Shared quantitative trait loci underlying the genetic correlation between continuous traits

Detecting natural selection in trait-trait coevolution

No phenotypic trait evolves independently of all other traits, but the cause of trait-trait coevolution is poorly understood. While the coevolution could arise simply from pleiotropic mutations that simultaneously affect the traits concerned, it could also result from multivariate natural selection favoring certain trait relationships. To gain a general mechanistic understanding of trait-trait coevolution, we examine the evolution of 220 cell morphology traits across 16 natural strains of the yeast Saccharomyces cerevisiae and the evolution of 24 wing morphology traits across 110 fly species of the family Drosophilidae, along with the variations of these traits among gene deletion or mutation accumulation lines (a.k.a. mutants). For numerous trait pairs, the phenotypic correlation among evolutionary lineages differs significantly from that among mutants. Specifically, we find hundreds of cases where the evolutionary correlation between traits is strengthened or reversed relative to the mutational correlation, which, according to our population genetic simulation, is likely caused by multivariate selection. Furthermore, we detect selection for enhanced modularity of the yeast traits analyzed. Together, these results demonstrate that trait-trait coevolution is shaped by natural selection and suggest that the pleiotropic structure of mutation is not optimal. Because the morphological traits analyzed here are chosen largely because of their measurability and thereby are not expected to be biased with regard to natural selection, our conclusion is likely general.

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection

Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a diverse barley (Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in diverse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.

A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree

Numerous questions in phylogenetic comparative biology revolve around the correlated evolution of two or more phenotypic traits on a phylogeny. In many cases, it may be sufficient to assume a constant value for the evolutionary correlation between characters across all the clades and branches of the tree. Under other circumstances, however, it is desirable or necessary to account for the possibility that the evolutionary correlation differs through time or in different sections of the phylogeny. Here, we present a method designed to fit a hierarchical series of models for heterogeneity in the evolutionary rates and correlation of two quantitative traits on a phylogenetic tree. We apply the method to two datasets: one for different attributes of the buccal morphology in sunfishes (Centrarchidae); and a second for overall body length and relative body depth in rock- and non-rock-dwelling South American iguanian lizards. We also examine the performance of the method for parameter estimation and model selection using a small set of numerical simulations.

Modularity and selection of nectar traits in the evolution of the selfing syndrome in Ipomoea lacunosa (Convolvulaceae)

Although the evolution of the selfing syndrome often involves reductions in floral size, pollen and nectar, few studies of selfing syndrome divergence have examined nectar. We investigate whether nectar traits have evolved independently of other floral size traits in the selfing syndrome, whether nectar traits diverged due to drift or selection, and the extent to which quantitative trait locus (QTL) analyses predict genetic correlations. We use F5 recombinant inbred lines (RILs) generated from a cross between Ipomoea cordatotriloba and Ipomoea lacunosa. We calculate genetic correlations to identify evolutionary modules, test whether trait divergence was due to selection, identify QTLs and perform correlation analyses to evaluate how well QTL properties reflect genetic correlations. Nectar and floral size traits form separate evolutionary modules. Selection has acted to reduce nectar traits in the selfing I. lacunosa. Genetic correlations predicted from QTL properties are consistent with observed genetic correlations. Changes in floral traits associated with the selfing syndrome reflect independent evolution of at least two evolutionary modules: nectar and floral size traits. We also demonstrate directional selection on nectar traits, which is likely to be independent of selection on floral size traits. Our study also supports the expected mechanistic link between QTL properties and genetic correlations.

The genetic basis of the root economics spectrum in a perennial grass

Construction economics of plant roots exhibit predictable relationships with root growth, death, and nutrient uptake strategies. Plant taxa with inexpensively constructed roots tend to more precisely explore nutrient hotspots than do those with costly constructed roots but at the price of more frequent tissue turnover. This trade-off underlies an acquisitive to conservative continuum in resource investment, described as the "root economics spectrum (RES)." Yet the adaptive role and genetic basis of RES remain largely unclear. Different ecotypes of switchgrass (Panicum virgatum) display root features exemplifying the RES, with costly constructed roots in southern lowland and inexpensively constructed roots in northern upland ecotypes. We used an outbred genetic mapping population derived from lowland and upland switchgrass ecotypes to examine the genetic architecture of the RES. We found that absorptive roots (distal first and second orders) were often "deciduous" in winter. The percentage of overwintering absorptive roots was decreased by northern upland alleles compared with southern lowland alleles, suggesting a locally-adapted conservative strategy in warmer and acquisitive strategy in colder regions. Relative turnover of absorptive roots was genetically negatively correlated with their biomass investment per unit root length, suggesting that the key trade-off in framing RES is genetically facilitated. We also detected strong genetic correlations among root morphology, root productivity, and shoot size. Overall, our results reveal the genetic architecture of multiple traits that likely impacts the evolution of RES and plant aboveground-belowground organization. In practice, we provide genetic evidence that increasing switchgrass yield for bioenergy does not directly conflict with enhancing its root-derived carbon sequestration.

Genetic architecture of divergence: the selfing syndrome in Ipomoea lacunosa

PREMISE

Highly selfing plant species frequently display a distinctive suite of traits termed the selfing syndrome. Here we tested the hypothesis that these traits are grouped into correlated evolutionary modules and determined the degree of independence between such modules.

METHODS

We evaluated phenotypic correlations and QTL overlaps in F2 offspring of a cross between the morning glories Ipomoea lacunosa and I. cordatotriloba and investigated how traits clustered into modules at both the phenotypic and genetic level. We then compared our findings to other QTL studies of the selfing syndrome.

RESULTS

In the I. lacunosa selfing syndrome, traits grouped into modules that displayed correlated evolution within but not between modules. QTL overlap predicted phenotypic correlations, and QTLs affecting the same trait module were significantly physically clustered in the genome. The genetic architecture of the selfing syndrome varied across systems, but the pattern of stronger within- than between-module correlation was widespread.

CONCLUSIONS

The genetic architecture we observe in the selfing syndrome is consistent with a growing understanding of floral morphological integration achieved via pleiotropy in clustered traits. This view of floral evolution is consistent with resource limitation or predation driving the evolution of the selfing syndrome, but invites further research into both the selective causes of the selfing syndrome and how genetic architecture itself evolves in response to changes in mating system.

Does geographic variation in thermal tolerance in Daphnia represent trade-offs or conditional neutrality?

Geographic variation in thermal tolerance in Daphnia seems to represent genetic load at the loci specifically responsible for heat tolerance resulting from conditional neutrality. We see no evidence of trade-offs between fitness-related traits at 25 °C vs. 10 °C or between two algal diets across Daphnia magna clones from a variety of locations representing the opposite ends of the distribution of long-term heat tolerance. Likewise, we found no evidence of within-environment trade-offs between heat tolerance and fitness-related traits in any of the environments. Neither short-term and long-term heat tolerance shows any consistent relationship with lipid fluorescence polarization and lipid peroxidation across clones or environments. Pervasive positive correlations between fitness-related traits indicate differences in genetic load rather than trade-off based local adaptation or thermal specialization. For heat tolerance such differences may be caused by either relaxation of stabilizing selection due to lower exposure to high temperature extremes, i.e., conditional neutrality, or by small effective population size followed by the recent range expansion.

The Genetic Architecture of Plant Defense Trade-offs in a Common Monkeyflower

Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a quantitative trait loci (QTL) mapping experiment involving a cross between 2 populations of common monkeyflower (Mimulus guttatus) that differ in growth rate as well as total concentration and arsenal composition of plant defense compounds, phenylpropanoid glycosides (PPGs). We find no evidence that pleiotropy underlies correlations between defense and growth rate. However, there is a strong genetic correlation between levels of total PPGs and flowering time that is largely attributable to a single shared QTL. While this result suggests a role for pleiotropy/close linkage, several other QTLs also contribute to variation in total PPGs. Additionally, divergent PPG arsenals are influenced by a number of smaller-effect QTLs that each underlie variation in 1 or 2 PPGs. This result indicates that chemical defense arsenals can be finely adapted to biotic environments despite sharing a common biochemical precursor. Together, our results show correlations between defense and life-history traits are influenced by pleiotropy or genetic linkage, but genetic constraints may have limited impact on future evolutionary responses, as a substantial proportion of variation in each trait is controlled by independent loci.

Variation in the seasonal germination niche across an elevational gradient: the role of germination cueing in current and future climates

PREMISE

The timing of germination has profound impacts on fitness, population dynamics, and species ranges. Many plants have evolved responses to seasonal environmental cues to time germination with favorable conditions; these responses interact with temporal variation in local climate to drive the seasonal climate niche and may reflect local adaptation. Here, we examined germination responses to temperature cues in Streptanthus tortuosus populations across an elevational gradient.

METHODS

Using common garden experiments, we evaluated differences among populations in response to cold stratification (chilling) and germination temperature and related them to observed germination phenology in the field. We then explored how these responses relate to past climate at each site and the implications of those patterns under future climate change.

RESULTS

Populations from high elevations had stronger stratification requirements for germination and narrower temperature ranges for germination without stratification. Differences in germination responses corresponded with elevation and variability in seasonal temperature and precipitation across populations. Further, they corresponded with germination phenology in the field; low-elevation populations germinated in the fall without chilling, whereas high-elevation populations germinated after winter chilling and snowmelt in spring and summer. Climate-change forecasts indicate increasing temperatures and decreasing snowpack, which will likely alter germination cues and timing, particularly for high-elevation populations.

CONCLUSIONS

The seasonal germination niche for S. tortuosus is highly influenced by temperature and varies across the elevational gradient. Climate change will likely affect germination timing, which may cascade to influence trait expression, fitness, and population persistence.

Insights into the genetic architecture of sexual dimorphism from an interspecific cross between two diverging Silene (Caryophyllaceae) species

The evolution of sexual dimorphism in species with separate sexes is influenced by the resolution of sexual conflicts creating sex differences through genetic linkage or sex-biased expression. Plants with different degrees of sexual dimorphism are thus ideal to study the genetic basis of sexual dimorphism. In this study we explore the genetic architecture of sexual dimorphism between Silene latifolia and Silene dioica. These species have chromosomal sex determination and differ in the extent of sexual dimorphism. To test whether QTL for sexually dimorphic traits have accumulated on the sex chromosomes and to quantify their contribution to species differences, we create a linkage map and performed QTL analysis of life history, flower and vegetative traits using an unidirectional interspecific F2 hybrid cross. We found support for an accumulation of QTL on the sex chromosomes and that sex differences explained a large proportion of the variance between species, suggesting that both natural and sexual selection contributed to species divergence. Sexually dimorphic traits that also differed between species displayed transgressive segregation. We observed a reversal in sexual dimorphism in the F2 population, where males tended to be larger than females, indicating that sexual dimorphism is constrained within populations but not in recombinant hybrids. This study contributes to the understanding of the genetic basis of sexual dimorphism and its evolution in Silene.

Co-inheritance of sea age at maturity and iteroparity in the Atlantic salmon vgll3 genomic region

Co-inheritance in life-history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life-history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around the vgll3 gene, and we used this opportunity demonstrate that these two traits are co-inherited around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturing vgll3 genotype (EE) compared to fish with the late-maturing genotype (LL). The L allele was dominant in individuals remaining only one year at sea before maturation, but the dominance was reversed, with the E allele being dominant in individuals maturing after two or more years at sea. Post hoc analysis indicated that iteroparous fish with the EE genotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, whereas this effect was not detected in fish with the LL genotype. These results broaden the functional link around the vgll3 genome region and help us understand constraints in the evolution of life-history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

A robust (long and thick) root system is characteristic of upland japonica rice adapted to drought conditions. Using deep sequencing and large scale phenotyping data of 795 rice accessions and an integrated strategy combining results from high resolution mapping by GWAS and linkage mapping, comprehensive analyses of genomic, transcriptomic and haplotype data, we identified large numbers of QTLs affecting rice root length and thickness (RL and RT) and shortlisted relatively few candidate genes for many of the identified small-effect QTLs. Forty four and 97 QTL candidate genes for RL and RT were identified, and five of the RL QTL candidates were validated by T-DNA insertional mutation; all have diverse functions and are involved in root development. This work demonstrated a powerful strategy for highly efficient cloning of moderate- and small-effect QTLs that is difficult using the classical map-based cloning approach. Population analyses of the 795 accessions, 202 additional upland landraces, and 446 wild rice accessions based on random SNPs and SNPs within robust loci suggested that there could be much less diversity in robust-root candidate genes among upland japonica accessions than in other ecotypes. Further analysis of nucleotide diversity and allele frequency in the robust loci among different ecotypes and wild rice accessions showed that almost all alleles could be detected in wild rice, and pyramiding of robust-root alleles could be an important genetic characteristic of upland japonica. Given that geographical distribution of upland landraces, we suggest that during domestication of upland japonica, the strongest pyramiding of robust-root alleles makes it a unique ecotype adapted to aerobic conditions.

Asian cultivated rice is well-known for its rich-within-species diversity with two major subspecies, indica and japonica and subpopulation differentiation. A robust (long and thick) root system that is characteristic of upland japonica rice represents a predominant ecotype grown under aerobic and rain-fed conditions. In this study, we identified candidate genes for root length and root thickness, and validated five root length candidates by T-DNA insertional mutations. Further analyses of an Asian cultivated and wild rice population were performed based on random SNPs and SNPs within robust loci. The findings hold promise for application in improving drought resistance and also reveal the adaptive domestication history of upland rice as a unique Asian cultivated rice ecotype.

Construction of an ultrahigh-density genetic linkage map for Jatropha curcas L. and identification of QTL for fruit yield

BACKGROUND

As an important biofuel plant, the demand for higher yield Jatropha curcas L. is rapidly increasing. However, genetic analysis of Jatropha and molecular breeding for higher yield have been hampered by the limited number of molecular markers available.

RESULTS

An ultrahigh-density linkage map for a Jatropha mapping population of 153 individuals was constructed and covered 1380.58 cM of the Jatropha genome, with average marker density of 0.403 cM. The genetic linkage map consisted of 3422 SNP and indel markers, which clustered into 11 linkage groups. With this map, 13 repeatable QTLs (reQTLs) for fruit yield traits were identified. Ten reQTLs, qNF-1, qNF-2a, qNF-2b, qNF-2c, qNF-3, qNF-4, qNF-6, qNF-7a, qNF-7b and qNF-8, that control the number of fruits (NF) mapped to LGs 1, 2, 3, 4, 6, 7 and 8, whereas three reQTLs, qTWF-1, qTWF-2 and qTWF-3, that control the total weight of fruits (TWF) mapped to LGs 1, 2 and 3, respectively. It is interesting that there are two candidate critical genes, which may regulate Jatropha fruit yield. We also identified three pleiotropic reQTL pairs associated with both the NF and TWF traits.

CONCLUSION

This study is the first to report an ultrahigh-density Jatropha genetic linkage map construction, and the markers used in this study showed great potential for QTL mapping. Thirteen fruit-yield reQTLs and two important candidate genes were identified based on this linkage map. This genetic linkage map will be a useful tool for the localization of other economically important QTLs and candidate genes for Jatropha.

A positive genetic correlation between hypoxia tolerance and heat tolerance supports a controversial theory of heat stress

We used quantitative genetics to test a controversial theory of heat stress, in which animals overheat when the demand for oxygen exceeds the supply. This theory, referred to as oxygen- and capacity-limited thermal tolerance, predicts a positive genetic correlation between hypoxia tolerance and heat tolerance. We demonstrate the first genetic correlation of this kind in a model organism, Drosophila melanogaster Genotypes more likely to fly under hypoxic stress (12% O₂) were also more likely to fly under heat stress (39°C). This finding prompts new questions about mechanisms and limits of adaptation to heat stress.

Interacting effects of genetic variation for seed dormancy and flowering time on phenology, life history, and fitness of experimental Arabidopsis thaliana populations over multiple generations in the field

Major alleles for seed dormancy and flowering time are well studied, and can interact to influence seasonal timing and fitness within generations. However, little is known about how this interaction controls phenology, life history, and population fitness across multiple generations in natural seasonal environments. To examine how seed dormancy and flowering time shape annual plant life cycles over multiple generations, we established naturally dispersing populations of recombinant inbred lines of Arabidopsis thaliana segregating early and late alleles for seed dormancy and flowering time in a field experiment. We recorded seasonal phenology and fitness of each genotype over 2 yr and several generations. Strong seed dormancy suppressed mid-summer germination in both early- and late-flowering genetic backgrounds. Strong dormancy and late-flowering genotypes were both necessary to confer a winter annual life history; other genotypes were rapid-cycling. Strong dormancy increased within-season fecundity in an early-flowering background, but decreased it in a late-flowering background. However, there were no detectable differences among genotypes in population growth rates. Seasonal phenology, life history, and cohort fitness over multiple generations depend strongly upon interacting genetic variation for dormancy and flowering. However, similar population growth rates across generations suggest that different life cycle genotypes can coexist in natural populations.

Immunogenomics of gastrointestinal nematode infection in ruminants - breeding for resistance to produce food sustainably and safely

Gastrointestinal nematode (GIN) infection of ruminants represents a major health and welfare challenge for livestock producers worldwide. The emergence of anthelmintic resistance in important GIN species and the associated animal welfare concerns have stimulated interest in the development of alternative and more sustainable strategies aimed at the effective management of the impact of GINs. These integrative strategies include selective breeding using genetic/genomic tools, grazing management, biological control, nutritional supplementation, vaccination and targeted selective treatment. In this review, the logic of selecting for "resistance" to GIN infection as opposed to "resilience" or "tolerance" is discussed. This is followed by a review of the potential application of immunogenomics to genetic selection for animals that have the capacity to withstand the impact of GIN infection. Advances in relevant genomic technologies are highlighted together with how these tools can be advanced to support the integration of immunogenomic information into ruminant breeding programmes.

Genetic dissection of adaptive form and function in rapidly speciating cichlid fishes

Genes of major phenotypic effects and strong genetic correlations can facilitate adaptation, direct selective responses, and potentially lead to phenotypic convergence. However, the preponderance of this type of genetic architecture in repeatedly evolved adaptations remains unknown. Using hybrids between Haplochromis chilotes (thick-lipped) and Pundamilia nyererei (thin-lipped) we investigated the genetics underlying hypertrophied lips and elongated heads, traits that evolved repeatedly in cichlids. At least 25 loci of small-to-moderate and mainly additive effects were detected. Phenotypic variation in lip and head morphology was largely independent. Although several QTL overlapped for lip and head morphology traits, they were often of opposite effects. The distribution of effect signs suggests strong selection on lips. The fitness implications of several detected loci were demonstrated using a laboratory assay testing for the association between genotype and variation in foraging performance. The persistence of low fitness alleles in head morphology appears to be maintained through antagonistic pleiotropy/close linkage with positive-effect lip morphology alleles. Rather than being based on few major loci with strong positive genetic correlations, our results indicate that the evolution of the Lake Victoria thick-lipped ecomorph is the result of selection on numerous loci distributed throughout the genome.

Trait Correlations in the Genomics Era

Thinking about the evolutionary causes and consequences of trait correlations has been dominated by quantitative genetics theory that is focused on hypothetical loci. Since this theory was initially developed, technology has enabled the identification of specific genetic variants that contribute to trait correlations. Here, we review studies of the genetic basis of trait correlations to ask: What has this new information taught us? We find that causal variants can be pleiotropic and/or linked in different ways, indicating that pleiotropy and linkage are not alternative genetic mechanisms. Further, many trait correlations have a polygenic basis, suggesting that both pleiotropy and linkage likely contribute. We discuss implications of these findings for the evolutionary causes and consequences of trait correlations.

High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population

Seeds per silique (SS), seed weight (SW), and silique length (SL) are important determinant traits of seed yield potential in rapeseed (Brassica napus L.), and are controlled by naturally occurring quantitative trait loci (QTLs). Mapping QTLs to narrow chromosomal regions provides an effective means of characterizing the genetic basis of these complex traits. Orychophragmus violaceus is a crucifer with long siliques, many SS, and heavy seeds. A novel B. napus introgression line with many SS was previously selected from multiple crosses (B. rapa ssp. chinesis × O. violaceus) × B. napus. In present study, a doubled haploid (DH) population with 167 lines was established from a cross between the introgression line and a line with far fewer SS, in order to detect QTLs for silique-related traits. By screening with a Brassica 60K single nucleotide polymorphism (SNP) array, a high-density linkage map consisting of 1,153 bins and spanning a cumulative length of 2,209.1 cM was constructed, using 12,602 high-quality polymorphic SNPs in the DH population. The average recombination bin densities of the A and C subgenomes were 1.7 and 2.4 cM, respectively. 45 QTLs were identified for the three traits in all, which explained 4.0-34.4% of the total phenotypic variation; 20 of them were integrated into three unique QTLs by meta-analysis. These unique QTLs revealed a significant positive correlation between SS and SL and a significant negative correlation between SW and SS, and were mapped onto the linkage groups A05, C08, and C09. A trait-by-trait meta-analysis revealed eight, four, and seven consensus QTLs for SS, SW, and SL, respectively, and five major QTLs (cqSS.A09b, cqSS.C09, cqSW.A05, cqSW.C09, and cqSL.C09) were identified. Five, three, and four QTLs for SS, SW, and SL, respectively, might be novel QTLs because of the existence of alien genetic loci for these traits in the alien introgression. Thirty-eight candidate genes underlying nine QTLs for silique-related traits were identified.

Genetic architecture and mechanism of seed number per pod in rapeseed: elucidated through linkage and near-isogenic line analysis

Seed number per pod (SNPP) is one of the major yield components and breeding targets in rapeseed that shows great variation and is invaluable for genetic improvement. To elucidate the genetic architecture and uncover the mechanism of SNPP, we identified five quantitative trait loci (QTLs) using the BnaZNRIL population, which were integrated with those of previous studies by physical map to demonstrate a complex and relatively complete genetic architecture of SNPP. A major QTL, qSN.A6, was successfully fine-mapped from 1910 to 267 kb using near-isogenic line (NIL). In addition, qSN.A6 exhibited an antagonistic pleiotropy on seed weight (SW), which is caused by a physiological interaction in which SNPP acts "upstream" of SW. Because the negative effect of qSN.A6 on SW cannot fully counteract its positive effect on SNPP, it also enhanced the final yield (17.4%), indicating its great potential for utilization in breeding. The following genetic and cytological experiments further confirmed that the different rate of ovule abortion was responsible for the ~5 seed difference between Zhongshuang11 and NIL-qSN.A6. This systematic approach to dissecting the comprehensive genetic architecture of SNPP and characterizing the underlying mechanism has advanced the understanding of SNPP and will facilitate the development of high-yield cultivars.

Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.)

To facilitate the pseudochromosomes assembly and gene cloning in rapeseed, we developed a reference genetic population/map (named BnaZNF2) from two sequenced cultivars, Zhongshuang11 and No.73290, those exhibit significant differences in many traits, particularly yield components. The BnaZNF2 genetic map exhibited perfect collinearity with the physical map of B. napus, indicating its high quality. Comparative mapping revealed several genomic rearrangements between B. napus and B. rapa or B. oleracea. A total of eight and 16 QTLs were identified for pod number and seed number per pod, respectively, and of which three and five QTLs are identical to previously identified ones, whereas the other five and 11 are novel. Two new major QTL respectively for pod number and seed number per pod, qPN.A06-1 and qSN.A06-1 (R(2 )= 22.8% and 32.1%), were colocalised with opposite effects, and only qPN.A06-1 was confirmed and narrowed by regional association analysis to 180 kb including only 33 annotated genes. Conditional QTL analysis and subsequent NILs test indicated that tight linkage, rather than pleiotropy, was the genetic causation of their colocalisation. Our study demonstrates potential of this reference genetic population/map for precise QTL mapping and as a base for positional gene cloning in rapeseed.

Detection of QTL for metabolic and agronomic traits in wheat with adjustments for variation at genetic loci that affect plant phenology

Mapping of quantitative trait loci associated with levels of individual metabolites (mQTL) was combined with the mapping of agronomic traits to investigate the genetic basis of variation and co-variation in metabolites, agronomic traits, and plant phenology in a field-grown bread wheat population. Metabolome analysis was performed using liquid chromatography-mass spectrometry resulting in identification of mainly polar compounds, including secondary metabolites. A total of 558 metabolic features were obtained from the flag leaves of 179 doubled haploid lines, of which 197 features were putatively identified, mostly as alkaloids, flavonoids and phenylpropanoids. Coordinated genetic control was observed for several groups of metabolites, such as organic acids influenced by two loci on chromosome 7A. Five major phenology-related loci, which were introduced as cofactors in the analyses, differed in their impact upon metabolic and agronomic traits with QZad-aww-7A having more impact on the expression of both metabolite and agronomic QTL than Ppd-B1, Vrn-A1, Eps, and QZad-aww-7D. This QTL study validates the utility of combining agronomic and metabolomic traits as an approach to identify potential trait enhancement targets for breeding selection and reinforces previous results that demonstrate the importance of including plant phenology in the assessment of useful traits in this wheat mapping population.

Genetic mapping of natural variation in schooling tendency in the threespine stickleback

Although there is a heritable basis for many animal behaviors, the genetic architecture of behavioral variation in natural populations remains mostly unknown, particularly in vertebrates. We sought to identify the genetic basis for social affiliation in two populations of threespine sticklebacks (Gasterosteus aculeatus) that differ in their propensity to school. Marine sticklebacks from Japan school strongly whereas benthic sticklebacks from a lake in Canada are more solitary. Here, we expanded on our previous efforts to identify quantitative trait loci (QTL) for differences in schooling tendency. We tested fish multiple times in two assays that test different aspects of schooling tendency: 1) the model school assay, which presents fish with a school of eight model sticklebacks; and 2) the choice assay, in which fish are given a choice between the model school and a stationary artificial plant. We found low-to-moderate levels of repeatability, ranging from 0.1 to 0.5, in schooling phenotypes. To identify the genomic regions that contribute to differences in schooling tendency, we used QTL mapping in two types of crosses: benthic × marine backcrosses and an F2 intercross. We found two QTL for time spent with the school in the model school assay, and one QTL for number of approaches to the school in the choice assay. These QTL were on three different linkage groups, not previously linked to behavioral differences in sticklebacks. Our results highlight the importance of using multiple crosses and robust behavioral assays to uncover the genetic basis of behavioral variation in natural populations.

Locally epistatic genomic relationship matrices for genomic association and prediction

In plant and animal breeding studies a distinction is made between the genetic value (additive plus epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this article, we argue that the breeder can take advantage of the epistatic marker effects in regions of low recombination. The models introduced here aim to estimate local epistatic line heritability by using genetic map information and combining local additive and epistatic effects. To this end, we have used semiparametric mixed models with multiple local genomic relationship matrices with hierarchical designs. Elastic-net postprocessing was used to introduce sparsity. Our models produce good predictive performance along with useful explanatory information.

The genetic architecture of coordinately evolving male wing pigmentation and courtship behavior in Drosophila elegans and Drosophila gunungcola

Many adaptive phenotypes consist of combinations of simpler traits that act synergistically, such as morphological traits and the behaviors that use those traits. Genetic correlations between components of such combinatorial traits, in the form of pleiotropic or tightly linked genes, can in principle promote the evolution and maintenance of these traits. In the Oriental Drosophila melanogaster species group, male wing pigmentation shows phylogenetic correlations with male courtship behavior; species with male-specific apical wing melanin spots also exhibit male visual wing displays, whereas species lacking these spots generally lack the displays. In this study, we investigated the quantitative genetic basis of divergence in male wing spots and displays between D. elegans, which possesses both traits, and its sibling species D. gunungcola, which lacks them. We found that divergence in wing spot size is determined by at least three quantitative trait loci (QTL) and divergence in courtship score is determined by at least four QTL. On the autosomes, QTL locations for pigmentation and behavior were generally separate, but on the X chromosome two clusters of QTL were found affecting both wing pigmentation and courtship behavior. We also examined the genetic basis of divergence in three components of male courtship, wing display, circling, and body shaking. Each of these showed a distinct genetic architecture, with some QTL mapping to similar positions as QTL for overall courtship score. Pairwise tests for interactions between marker loci revealed evidence of epistasis between putative QTL for wing pigmentation but not those for courtship behavior. The clustering of X-linked QTL for male pigmentation and behavior is consistent with the concerted evolution of these traits and motivates fine-scale mapping studies to elucidate the nature of the contributing genetic factors in these intervals.

Genetic susceptibility to type 2 diabetes and obesity: from genome-wide association studies to rare variants and beyond

During the past 7 years, genome-wide association studies have shed light on the contribution of common genomic variants to the genetic architecture of type 2 diabetes, obesity and related intermediate phenotypes. The discoveries have firmly established more than 175 genomic loci associated with these phenotypes. Despite the tight correlation between type 2 diabetes and obesity, these conditions do not appear to share a common genetic background, since they have few genetic risk loci in common. The recent genetic discoveries do however highlight specific details of the interplay between the pathogenesis of type 2 diabetes, insulin resistance and obesity. The focus is currently shifting towards investigations of data from targeted array-based genotyping and exome and genome sequencing to study the individual and combined effect of low-frequency and rare variants in metabolic disease. Here we review recent progress as regards the concepts, methodologies and derived outcomes of studies of the genetics of type 2 diabetes and obesity, and discuss avenues to be investigated in the future within this research field.

Extensive functional pleiotropy of REVOLUTA substantiated through forward genetics

In plants, genes may sustain extensive pleiotropic functional properties by individually affecting multiple, distinct traits. We discuss results from three genome-wide association studies of approximately 400 natural poplar (Populus trichocarpa) accessions phenotyped for 60 ecological/biomass, wood quality, and rust fungus resistance traits. Single-nucleotide polymorphisms (SNPs) in the poplar ortholog of the class III homeodomain-leucine zipper transcription factor gene REVOLUTA (PtREV) were significantly associated with three specific traits. Based on SNP associations with fungal resistance, leaf drop, and cellulose content, the PtREV gene contains three potential regulatory sites within noncoding regions at the gene's 3' end, where alternative splicing and messenger RNA processing actively occur. The polymorphisms in this region associated with leaf abscission and cellulose content are suggested to represent more recent variants, whereas the SNP associated with leaf rust resistance may be more ancient, consistent with REV's primary role in auxin signaling and its functional evolution in supporting fundamental processes of vascular plant development.

The PGPR strain Phyllobacterium brassicacearum STM196 induces a reproductive delay and physiological changes that result in improved drought tolerance in Arabidopsis

Understanding how biotic interactions can improve plant tolerance to drought is a challenging prospect for agronomy and ecology. Plant growth-promoting rhizobacteria (PGPR) are promising candidates but the phenotypic changes induced by PGPR under drought remain to be elucidated. We investigated the effects of Phyllobacterium brassicacearum STM196 strain, a PGPR isolated from the rhizosphere of oilseed rape, on two accessions of Arabidopsis thaliana with contrasting flowering time. We measured multiple morphophysiological traits related to plant growth and development in order to quantify the added value of the bacteria to drought-response strategies of Arabidopsis in soil conditions. A delay in reproductive development induced by the bacteria resulted in a gain of biomass that was independent of the accession and the watering regime. Coordinated changes in transpiration, ABA content, photosynthesis and development resulted in higher water-use efficiency and a better tolerance to drought of inoculated plants. Our findings give new insights into the ecophysiological bases by which PGPR can confer stress tolerance to plants. Rhizobacteria-induced delay in flowering time could represent a valuable strategy for increasing biomass yield, whereas rhizobacteria-induced improvement of water use is of particular interest in multiple scenarios of water availability.

Quantitative trait locus and haplotype analyses of wild and crop-mimic traits in U.S. weedy rice

Conspecific weeds retained characteristics from wild ancestors and also developed crop mimicries for adaptation and competitiveness. This research was conducted to identify quantitative trait loci (QTL) associated with the wild and crop-mimic traits and to determine haplotype variants for QTL-rich regions in U.S. weedy rice. An F2 population from the cross between a cultivated (EM93-1) and a U.S. weedy (US1) rice line was evaluated for six wild and eight crop-mimic traits in a greenhouse to identify the QTL. A core collection of 27 U.S. weedy red rice lines and 14 AA-genome wild rice lines were determined for the haplotype variants. A total of 49 QTL were identified, with 45 collocated as clusters on 14 genomic segments. The number of haplotypes across the 14 segments was lower in the weedy (6.1 ± 2.4) than in the wild (7.5 ± 1.8) rice sample. Both samples shared ~50% haplotypes (wild-like). The EM93-1-like haplotypes accounted for a greater proportion (30 ± 26%) of the haplotypes in the weedy than in the wild (7 ± 10%) rice. Based on haplotype patterns for the 14 QTL cluster regions, 26 of the 28 red rice lines were clustered into two groups corresponding to the black-hull awned and straw-hull awnless morphological types, respectively. The QTL analysis demonstrated that conspecific weed-crop differentiation involved many genomic segments with multiple loci regulating natural variation for adaptation and competitiveness. The haplotype analysis revealed that U.S. weedy rice retained large blocks of linkage disequilibrium for the multiple loci from the wild relatives and also incorporated haplotypes from cultivars.

Genetic architecture of flowering time differentiation between locally adapted populations of Arabidopsis thaliana

To gain an understanding of the genetic basis of adaptation, we conducted quantitative trait locus (QTL) mapping for flowering time variation between two winter annual populations of Arabidopsis thaliana that are locally adapted and display distinct flowering times. QTL mapping was performed with large (n = 384) F(2) populations with and without vernalization, in order to reveal both the genetic basis of a vernalization requirement and that of variation in flowering time given vernalization. In the nonvernalization treatment, none of the Sweden parents flowered, whereas all of the Italy parents and 42% of the F(2)s flowered. We identified three QTLs for flowering without vernalization, with much of the variation being attributed to a QTL co-localizing with FLOWERING LOCUS C (FLC). In the vernalization treatment, all parents and F(2)s flowered, and six QTLs of small to moderate effect were revealed, with underlying candidate genes that are members of the vernalization pathway. We found no evidence for a role of FRIGIDA in the regulation of flowering times. These results contribute to a growing body of evidence aimed at the identification of ecologically relevant genetic variation for flowering time in Arabidopsis, and set the stage for functional studies to determine the link between flowering time loci and fitness.

Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions

The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct Q(ST)-F(ST) comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.

The genetic basis for natural variation in heteroblasty in Antirrhinum

Heteroblasty refers to the changes in leaf shape and size (allometry) along stems. Although evolutionary changes involving heteroblasty might contribute to leaf diversity, little is known of the extent to which heteroblasty differs between species or how it might relate to other aspects of allometry or other developmental transitions. Here, we develop a computational model that can quantify differences in leaf allometry between Antirrhinum (snapdragon) species, including variation in heteroblasty. It allows the underlying genes to be mapped in inter-species hybrids, and their effects to be studied in similar genetic backgrounds. Heteroblasty correlates with overall variation in leaf allometry, so species with smaller, rounder leaves produce their largest leaves earlier in development. This involves genes that affect both characters together and is exaggerated by additional genes with multiplicative effects on leaf size. A further heteroblasty gene also alters leaf spacing, but none affect other developmental transitions, including flowering. We suggest that differences in heteroblasty have co-evolved with overall leaf shape and size in Antirrhinum because these characters are constrained by common underlying genes. By contrast, heteroblasty is not correlated with other developmental transitions, with the exception of internode length, suggesting independent genetic control and evolution.

Genetical genomics identifies the genetic architecture for growth and weevil resistance in spruce

In plants, relationships between resistance to herbivorous insect pests and growth are typically controlled by complex interactions between genetically correlated traits. These relationships often result in tradeoffs in phenotypic expression. In this study we used genetical genomics to elucidate genetic relationships between tree growth and resistance to white pine terminal weevil (Pissodes strobi Peck.) in a pedigree population of interior spruce (Picea glauca, P. engelmannii and their hybrids) that was growing at Vernon, B.C. and segregating for weevil resistance. Genetical genomics uses genetic perturbations caused by allelic segregation in pedigrees to co-locate quantitative trait loci (QTLs) for gene expression and quantitative traits. Bark tissue of apical leaders from 188 trees was assayed for gene expression using a 21.8K spruce EST-spotted microarray; the same individuals were genotyped for 384 SNP markers for the genetic map. Many of the expression QTLs (eQTL) co-localized with resistance trait QTLs. For a composite resistance phenotype of six attack and oviposition traits, 149 positional candidate genes were identified. Resistance and growth QTLs also overlapped with eQTL hotspots along the genome suggesting that: 1) genetic pleiotropy of resistance and growth traits in interior spruce was substantial, and 2) master regulatory genes were important for weevil resistance in spruce. These results will enable future work on functional genetic studies of insect resistance in spruce, and provide valuable information about candidate genes for genetic improvement of spruce.

Makeup of the genetic correlation between milk production traits using genome-wide single nucleotide polymorphism information

The correlated responses between traits may differ depending on the makeup of genetic covariances, and may differ from the predictions of polygenic covariances. Therefore, the objective of the present study was to investigate the makeup of the genetic covariances between the well-studied traits: milk yield, fat yield, protein yield, and their percentages in more detail. Phenotypic records of 1,737 heifers of research farms in 4 different countries were used after homogenizing and adjusting for management effects. All cows had a genotype for 37,590 single nucleotide polymorphisms (SNP). A bayesian stochastic search variable selection model was used to estimate the SNP effects for each trait. About 0.5 to 1.0% of the SNP had a significant effect on 1 or more traits; however, the SNP without a significant effect explained most of the genetic variances and covariances of the traits. Single nucleotide polymorphism correlations differed from the polygenic correlations, but only 10 regions were found with an effect on multiple traits; in 1 of these regions the DGAT1 gene was previously reported with an effect on multiple traits. This region explained up to 41% of the variances of 4 traits and explained a major part of the correlation between fat yield and fat percentage and contributes to asymmetry in correlated response between fat yield and fat percentage. Overall, for the traits in this study, the infinitesimal model is expected to be sufficient for the estimation of the variances and covariances.

Inbreeding-stress interactions: evolutionary and conservation consequences

The effect of environmental stress on the magnitude of inbreeding depression has a long history of intensive study. Inbreeding-stress interactions are of great importance to the viability of populations of conservation concern and have numerous evolutionary ramifications. However, such interactions are controversial. Several meta-analyses over the last decade, combined with omic studies, have provided considerable insight into the generality of inbreeding-stress interactions, its physiological basis, and have provided the foundation for future studies. In this review, we examine the genetic and physiological mechanisms proposed to explain why inbreeding-stress interactions occur. We specifically examine whether the increase in inbreeding depression with increasing stress could be due to a concomitant increase in phenotypic variation, using a larger data set than any previous study. Phenotypic variation does usually increase with stress, and this increase can explain some of the inbreeding-stress interaction, but it cannot explain all of it. Overall, research suggests that inbreeding-stress interactions can occur via multiple independent channels, though the relative contribution of each of the mechanisms is unknown. To better understand the causes and consequences of inbreeding-stress interactions in natural populations, future research should focus on elucidating the genetic architecture of such interactions and quantifying naturally occurring levels of stress in the wild.

The genetic architecture of a complex ecological trait: host plant use in the specialist moth, Heliothis subflexa

We used genetic mapping to examine the genetic architecture of differences in host plant use between two species of noctuid moths, Heliothis subflexa, a specialist on Physalis spp., and its close relative, the broad generalist H. virescens. We introgressed H. subflexa chromosomes into the H. virescens background and analyzed 1462 backcross insects. The effects of H. subflexa-origin chromosomes were small when measured as the percent variation explained in backcross populations (0.2-5%), but were larger when considered in relation to the interspecific difference explained (1.5-165%). Most significant chromosomes had effects on more than one trait, and their effects varied between years, sexes, and genetic backgrounds. Different chromosomes could produce similar phenotypes, suggesting that the same trait might be controlled by different chromosomes in different backcross populations. It appears that many loci of small effect contribute to the use of Physalis by H. subflexa. We hypothesize that behavioral changes may have paved the way for physiological adaptation to Physalis by the generalist ancestor of H. subflexa and H. virescens.

Identification of a major QTL for silique length and seed weight in oilseed rape (Brassica napus L.)

Silique length (SL) and seed weight (SW) are two important yield-related traits controlled by quantitative trait loci (QTL) in oilseed rape (Brassica napus L.). The genetic bases underlying these two traits are largely unknown at present. In this study, we conducted QTL analyses for SL and SW using 186 recombinant inbred lines (RILs) derived from a cross between S1, an EMS mutant with extremely long siliques and large seeds, and S2, an inbred line with regular silique length and seed size. RILs were grown in Wuhan in the 2008/09 (SS09) and 2009/10 (SS10) growing seasons, and mean SL and SW for each line were investigated. Ten non-redundant QTL were identified for SL. Of these, a major QTL, cqSLA9, consistently explained as much as 53.4% of SL variation across environments. The others are minor QTL and individually explained less than 10% of the SL variation. Nine non-redundant QTL were identified for SW. Of which, one major QTL, cqSWA9, explained as much as 28.2% of the total SW variation in the SS09 and SS10 environments. In addition, three additive by additive interactions with small effects were detected for SL, and no interactions were detected for SW. Interestingly, the two major QTL, cqSLA9 for SL and cqSWA9 for SW colocalized in the same chromosomal region and were integrated into a unique QTL, uqA9. The S1 allele at this locus increases both SL and SW, suggesting that uqA9 has pleiotropic effects on both SL and SW. The existence and effect of uqA9 was confirmed in genetically different RILs derived from the cross between S1 and No2127, a resynthesized DH line having regular silique length and seed size. Individuals in one residual heterozygous line for cqSLA9 showed significant difference in silique length. The results in this study revealed that silique length in the S1 mutant is mainly controlled by the cqSLA9 locus, which will be suitable for fine mapping and marker-assisted selection in rapeseed breeding for high yield.

Confirmation of two quantitative trait loci regions for nematode resistance in commercial British terminal sire breeds

Sheep internal parasites (nematodes) remain a major health challenge and are costly for pasture-based production systems. Most current breeding programmes for nematode resistance are based on indicator traits such as faecal egg counts (FEC), which are costly and laborious to collect. Hence, genetic markers for resistance would be advantageous. However, although some quantitative trait loci (QTL) have been identified, these QTL are often not consistent across breeds and few breeding strategies for nematode resistance in sheep are currently using molecular information. In this study, QTL for nematode resistance on ovine chromosomes (OAR) 3 and 14, previously identified in the Blackface breed, were explored using commercial Suffolk (n = 336) and Texel lambs (n = 879) sampled from terminal sire breeder flocks in the United Kingdom. FEC were used as the indicator trait for nematode resistance, and these were counted separately for Nematodirus and Strongyles genera. Microsatellite markers were used to map the QTL and the data were analysed using interval mapping regression techniques and variance component analysis. QTL for Nematodirus and Strongyles FEC were found to be segregating on OAR3 at 5% chromosome region-wide significance threshold in both Suffolk and Texel sheep, and Nematodirus FEC QTL were segregating on OAR14 in both breeds. In addition, QTL for growth traits were also found to be segregating at 5% chromosome region-wide on OAR3 and OAR14. The confirmation that FEC QTL segregate in the same position in three widely used breeds widens their potential applicability to purebred Blackface, Suffolk and Texel sheep, with benefits likely to be observed in their commercial crossbred progeny.

Why are not all chilies hot? A trade-off limits pungency

Evolutionary biologists increasingly recognize that evolution can be constrained by trade-offs, yet our understanding of how and when such constraints are manifested and whether they restrict adaptive divergence in populations remains limited. Here, we show that spatial heterogeneity in moisture maintains a polymorphism for pungency (heat) among natural populations of wild chilies (Capsicum chacoense) because traits influencing water-use efficiency are functionally integrated with traits controlling pungency (the production of capsaicinoids). Pungent and non-pungent chilies occur along a cline in moisture that spans their native range in Bolivia, and the proportion of pungent plants in populations increases with greater moisture availability. In high moisture environments, pungency is beneficial because capsaicinoids protect the fruit from pathogenic fungi, and is not costly because pungent and non-pungent chilies grown in well-watered conditions produce equal numbers of seeds. In low moisture environments, pungency is less beneficial as the risk of fungal infection is lower, and carries a significant cost because, under drought stress, seed production in pungent chilies is reduced by 50 per cent relative to non-pungent plants grown in identical conditions. This large difference in seed production under water-stressed (WS) conditions explains the existence of populations dominated by non-pungent plants, and appears to result from a genetic correlation between pungency and stomatal density: non-pungent plants, segregating from intra-population crosses, exhibit significantly lower stomatal density (p = 0.003), thereby reducing gas exchange under WS conditions. These results demonstrate the importance of trait integration in constraining adaptive divergence among populations.

Accuracy of multi-trait genomic selection using different methods

Background

Genomic selection has become a very important tool in animal genetics and is rapidly emerging in plant genetics. It holds the promise to be particularly beneficial to select for traits that are difficult or expensive to measure, such as traits that are measured in one environment and selected for in another environment. The objective of this paper was to develop three models that would permit multi-trait genomic selection by combining scarcely recorded traits with genetically correlated indicator traits, and to compare their performance to single-trait models, using simulated datasets.

Methods

Three (SNP) Single Nucleotide Polymorphism based models were used. Model G and BCπ0 assumed that contributed (co)variances of all SNP are equal. Model BSSVS sampled SNP effects from a distribution with large (or small) effects to model SNP that are (or not) associated with a quantitative trait locus. For reasons of comparison, model A including pedigree but not SNP information was fitted as well.

Results

In terms of accuracies for animals without phenotypes, the models generally ranked as follows: BSSVS > BCπ0 > G > > A. Using multi-trait SNP-based models, the accuracy for juvenile animals without any phenotypes increased up to 0.10. For animals with phenotypes on an indicator trait only, accuracy increased up to 0.03 and 0.14, for genetic correlations with the evaluated trait of 0.25 and 0.75, respectively.

Conclusions

When the indicator trait had a genetic correlation lower than 0.5 with the trait of interest in our simulated data, the accuracy was higher if genotypes rather than phenotypes were obtained for the indicator trait. However, when genetic correlations were higher than 0.5, using an indicator trait led to higher accuracies for selection candidates. For different combinations of traits, the level of genetic correlation below which genotyping selection candidates is more effective than obtaining phenotypes for an indicator trait, needs to be derived considering at least the heritabilities and the numbers of animals recorded for the traits involved.

Genetics of incipient speciation in Drosophila mojavensis. III. Life-history divergence in allopatry and reproductive isolation

We carried out a three-tiered genetic analysis of egg-to-adult development time and viability in ancestral and derived populations of cactophilic Drosophila mojavensis to test the hypothesis that evolution of these life-history characters has shaped premating reproductive isolation in this species. First, a common garden experiment with 11 populations from Baja California and mainland Mexico and Arizona reared on two host species revealed significant host plant X region and population interactions for viability and development time, evidence for host plant adaptation. Second, replicated line crosses with flies reared on both hosts revealed autosomal, X chromosome, cytoplasmic, and autosome X cactus influences on development time. Viability differences were influenced by host plants, autosomal dominance, and X chromosomal effects. Many of the F(1) , F(2) , and backcross generations showed evidence of heterosis for viability. Third, a QTL analysis of male courtship song and epicuticular hydrocarbon variation based on 1688 Baja × mainland F(2) males also revealed eight QTL influencing development time differences. Mainland alleles at six of these loci were associated with longer development times, consistent with population-level differences. Eight G × E interactions were also detected caused by longer development times of mainland alleles expressed on a mainland host with smaller differences among Baja genotypes reared on the Baja host plant. Four QTL influenced both development time and epicuticular hydrocarbon differences associated with courtship success, and there was a significant QTL-based correlation between development time and cuticular hydrocarbon variation. Thus, the regional shifts in life histories that evolved once D. mojavensis invaded mainland Mexico from Baja California by shifting host plants were genetically correlated with variation in cuticular hydrocarbon-based mate preferences.

Switch between life history strategies due to changes in glycolytic enzyme gene dosage in Saccharomyces cerevisiae

Adaptation is the process whereby a population or species becomes better fitted to its habitat through modifications of various life history traits which can be positively or negatively correlated. The molecular factors underlying these covariations remain to be elucidated. Using Saccharomyces cerevisiae as a model system, we have investigated the effects on life history traits of varying the dosage of genes involved in the transformation of resources into energy. Changing gene dosage for each of three glycolytic enzyme genes (hexokinase 2, phosphoglucose isomerase, and fructose-1,6-bisphosphate aldolase) resulted in variation in enzyme activities, glucose consumption rate, and life history traits (growth rate, carrying capacity, and cell size). However, the range of effects depended on which enzyme was expressed differently. Most interestingly, these changes revealed a genetic trade-off between carrying capacity and cell size, supporting the discovery of two extreme life history strategies already described in yeast populations: the "ants," which have lower glycolytic gene dosage, take up glucose slowly, and have a small cell size but reach a high carrying capacity, and the "grasshoppers," which have higher glycolytic gene dosage, consume glucose more rapidly, and allocate it to a larger cell size but reach a lower carrying capacity. These results demonstrate antagonist pleiotropy for glycolytic genes and show that altered dosage of a single gene drives a switch between two life history strategies in yeast.

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.

Principal-component-based multivariate regression for genetic association studies of metabolic syndrome components

Background

Quantitative traits often underlie risk for complex diseases. For example, weight and body mass index (BMI) underlie the human abdominal obesity-metabolic syndrome. Many attempts have been made to identify quantitative trait loci (QTL) over the past decade, including association studies. However, a single QTL is often capable of affecting multiple traits, a quality known as gene pleiotropy. Gene pleiotropy may therefore cause a loss of power in association studies focused only on a single trait, whether based on single or multiple markers.

Results

We propose using principal-component-based multivariate regression (PCBMR) to test for gene pleiotropy with comprehensive evaluation. This method generates one or more independent canonical variables based on the principal components of original traits and conducts a multivariate regression to test for association with these new variables. Systematic simulation studies have shown that PCBMR has great power. PCBMR-based pleiotropic association studies of abdominal obesity-metabolic syndrome and its possible linkage to chromosomal band 3q27 identified 11 susceptibility genes with significant associations. Whereas some of these genes had been previously reported to be associated with metabolic traits, others had never been identified as metabolism-associated genes.

Conclusions

PCBMR is a computationally efficient and powerful test for gene pleiotropy. Application of PCBMR to abdominal obesity-metabolic syndrome indicated the existence of gene pleiotropy affecting this syndrome.