Pleiotropy or linkage? Their relative contributions to the genetic correlation of quantitative traits and detection by multitrait GWA studies

Impacts of pleiotropy and migration on repeated genetic adaptation

Observations of genetically repeated evolution (repeatability) in complex organisms are incongruent with the Fisher-Orr model, which implies that repeated use of the same gene should be rare when mutations are pleiotropic (i.e. affect multiple traits). When spatially divergent selection occurs in the presence of migration, mutations of large effect are more strongly favored, and hence, repeatability is more likely, but it is unclear whether this observation is limited by pleiotropy. Here, we explore this question using individual-based simulations of a two-patch model incorporating multiple quantitative traits governed by mutations with pleiotropic effects. We explore the relationship between fitness trade-offs and repeatability by varying the alignment between mutation effect and spatial variation in trait optima. While repeatability decreases with increasing trait dimensionality, trade-offs in mutation effects on traits do not strongly limit the contribution of a locus of large effect to repeated adaptation, particularly under increased migration. These results suggest that repeatability will be more pronounced for local rather than global adaptation. Whereas pleiotropy limits repeatability in a single-population model, when there is local adaptation with gene flow, repeatability can occur if some loci are able to produce alleles of large effect, even when there are pleiotropic trade-offs.

Meristic co-evolution and genomic co-localization of lateral line scales and vertebrae in Central American cichlid fishes

Meristic traits are often treated as distinct phenotypes that can be used to differentiate and delineate recently diverged species. For instance, the number of lateral line scales and vertebrae, two traits that vary substantially among Neotropical Heroine cichlid species, have been previously suggested to co-evolve. These meristic traits could co-evolve due to shared adaptive, developmental, or genetic factors. If they were found to be genetically or developmentally non-independent, this might require a more general re-evaluation of their role in evolutionary or taxonomic studies. We expanded a previous analysis of correlated evolution of meristic traits (lateral line scales and vertebrae counts) in these fishes to include a range of phylogenetic reconstructions as well as the analyses of 13 Nicaraguan Midas cichlid species (Amphilophus spp.). Additionally, we performed qualitative traits locus (QTL) mapping in a F2 laboratory-reared hybrid population from two ecologically divergent Midas cichlid fish species to discover and evaluate whether genomic co-segregation might explain the observed patterns of meristic co-evolution. Meristic values for these traits were found to morphologically differentiate some species of the Midas cichlid adaptive radiation. Our QTL analysis pinpointed several genomic regions associated with divergence in these traits and highlighted the potential for genomic co-segregation of the lateral line and vertebrae numbers on two chromosomes. Further, our phylogenetic comparative analyses consistently recovered a significant positive evolutionary correlation between the counts of lateral line scale and vertebrae numbers in Neotropical cichlids. Hence, the findings of genomic co-segregation could partially explain the co-evolution of these two meristic traits in these species. Continuing to unravel the genetic architecture governing meristic divergence helps to better understand both trait correlations and the utility of meristic traits in taxonomic diagnoses and how traits in phenotypes might be expected to co-evolve.

Childhood Reading Ability and Pain in Childhood Through to Midlife

Dyslexia and pain have recently been shown to correlate on a genetic level, but there has been little exploration of this association on the phenotypic level despite reports of increased pain in Attention Deficit Hyperactivity Disorder, which commonly co-occurs with dyslexia. In this study we test for an association between reading ability, which is the primary feature of dyslexia, and pain both in childhood and adulthood. Logistic regression modeling was used to test associations between reading ability in childhood and pain from childhood to midlife in a large UK birth cohort; the 1958 National Child Development Study. Associations were found between poor childhood reading ability and increased headache and abdominal pain in childhood, and between poor childhood reading ability and headache, eye pain, back pain, and rheumatism in adulthood. Mediation analyses indicated that socioeconomic status (defined by employment) fully mediated the association between poor reading ability in childhood and back pain at age 42. By contrast, the association between reading ability and eye pain acted independently of socioeconomic status. Different mechanisms were thus indicated for the association of reading with different pain types, including manual labor and a potential shared biological pathway. PERSPECTIVE: This study found a relationship between poor reading ability in childhood and pain in childhood and adulthood. Those with reading difficulties should be monitored for pain symptoms. Future research may uncover shared biological mechanisms, increasing our understanding of pain and potential treatments.

Genomic determinants, architecture, and constraints in drought-related traits in Corymbia calophylla

BACKGROUND

Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla.

RESULTS

We found 273 genomic variants determining traits with moderate heritability (h2SNP = 0.26-0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions.

CONCLUSIONS

Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.

Epistasis and pleiotropy-induced variation for plant breeding

Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy-based phenotypic trade-offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non-pleiotropy-induced variation, and genotype × environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large-scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.

Rapid evolutionary change in trait correlations of single proteins

Many organismal traits are genetically determined and covary in evolving populations. The resulting trait correlations can either help or hinder evolvability - the ability to bring forth new and adaptive phenotypes. The evolution of evolvability requires that trait correlations themselves must be able to evolve, but we know little about this ability. To learn more about it, we here study two evolvable systems, a yellow fluorescent protein and the antibiotic resistance protein VIM-2 metallo beta-lactamase. We consider two traits in the fluorescent protein, namely the ability to emit yellow and green light, and three traits in our enzyme, namely the resistance against ampicillin, cefotaxime, and meropenem. We show that correlations between these traits can evolve rapidly through both mutation and selection on short evolutionary time scales. In addition, we show that these correlations are driven by a protein's ability to fold, because single mutations that alter foldability can dramatically change trait correlations. Since foldability is important for most proteins and their traits, mutations affecting protein folding may alter trait correlations mediated by many other proteins. Thus, mutations that affect protein foldability may also help shape the correlations of complex traits that are affected by hundreds of proteins.

The genomic basis of nitrogen utilization efficiency and trait plasticity to improve nutrient stress tolerance in cultivated sunflower

Maintaining crop productivity is challenging as population growth, climate change, and increasing fertilizer costs necessitate expanding crop production to poorer lands whilst reducing inputs. Enhancing crops' nutrient use efficiency is thus an important goal, but requires a better understanding of related traits and their genetic basis. We investigated variation in low nutrient stress tolerance in a diverse panel of cultivated sunflower genotypes grown under high and low nutrient conditions, assessing relative growth rate (RGR) as performance. We assessed variation in traits related to nitrogen utilization efficiency (NUtE), mass allocation, and leaf elemental content. Across genotypes, nutrient limitation generally reduced RGR. Moreover, there was a negative correlation between vigor (RGR in control) and decline in RGR in response to stress. Given this trade-off, we focused on nutrient stress tolerance independent of vigor. This tolerance metric correlated with the change in NUtE, plasticity for a suite of morphological traits, and leaf element content. Genome-wide associations revealed regions associated with variation and plasticity in multiple traits, including two regions with seemingly additive effects on NUtE change. Our results demonstrate potential avenues for improving sunflower nutrient stress tolerance independent of vigor, and highlight specific traits and genomic regions that could play a role in enhancing tolerance.

Exploitation of the Genetic Variability of Diverse Metric Traits of Durum Wheat (Triticum turgidum L. ssp. durum Desf.) Cultivars for Local Adaptation to Semi-Arid Regions of Algeria

Abiotic stresses pose significant challenges to wheat farming, yet exploiting the genetic variability within germplasm collections offers an opportunity to effectively address these challenges. In this study, we investigated the genetic diversity of key agronomic traits among twenty durum wheat cultivars, with the intention to pinpoint those better suited to semi-arid conditions. Field trials were conducted at the ITGC-FDPS Institute, Setif, Algeria, during the winter season of 2021/22. A completely randomized design was used with three replicates. Statistical analyses revealed significant variation among the genotypes for most of the studied traits, with some cultivars exhibiting a superior performance in a stressful environment. Notably, traits like the number of grains per spike (NGS) and the grain yield (GY) displayed high genotypic coefficients of variation (CVg). Except for membrane thermostability (MT) and biological yield (BY), the majority of the assessed traits exhibited moderate-to-high heritability estimates. Genotypic and phenotypic correlation studies have confirmed the importance of many yield-related traits in the expression of GY. The harvest index (HI) underscored the highest genotypic direct effect on GY, followed closely by spike number (SN), serving as consistent pathways through which most of the measured traits indirectly influenced GY. The cluster analysis categorized the durum wheat cultivars into seven distinct clusters. The largest inter-cluster distance was observed between clusters G3 and G4 (D2 = 6145.86), reflecting maximum dissimilarity between the individuals of these clusters. Hybridizing divergent clusters may benefit future breeding programs aiming to develop potential durum wheat varieties through cross combinations. This study's findings contribute to sustainable agriculture efforts by facilitating the selection of genotypes with enhanced resilience and productivity, particularly for cultivation in challenging semi-arid regions.

Glycemic traits and colorectal cancer survival in a cohort of South Korean patients: A Mendelian randomization analysis

BACKGROUND

Clinical diabetic traits have been reported to be associated with increased colorectal cancer (CRC) risk in observational studies. Using the Mendelian randomization (MR) analysis method, we examined the causal association between glycemic traits, such as fasting glucose (FG), fasting insulin (FI), and glycosylated hemoglobin A1c (HbA1c), and survival in a cohort of CRC patients.

METHODS

We conducted a two-sample MR analysis among a cohort of patients with locally advanced CRC at Seoul National University Hospital. Single-nucleotide polymorphisms robustly associated (p < 5 × 10-8 ) with the three glycemic traits were obtained from the Meta-Analyses of Glucose and Insulin-related traits Consortium, Asian Genetic Epidemiology Network, and Korea Biobank Array. Three-year and 5-year overall survival (OS) and progression-free survival (PFS) were used as outcomes. Survival analysis was conducted using subgroup analysis by cancer stage and subsite in a multivariate Cox proportional hazards model adjusted for age and sex to examine whether glycemic traits affected survival.

RESULTS

A total of 509 patients were included in our final analysis. MR analysis showed that HbA1c levels were associated with poor 3-year OS (β = 4.20, p = 0.02). Sensitivity analyses did not show evidence of any violations of the MR assumptions. In the cancer subgroup analysis of the Cox proportional hazards model, pooled hazard ratios for FG were significantly associated with poor 3-year OS and PFS regardless of cancer stage. FI was not significantly associated with any 3-year survival endpoints. Among Stage III patients, three glycemic traits were significantly associated with both 5-year OS and PFS. Location-specific subgroup analysis showed a significant association between three glycemic traits and 5-year PFS in patients with left-sided colon cancer. FG was associated with poor 3-year survival for colon cancer but not rectal cancer.

CONCLUSIONS

Our results suggest that FG and HbA1c could be used to predict prognosis in CRC patients. Lifestyle and/or pharmacological interventions targeting glycemic traits could help improve survival for CRC patients.

Simulation of dual-purpose chicken breeding programs implementing gene editing

BACKGROUND

In spite of being controversial and raising ethical concerns, the application of gene editing is more likely to be accepted when it contributes to improving animal welfare. One of the animal welfare and ethical issues in chicken breeding is chick culling, the killing of the male layer chicks after hatching due to the poor fattening performance. Although establishing dual-purpose chicken lines could solve this problem, unfavorable genetic correlations between egg and meat production traits hindered their competitiveness. Although it is also controversial in ethical terms, gene editing may accelerate genetic progress in dual-purpose chicken and alleviate the ethical concerns from chick culling.

RESULTS

The simulation compared the utility improvement in dual-purpose use under two breeding schemes: one consisting in the improvement of the laying hens, and the second in the improvement of a synthetic line obtained from a layer broiler cross. In each breeding scheme, the breeding programs were simulated with and without gene editing. Polygenic breeding values and 500 simulated quantitative trait loci (QTL) with different levels of pleiotropy caused negative correlations between egg production, meat production, and overall health. The results of the simulation demonstrated that genetic gain could be accelerated by at most 81% for several generations if gene editing was used. The actual increase in genetic gain depended on the number of single nucleotide polymorphisms (SNPs) being edited per animal. The rate of genetic improvement became equal in scenarios with and without gene editing after 20 generations. This is because the remaining segregating QTL had small effects and their edition would have negative overall health effects from potential off-target edits. Although gene editing can improve genetic gain in quantitative traits, it can only be recommended as long as QTL with reasonable effect sizes are segregating and detectable.

CONCLUSIONS

This simulation demonstrates the potential of gene editing to accelerate the simultaneous improvement of negatively correlated traits. When the risk of negative consequences from gene editing persists, the number of SNPs to be edited should be chosen carefully to obtain the optimal genetic gain.

The genomic architecture of continuous plumage colour variation in the European barn owl (Tyto alba)

The maintenance of colour variation in wild populations has long fascinated evolutionary biologists, although most studies have focused on discrete traits exhibiting rather simple inheritance patterns and genetic architectures. However, the study of continuous colour traits and their potentially oligo- or polygenic genetic bases remains rare in wild populations. We studied the genetics of the continuously varying white-to-rufous plumage coloration of the European barn owl (Tyto alba) using a genome-wide association approach on the whole-genome data of 75 individuals. We confirmed a mutation at the melanocortin-1-receptor gene (MC1R) is involved in the coloration and identified two new regions, located in super-scaffolds 9 and 42. The combination of the three regions explains most of the colour variation (80.37%, 95% credible interval 58.45-100%). One discovered region, located in the sex chromosome, differs between the most extreme colorations in owls sharing a specific MC1R genotype. This region may play a role in the colour sex dimorphism of this species, possibly in interaction with the autosomal MC1R. We thus provide insights into the genetic architecture of continuous colour variation, pointing to an oligogenic basis with potential epistatic effects among loci that should aid future studies understanding how continuous colour variation is maintained in nature.

Natural variations of HvSRN1 modulate the spike rachis node number in barley

Grain number, one of the major determinants of yield in Triticeae crops, is largely determined by spikelet number and spike rachis node number (SRN). Here, we identified three quantitative trait loci (QTLs) for SRN using 145 recombinant inbred lines derived from a barley R90/1815D cross. qSRN1, the major-effect QTL, was mapped to chromosome 2H and explained up to 38.77% of SRN variation. Map-based cloning revealed that qSRN1 encodes the RAWUL domain-containing protein HvSRN1. Further analysis revealed that two key SNPs in the HvSRN1 promoter region (∼2 kb upstream of the transcription start site) affect the transcript level of HvSRN1 and contribute to variation in SRN. Similar to its orthologous proteins OsLAX2 and ZmBA2, HvSRN1 showed protein-protein interactions with HvLAX1, suggesting that the LAX2-LAX1 model for spike morphology regulation may be conserved in Poaceae crops. CRISPR-Cas9-induced HvSRN1 mutants showed reduced SRN but increased grain size and weight, demonstrating a trade-off effect. Our results shed light on the role of HvSRN1 variation in regulating the balance between grain number and weight in barley.

Linkage drag analysis in three Aegilops speltoides introgressions carrying Sr47 in modern durum and hard red spring wheat germplasm

KEY MESSAGE

Yield and quality tests of wheat lines derived from RWG35 show they carry little, or no linkage drag and are the preferred source of Sr47 for stem rust resistance. Three durum wheat (Triticum turgidum L. subsp. durum) lines, RWG35, RWG36, and RWG37 carrying slightly different Aegilops speltoides introgressions, but each carrying the Sr47 stem rust resistance gene, were backcrossed to three durum and three hard red spring (HRS) wheat (Triticum aestivum L.) cultivars to produce 18 backcross populations. Each population was backcrossed to the recurrent parent six times and prepared for yield trials to test for linkage drag. Lines carrying the introgression (S-lines) were compared to euploid sibling lines (W-lines) and their parent. Yield trials were conducted from 2018 to 2021 at three locations. Three agronomic and several quality traits were studied. In durum, lines derived from RWG35 had little or no linkage drag. Lines derived from RWG36 and RWG37 still retained linkage drag, most notably involving yield and thousand kernel weight, but also test weight, falling number, kernel hardness index, semolina extract, semolina protein content, semolina brightness, and peak height. In HRS wheat, the results were more complex, though the general result of RWG35 lines having little or no linkage drag and RWG36 and RWG37 lines retaining linkage drag still applied. But there was heterogeneity in the Glenn35S lines, and Linkert lines had problems combining with the Ae. speltoides introgressions. We concluded that introgressions derived from RWG35 either had eliminated linkage drag or any negative effects were minor in nature. We recommend that breeders who wish to incorporate Sr47 into their cultivars should work exclusively with germplasm derived from RWG35.

Combination of meta-analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean

Increasing seed yield in common bean could help to improve food security and reduce malnutrition globally due to the high nutritional quality of this crop. However, the complex genetic architecture and prevalent genotype by environment interactions for seed yield makes increasing genetic gains challenging. The aim of this study was to identify the most consistent genomic regions related with seed yield components and phenology reported in the last 20 years in common bean. A meta-analysis of quantitative trait locus (QTL) for seed yield components and phenology (MQTL-YC) was performed for 394 QTL reported in 21 independent studies under sufficient water and drought conditions. In total, 58 MQTL-YC over different genetic backgrounds and environments were identified, reducing threefold on average the confidence interval (CI) compared with the CI for the initial QTL. Furthermore, 40 MQTL-YC identified were co-located with 210 SNP peak positions reported via genome-wide association (GWAS), guiding the identification of candidate genes. Comparative genomics among these MQTL-YC with MQTL-YC reported in soybean and pea allowed the identification of 14 orthologous MQTL-YC shared across species. The integration of MQTL-YC, GWAS, and comparative genomics used in this study is useful to uncover and refine the most consistent genomic regions related with seed yield components for their use in plant breeding.

A pleiotropic chemoreceptor facilitates the production and perception of mating pheromones

Optimal mating decisions depend on the robust coupling of signal production and perception because independent changes in either could carry a fitness cost. However, since the perception and production of mating signals are often mediated by different tissues and cell types, the mechanisms that drive and maintain their coupling remain unknown for most animal species. Here, we show that in Drosophila, behavioral responses to, and the production of, a putative inhibitory mating pheromone are co-regulated by Gr8a, a member of the Gustatory receptor gene family. Specifically, through behavioral and pheromonal data, we found that Gr8a independently regulates the behavioral responses of males and females to a putative inhibitory pheromone, as well as its production in the fat body and oenocytes of males. Overall, these findings provide a relatively simple molecular explanation for how pleiotropic receptors maintain robust mating signaling systems at the population and species levels.

Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom

Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.

Genome-wide association studies reveal putative QTLs for physiological traits under contrasting phosphorous conditions in wheat (Triticum aestivum L.)

A Genome-wide association (GWAS) study was conducted for phosphorous (P)-use responsive physiological traits in bread wheat at the seedling stage under contrasting P regimes. A panel of 158 diverse advanced breeding lines and released varieties, and a set of 10,800 filtered single nucleotide polymorphism (SNP) markers were used to study marker-trait associations over the eight shoot traits. Principle component analysis separated the two environments (P regimes) because of the differential response of the traits indicating the essentiality of the separate breeding programmes for each environment. Significant variations for genotypic, environmental, and genotype × environment (GEI) effects were observed for all the traits in the combined analysis of variance with moderately high broad sense heritability traits (0.50–0.73). With the different algorithms of association mapping viz., BLINK, FarmCPU, and MLM, 38 unique QTLs under non-limiting P (NLP) and 45 QTLs for limiting P (LP) conditions for various shoot traits were identified. Some of these QTLs were captured by all three algorithms. Interestingly, a Q.iari.dt.sdw.1 on chromosome 1D was found to explain the significant variations in three important physiological traits under non-limiting phosphorus (NLP) conditions. We identified the putative candidate genes for QTLs namely Q.iari.dt.chl.1, Q.iari.dt.sdw.16, Q.iari.dt.sdw.9 and Q.iari.dt.tpc.1 which are potentially involved in the mechanism regulating phosphorus use efficiency through improved P absorption due to improved root architectural traits and better mobilization such as sulfotransferase involved in postembryonic root development, WALLS ARE THIN1 (WAT1), a plant-specific protein that facilitates auxin export; lectin receptor-like kinase essentially involved in plant development, stress response during germination and lateral root development and F-box component of the SKP-Cullin-F box E3 ubiquitin ligase complex and strigolactone signal perception. Expression profiling of putative genes located in identified genomic regions against the wheat expression atlas revealed their significance based on the expression of these genes for stress response and growth development processes in wheat. Our results thus provide an important insight into understanding the genetic basis for improving PUE under phosphorus stress conditions and can shape the future breeding programme by developing and integrating molecular markers for these difficult-to-score important traits.

Unraveling coevolutionary dynamics using ecological genomics

Coevolutionary interactions, from the delicate co-dependency in mutualistic interactions to the antagonistic relationship of hosts and parasites, are a ubiquitous driver of adaptation. Surprisingly, little is known about the genomic processes underlying coevolution in an ecological context. However, species comprise genetically differentiated populations that interact with temporally variable abiotic and biotic environments. We discuss the recent advances in coevolutionary theory and genomics as well as shortcomings, to identify coevolving genes that take into account this spatial and temporal variability of coevolution, and propose a practical guide to understand the dynamic of coevolution using an ecological genomics lens.

Pleiotropy or linkage? Their relative contributions to the genetic correlation of quantitative traits and detection by multitrait GWA studies

Genetic correlations between traits may cause correlated responses to selection. Previous models described the conditions under which genetic correlations are expected to be maintained. Selection, mutation, and migration are all proposed to affect genetic correlations, regardless of whether the underlying genetic architecture consists of pleiotropic or tightly linked loci affecting the traits. Here, we investigate the conditions under which pleiotropy and linkage have different effects on the genetic correlations between traits by explicitly modeling multiple genetic architectures to look at the effects of selection strength, degree of correlational selection, mutation rate, mutational variance, recombination rate, and migration rate. We show that at mutation-selection(-migration) balance, mutation rates differentially affect the equilibrium levels of genetic correlation when architectures are composed of pairs of physically linked loci compared to architectures of pleiotropic loci. Even when there is perfect linkage (no recombination within pairs of linked loci), a lower genetic correlation is maintained than with pleiotropy, with a lower mutation rate leading to a larger decrease. These results imply that the detection of causal loci in multitrait association studies will be affected by the type of underlying architectures, whereby pleiotropic variants are more likely to be underlying multiple detected associations. We also confirm that tighter linkage between nonpleiotropic causal loci maintains higher genetic correlations at the traits and leads to a greater proportion of false positives in association analyses.