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.     

Phenotypic and genetic analysis of reproductive traits in horse populations with different breeding purposes

Reproductive traits have a major influence on the economic effectiveness of horse breeding. However, there is little information available. We evaluated the use of reproductive traits as selection criteria in official breeding programs to increase the reproductive efficiency of breeding studs, analysing 696 690 records from the pedigree data of eight Spanish horse populations, with different breeding purposes. The reproductive parameters studied in both sexes were age at first foaling (AFF), age at last foaling, average reproductive life and generational interval. In the females, the average interval between foaling (AIF) and interval between first and second foaling were also studied. There were clear differences between sexes and breeds, which may be due to management practices, breeding purposes and the status of the populations, rather than to differences in actual physiological conditions. Riding mares were the most precocious (AFF, 1937.64 to 2255.69 days) and had a more intensive reproductive use (AIF, 625.83 to 760.07 days), whereas sires used for meat production were the most precocious males (AFF, 1789.93 to 1999.75 days), although they had a shorter reproductive life (1564.34 to 1797.32 days). Heritabilities (0.02 to 0.42 in females and 0.04 to 0.28 in males) evidenced the genetic component of the reproductive traits, with Sport Horses having the higher average values. These results support the selection by AFF to improve reproductive aspects because of its medium–high heritability and its positive correlations with other important reproductive traits. The inclusion of the AIF is also recommended in sport populations, because this determines the length of the breaks between foaling and conditions the reproductive performance of the dams, as well as their selective intensity, genetic gain and genetic improvement. It is therefore an important economic parameter in breeding studs.     

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.     

Somatic embryogenesis from different tissues of Spanish populations of maritime pine

The somatic embryogenesis (SE) capacity of megagametophytes belonging to Continental and Mediterranean Spanish provenances of maritime pine (Pinus pinaster Aiton) was studied, noting factors (megagametophyte developmental stage and culture medium) that enhanced the induction and establishment of SE lines. In both provenances, initiation and establishment of embryogenic calli was higher on megagametophytes in which the dominant zygotic embryo had begun to develop. In the Mediterranean provenance, however, SE lines were also established from megagametophytes enclosing zygotic embryos with well-developed cotyledons. A modified Litvay medium (mLV) containing 9.9???M 2,4-dichlorophenoxyacetic acid (2,4-D) and 4.4???M 6-benzyladenine (BA) was superior to DCR medium containing 13.6???M 2,4-D and 4.4???M BA for SE induction, but there were no differences between media in terms of the number of SE lines established after 4?months in culture (153 vs. 155 established SE lines, for mLV and DCR media respectively). Of the 26 embryogenic lines tested for maturation, 15 (58?%) produced cotyledonary somatic embryos and 75?% of these gave rise to plants on germination medium. SE-like cultures from adult maritime pine trees were also initiated, but embryogenic lines could not be established. This is the first report on the production of SE in maritime pine of Continental and Mediterranean origin. The micropropagation protocols presented here provide an important tool for the vegetative multiplication of selected families and breeding programs for maritime pines from Spain.     

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.

     

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.     

The genetic architecture of sexually selected traits in two natural populations of Drosophila montana

We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power.     

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.

     

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.     

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.     

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.