. Methods: To identify quantitative trait loci influencing triglycerides, we conducted a genome-wide linkage scan on data from 485 Australian adult dizygotic twin pairs. Prior to linkage analysis, triglyceride values were adjusted for the effects of covariates including age, sex, time since last meal, time of blood collection (CT) and time to plasma separation. Results: The heritability estimate for ln(triglyceride) adjusted for all above fixed effects was 0.49. The highest multipoint LOD score observed was 2.94 (genome-wide p=0.049) on chromosome 7 (at 65cM). This 7p region contains several candidate genes. Two other regions with suggestive multipoint LOD scores were also identified on chromosome 4 (LOD score=2.26 at 62cM) and chromosome X (LOD score=2.01 at 81cM). Conclusions: The linkage peaks found represent newly identified regions for more detailed study, in particular the significant linkage observed on chromosome 7p13. \ (c) 2006 Elsevier B.V. All rights reserved.

Genetic and environmentally derived variation in the cell wall composition of miscanthus and implications for thermo-chemical conversion

Fifteen Miscanthus genotypes grown in five locations across Europe were analysed to investigate the influence of genetic and environmental factors on cell wall composition. Chemometric techniques combining near infrared reflectance spectroscopy and conventional chemical analyses were used to construct calibration models for determination of acid detergent lignin, acid detergent fibre, and neutral detergent fibre from sample spectra. The developed equations were shown to predict cell wall components with a good degree of accuracy and significant genetic and environmental variation was identified. The influence of nitrogen and potassium fertiliser on the dry matter yield and cell wall composition of M. x giganteus was investigated. A detrimental affect on feedstock quality was observed to result from application of these inputs which resulted in an overall reduction in concentrations of cell wall components and increased accumulation of ash within the biomass. Pyrolysis-gas chromatography-mass spectrometry and thermo-gravimetric analysis indicates that genotypes other than the commercially cultivated M. x giganteus have potential for use in energy conversion processes and in the bio-refining. The yields and quality parameters of the pyrolysis liquids produced from Miscanthus compared favourably with that produced from SRC willow and produced a more stable pyrolysis liquid with a higher lower heating value. Overall, genotype had a more significant effect on cell wall composition than environment. This indicates good potential for dissection of this trait by QTL analysis and also for plant breeding to produce new genotypes with improved feedstock characteristics for energy conversion.

Molecular Typing, Virulence Traits and Antimicrobial Resistance of Diabetic Foot Staphylococci

Diabetes mellitus is a major chronic disease that continues to increase significantly. One of the most important and costly complications of diabetes are foot infections that may be colonized by pathogenic and antimicrobial resistant bacteria, harboring several virulence factors, that could impair its successful treatment. Staphylococcus aureus is one of the most prevalent isolate in diabetic foot infections, together with aerobes and anaerobes.

Banana agronomy – can unravelling the Musa genome help?

Unravelling the Musa genome allows genes and alleles linked to desired traits to be identified. Short stature and early flowering are desirable agronomic features of banana, as they are of bread wheat (Triticum aestivum). In wheat they were achieved through knowledge of the physiology and genetics of vernalization and photoperiod during development. Bananas and plantains have a facultative long-day response to photoperiod, as do wheat and wall cress (Arabidopsis thaliana). Using keyword searches of the genome of Musa acuminata 'Pahang' we found homologues of the genes of either T. aestivum or Arabidopsis that govern responses to vernalization and photoperiod. This knowledge needs to be interpreted in the context of plant development. Bananas have juvenile, mid-vegetative and reproductive phases of development. Leaf and bunch 'clocks' operate concurrently throughout the juvenile and mid-vegetative phases. In the mid-vegetative phase the plant becomes sensitive to photoperiod. Increased sensitivity to photoperiod reduces the overall pace of the bunch clock without affecting the leaf clock. Separation of the clocks changes the link between leaf number and time of flowering. The 'critical' quantitative trait for the time of flowering is the pace of the bunch clock up to bunch initiation. For bunch size it is the duration of the subsequent phase of female hand formation. Plants with either a short juvenile phase or a faster bunch clock in the mid-vegetative phase will produce fewer leaves and bunch early. In turn, independent manipulation of hand number per bunch and/or fruit per hand will provide manageable bunches with appropriate fruit size. Using published data we explore relationships between plant height, leaf number, bunch weight and hand number among bananas and plantains. Identifying and then manipulating the appropriate genes in Musa opens opportunities for earlier flowering, leading to plants with desirable agronomic qualities.

Some problems and errors in cytogenetic biodosimetry

Human radiosensitivity is a quantitative trait that is generally subject to binomial distribution. Individual radiosensitivity, however, may deviate significantly from the mean (by 2-3 standard deviations). Thus, the same dose of radiation may result in different levels of genotoxic damage (commonly measured as chromosome aberration rates) in different individuals. There is significant genetic component in individual radiosensitivity. It is related to carriership of variant alleles of various single-nucleotide polymorphisms (most of these in genes coding for proteins functioning in DNA damage identification and repair); carriership of different number of alleles producing cumulative effects; amplification of gene copies coding for proteins responsible for radioresistance, mobile genetic elements, and others. Among the other factors influencing individual radioresistance are: radioadaptive response; bystander effect; levels of endogenous substances with radioprotective and antimutagenic properties and environmental factors such as lifestyle and diet, physical activity, psychoemotional state, hormonal state, certain drugs, infections and others. These factors may have radioprotective or sensibilising effects. Apparently, there are too many factors that may significantly modulate the biological effects of ionising radiation. Thus, conventional methodologies for biodosimetry (specifically, cytogenetic methods) may produce significant errors if personal traits that may affect radioresistance are not accounted for.

A genome scan for eye color in 502 twin families: Most variation is due to a QTL on chromosome 15q

We have rated eye color on a 3-point scale (1=blue/grey, 2=hazel/green, 3=brown) in 502 twin families and carried out a 5-10 cM genome scan (400-757 markers). We analyzed eye color as a threshold trait and performed multipoint sib pair linkage analysis using variance components analysis in Mx. A lod of 19.2 was found at the marker D15S1002, less than 1 cM from OCA2, which has been previously implicated in eye color variation. We estimate that 74% of variance in eye color liability is due to this QTL and a further 18% due to polygenic effects. However, a large shoulder on this peak suggests that other loci affecting eye color may be telomeric of OCA2 and inflating the QTL estimate. No other peaks reached genome-wide significance, although lods >2 were seen on 5p and 14q and lods >1 were additionally seen on chromosomes 2, 3, 6, 7, 8, 9, 17 and 18. Most of these secondary peaks were reduced or eliminated when we repeated the scan as a two locus analysis with the 15q linkage included, although this does not necessarily exclude them as false positives. We also estimated the interaction between the 15q QTL and the other marker locus but there was only minor evidence for additive x additive epistasis. Elaborating the analysis to the full two-locus model including non-additive main effects and interactions did not strengthen the evidence for epistasis. We conclude that most variation in eye color in Europeans is due to polymorphism in OCA2 but that there may be modifiers at several other loci.

Étude d'un locus pour trait quantitatif de l'hypertension sur le chromosome 3 du rat Dahl Salt-Sensitive

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.