Evolution of genetic variation for condition-dependent traits in stalk-eyed flies

Sexual selection has been proposed to increase genetic variation for condition-dependent ornaments. The condition capture model predicts the genetic variance for a sexually selected trait from the genetic variance in condition and the slope of the relationship between the ornament and condition. Assuming that body size reflects condition we assess the efficacy of this model using six species of stalk-eyed flies (Diopsidae). Prior evidence indicates that male eye span exhibits strong condition dependence and is under sexual selection in sexually dimorphic but not monomorphic species. In contrast, thorax width is weakly related to condition and probably under stabilizing selection. We estimated additive genetic variances for eye span, body length and thorax width from half-sib breeding studies and found that the condition capture model explained 97% of the variation in eye span genetic variance but only 7% of thorax width genetic variance. Comparison of phylogenetically independent contrasts revealed that evolutionary change in male eye span genetic variance is due to evolutionary change in the allometric relationship between eye span and condition: not to evolutionary change in genetic variance for condition. These results suggest that sexual selection can accelerate evolutionary change in condition-dependent male ornaments by increasing the genetic variation available for selection.     

Mapping QTL for agronomic traits in breeding populations

Detection of quantitative trait loci (QTL) in breeding populations offers the advantage that these QTL are of direct relevance for the improvement of crops via knowledge-based breeding. As phenotypic data are routinely generated in breeding programs and the costs for genotyping are constantly decreasing, it is tempting to exploit this information to unravel the genetic architecture underlying important agronomic traits in crops. This review characterizes the germplasm from breeding populations available for QTL detection, provides a classification of the different QTL mapping approaches that are available, and highlights important considerations concerning study design and biometrical models suitable for QTL analysis.     

Monitoring and managing genetic variation in group breeding populations without individual pedigrees

The genetic management of captive populations to conserve genetic variation is currently based on analyses of individual pedigrees to infer inbreeding and kinship coefficients and values of individuals as breeders. Such analyses require that individual pedigrees are known and individual pairing (mating) can be controlled. Many species in captivity, however, breed in groups due to various reasons, such as space constraints and fertility considerations for species living naturally in social groups, and thus have no pedigrees available for the traditional genetic analyses and management. In the absence of individual pedigree, such group breeding populations can still be genetically monitored, evaluated and managed by suitable population genetics models using population level information (such as census data). This article presents a simple genetic model of group breeding populations to demonstrate how to estimate the genetic variation maintained within and among populations and to optimise management based on these estimates. A numerical example is provided to illustrate the use of the proposed model. Some issues relevant to group breeding, such as the development and robustness evaluation of the population genetics model appropriate for a particular species under specific management and recording systems and the genetic monitoring with markers, are also briefly discussed.     

Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations

Though epistasis has long been postulated to have a critical role in genetic regulation of important pathways as well as provide a major source of variation in the process of speciation, the importance of epistasis for genomic selection in the context of plant breeding is still being debated. In this paper, we report the results on the prediction of genetic values with epistatic effects for 280 accessions in the Nebraska Wheat Breeding Program using adaptive mixed least absolute shrinkage and selection operator (LASSO). The development of adaptive mixed LASSO, originally designed for association mapping, for the context of genomic selection is reported. The results show that adaptive mixed LASSO can be successfully applied to the prediction of genetic values while incorporating both marker main effects and epistatic effects. Especially, the prediction accuracy is substantially improved by the inclusion of two-locus epistatic effects (more than onefold in some cases as measured by cross-validation correlation coefficient), which is observed for multiple traits and planting locations. This points to significant potential in using non-additive genetic effects for genomic selection in crop breeding practices.     

Heritabilities and genetic correlations for estimated growth curve parameters in maritime pine

Height growth curves and several other characters were measured in five maritime pine (Pinus pinaster Ait) progeny tests aged from 18 to 27 years (about half the rotation age), with sample sizes of 272–1555 trees. These curves were fitted with a reparametrized Lundqvist-Matèrn sigmoidal growth function with global estimation of two of the four parameters. Each curve was characterized by two parameters:

the maximal growth rate (r), approximately proportional to the stem height at age 16 years, and essentially determined by the height increments around age 6 years.

the asymptote (A), which is an extrapolation of growth after the measurement age. A is essentially determined by the latter growth period (around age 20 years), and is also related to the shape of the observed curve.

The modelling framework appeared to be well suited to the characteristics of the data studied, and the estimation standard errors of the parameters were reasonably low. The heritabilities yielded for the growth curve parameters were high, similar to the heritabilities of cumulative heights. The genetic correlation between r and A was low, pointing to a poor juvenile-mature correlation. Discrepancies from one trial to another in heritabilities and in the correlation pattern were observed, they probably originated from environmental stresses. Maritime pine is actually selected using height and butt angle of lean at age 10 years as criteria. Improvements in the breeding program are suggested.     

Among-population variation and plasticity to drought of Atlantic,Mediterranean, and interprovenance hybrid populations of maritime pine

Maritime pine grows naturally under a wide range of climatic conditions, from strongly Atlantic to strongly Mediterranean. Aiming to improve our understanding of the genetic structure and inheritance of drought resistance strategies in the species, we conducted an environmentally controlled experiment to assess the genetic variation and plasticity to drought of Atlantic and Mediterranean populations, and the interprovenance hybrids between them. Hybridization could also help to provide new genetic material for use in transitional areas between the two regions, for which reproductive materials of good quality are generally lacking. Plastic responses to water stress appeared to be highly conserved among populations, with a common conservative isohydric strategy based on promoting growth when water was abundant, and stopping it when water became limiting. We found, however, a strong intraspecific variation in biomass allocation patterns. The Atlantic populations showed a risky growth-based strategy with a larger amount of juvenile needles, whereas Mediterranean populations showed a more conservative strategy, minimizing aerial growth and increasing the proportion of adult needles that is more resistant to water loss. Hybrid populations performed more similarly to the Mediterranean parent, suggesting a dominance of the Mediterranean-like characteristics. Some of the tested hybrid populations, however, combined high growth with traits of drought adaptation, and thus represent potentially interesting materials for use in transitional regions between the two climate zones.     

Maintenance of genetic variation in quantitative traits of a woodland rodent during generations of captive breeding

Breeding programs to conserve diversity are predicated on the assumption that genetic variation in adaptively important traits will be lost in parallel to the loss of variation at neutral loci. To test this assumption, we monitored quantitative traits across 18 generations of Peromyscus leucopus mice propagated with protocols that mirror breeding programs for threatened species. Ears, hind feet, and tails became shorter, but changes were reversible by outcrossing and therefore were due to accumulated inbreeding. Heritability of ear length decreased, because of an increase in phenotypic variance rather than the expected decrease in additive genetic variance. Additive genetic variance in hind foot length increased. This trait initially had low heritability but large dominance or common environmental variance contributing to resemblance among full-sibs. The increase in the additive component indicates that there was conversion of interaction variances to additive variance. For no trait did additive genetic variation decrease significantly across generations. These findings indicate that the restructuring of genetic variance that occurs with genetic drift and novel selection in captivity can prevent or delay the loss of phenotypic and heritable variation, providing variation on which selection can act to adapt populations to captivity and perhaps later to readapt to more natural habitats after release. Therefore, the importance of minimizing loss of gene diversity from conservation breeding programs for threatened wildlife species might lie in preventing immediate reduction in individual fitness due to inbreeding and protecting allelic diversity for long-term evolutionary change, more so than in protecting variation in quantitative traits for rapid re-adaptation to wild environments.     

Investigating successive Australian barley breeding populations for stable resistance to leaf rust

Key message

Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene Rph20 to provide stable leaf rust resistance across environments.

Abstract

Stable resistance to barley leaf rust (BLR, caused by Puccinia hordei) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with Rph20 to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene Rph20 was the only active resistance region consistently detected across BPs. Of the QTL identified, RphQ27 on chromosome 6HL was considered the best candidate for pairing with Rph20. RphQ27 did not align or share proximity with known genes and was detected in three of the four BPs. The combination of RphQ27 and Rph20 was of low frequency in the breeding material; however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across diverse environments.

     

Clonal variation for shoot ontogenetic heteroblasty in maritime pine (Pinus pinaster Ait.)

Pine seedling shoots undergo sharp heteroblastic changes during the early ontogenetic stages. The rate of these changes has been seen to vary between species and provenances within species, but there is a marked lack of information about its genetic control at the lower hierarchical levels. We used clonal replicates of maritime pine to determine broad-sense heritability of shoot ontogenetic heteroblasty and its correlation to rooting ability. We applied a simple ontogenetic index based on the proportion of basal nodes with secondary needles in rooted cuttings of 15 clones from 9 environmentally contrasting origins. We found a high clonal heritability for shoot ontogenetic index and a moderately high heritability for rooting ability, but both genetic and phenotypic correlations between these two traits were weak and non-significant. These results indicate that both developmental phenomena are genetically controlled, but not strictly associated in this species.     

Molecular diversity of sunflower populations maintained as genetic resources is affected by multiplication processes and breeding for major traits

Key message

SNP genotyping of 114 cultivated sunflower populations showed that the multiplication process and the main traits selected during breeding of sunflower cultivars drove molecular diversity of the populations.

Abstract

The molecular diversity in a set of 114 cultivated sunflower populations was studied by single-nucleotide polymorphism genotyping. These populations were chosen as representative of the 400 entries in the INRA collection received or developed between 1962 and 2011 and made up of land races, open-pollinated varieties, and breeding pools. Mean allele number varied from 1.07 to 1.90. Intra-population variability was slightly reduced according to the number of multiplications since entry but some entries were probably largely homozygous when received. A principal component analysis was used to study inter-population variability. The first 3 axes accounted for 17% of total intra-population variability. The first axis was significantly correlated with seed oil content, more closely than just the distinction between oil and confectionary types. The second axis was related to the presence or absence of restorer genes and the third axis to flowering date and possibly to adaptation to different climates. Our results provide arguments highlighting the effect of the maintenance process on the within population genetic variability as well as on the impact of breeding for major agronomic traits on the between population variability of the collection. Propositions are made to improve sunflower population maintenance procedures to keep maximum genetic variability for future breeding.

     

Water-deficit-responsive proteins in maritime pine

We have isolated three receptor-like kinase cDNAs from an Arabidopsis flower cDNA library by PCR using degenerate oligonucleotide primers for conserved domains of protein kinases. Cloning and sequencing of the full-length cDNAs, designated RKF1 to 3 (receptor-like kinase in flowers), showed that the putative extracellular domain of the RKF1 protein contains 13 tandem repeats of leucine-rich sequences and those of RKF2 and RKF3 have no significant homology with other plant sequences. RNA blot analysis revealed that the RKF1 mRNA is highly expressed in stamens while RKF2 and RKF3 mRNAs are present at low levels in all organs examined. In situ localization experiments indicated that the RKF1 mRNA is detectable in early flower primordia and during stamen development. In addition, when fused to a GUS reporter gene, the RKF1 promoter directed high GUS expression in pollen grains. Recombinant RKF1, produced in Escherichia coli, was found to have kinase activity with serine/threonine specificity in vitro.     

Genetic variation of pine in natural Crimean populations and in artificial populations in Krivbass

The comparative analysis of the genetic variation in the plantations of Pinus pallasiana D. Don in Krivbass and the Crimean populations has been conducted using the electrophoretic division of isoenzymes of 10 geneenzymous systems, encoded by 23 loci. In the artificial plantations of industrial ecotopes of Krivbass the level of genetic variation has been higher than in natural stands of Pinus pallasiana D. Don. within the range of one microslope in the Mountainous Crimea. The Nei' s genetic distance (Dn) between two regions varied within 0.016 to 0.026.     

Evolution in heterogeneous environments and the potential of maintenance of genetic variation in traits of adaptive significance

The maintenance of genetic variation in traits of adaptive significance has been a major dilemma of evolutionary biology. Considering the pattern of increased genetic variation associated with environmental clines and heterogeneous environments, selection in heterogeneous environments has been proposed to facilitate the maintenance of genetic variation. Some models examining whether genetic variation can be maintained, in heterogeneous environments are reviewed. Genetic mechanisms that constrain evolution in quantitative genetic traits indicate that genetic variation can be maintained but when is not clear. Furthermore, no comprehensive models have been developed, likely due to the genetic and environmental complexity of this issue. Therefore, I have suggested two empirical approaches to provide insight for future theoretical and empirical research. Traditional path analysis has been a very powerful approach for understanding phenotypic selection. However, it requires substantial information on the biology of the study system to construct a causal model and alternatives. Exploratory path analysis is a data driven approach that uses the statistical relationships in the data to construct a set of models. For example, it can be used for understanding phenotypic selection in different environments, where there is no prior information to develop path models in the different environments. Data from Brassica rapa grown in different nutrients indicated that selection changed in the different environments. Experimental evolutionary studies will provide direct tests as to when genetic variation is maintained.     

Levels of genetic variation captured by four descendant populations of pinyon pine (Pinus edulis Engelm.)

An isolated cluster of populations of pinyon pine, Pinus edulis Engelm., was used to study the evolutionary dynamics of the founding of new populations. A large population at Owl Creek Canyon, Colorado, is 150 to 200 km to the north from the main distribution of pinyon pine. The population at Owl Creek was established approximately 450 years ago following long-distance dispersal and it is apparently the source of four tiny descendant populations that have been established in close proximity (5.2–11.2 km) within the last century. Genetic variation was estimated with an electrophoretic survey of proteins. Eight of ten proteins were polymorphic in the analysed populations. The recently established populations showed a reduction in the levels of heterozygosity and a decrease in the mean number of alleles per locus, particularly the two smaller (n<20) and also more distant sites from Owl Creek (Windy Site and Hewlett Gulch).Measures of genetic diversity among populations were consistent with the hypothesis that the four young populations have their source in Owl Creek. In addition, the detected inbreeding might be attributable to the caching of related seeds by birds foraging at the source population. The implications of these results for the management of widespread species, such as pinyon pine, are discussed.     

Integrating candidate gene and quantitative genetic approaches to understand variation in timing of breeding in wild tit populations

Two commonly used techniques for estimating the effect of genes on traits in wild populations are the candidate gene approach and quantitative genetic analyses. However, whether these two approaches measure the same underlying processes remains unresolved. Here, we use these two methods to test whether they are alternative or complementary approaches to understanding genetic variation in the timing of reproduction - a key trait involved in adaptation to climate change - in wild tit populations. Our analyses of the candidate gene Clock show weak correlates with timing variables in blue tits, but no association in great tits, confirming earlier results. Quantitative genetic analyses revealed very low levels of both direct (female) and indirect (male) additive genetic variation in timing traits for both species, in contrast to previous studies on these traits, and much lower than generally assumed. Hence, neither method suggests strong genetic effects on the timing of breeding in birds, and further work should seek to assess the generality of these conclusions. We discuss how differences in the genetic control of traits, species life-history and confounding environmental variables may determine how useful integrating these two techniques is to understand the phenotypic variation in wild populations.     

Patterns of genetic variation in anthropogenically impacted populations

Genetic variation is considered critical for allowing natural populations to adapt to their changing environment, and yet the effects of human disturbance on genetic variation in the wild are poorly understood. Different types of human disturbances may genetically impact natural populations in a predictable manner and so the aim of this study was to provide an overview of these changes using a quantitative literature review approach. I examined both allozyme and microsatellite estimates of genetic variation from peer-reviewed journals, using the mean number of alleles per locus and expected heterozygosity as standardized metrics. Populations within each study were categorized according to the type of human disturbance experienced (“hunting/harvest”, “habitat fragmentation”, or “pollution”), and taxon-specific, as well as time- and context-dependent disturbance effects were considered. I found that human disturbances are associated with weak, but consistent changes in neutral genetic variation within natural populations. The direction of change was dependent on the type of human disturbance experienced, with some forms of anthropogenic challenges consistently decreasing genetic variation from background patterns (e.g., habitat fragmentation), whereas others had no effect (e.g., hunting/harvest) or even slightly increased genetic variation (e.g., pollution). These same measures appeared sensitive to both the time of origin and duration of the disturbance as well. This suggests that the presence or absence, strength, type, as well as the spatial and temporal scale of human disturbance experienced may warrant careful consideration when conservation management plans are formulated for natural populations, with particular attention paid to the effects of habitat fragmentation.     

Quantitative genetic approach for assessing invasiveness: geographic and genetic variation in life-history traits

Predicting the spread of invasive species is a challenge for modern ecology. Although many invasive species undergo genetic bottlenecks during introduction to new areas resulting in a loss of genetic diversity, successful invaders manage to flourish in novel environments either because of pre-adaptations or because important traits contain adaptive variation enabling rapid adaptation to changing conditions. To predict and understand invasion success, it is crucial to analyse these features. We assessed the potential of a well-known invader, the Colorado potato beetle (Leptinotarsa decemlineata), to expand north of its current range in Europe. A short growing season and harsh overwintering conditions are apparent limiting factors for this species’ range. By rearing full-sib families from four geographically distinct populations (Russia, Estonia, Poland, Italy) at two fluctuating temperature regimes, we investigated (a) possible differences in survival, development time, and body size among populations and (b) the amount of adaptive variation within populations in these traits. All populations were able to complete their development in cooler conditions than in their current range. A significant genotype–environment interaction for development time and body size suggests the presence of adaptive genetic variation, indicating potential to adapt to cooler conditions. The northernmost population had the highest survival rates and fastest development times on both temperature regimes, suggesting pre-adaptation to cooler temperatures. Other populations had minor differences in development times. Interestingly, this species lacks the classical trade-off between body size and development time which could have contributed to its invasion potential. This study demonstrates the importance of considering both ecological and evolutionary aspects when assessing invasion risk.