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bioRxiv2026

Genetic basis of Cassava (Manihot esculenta Crantz) plant architecture and its relevance for selection of farmer-preferred varieties

Plant architecture, the spatial configuration of stems, branches, leaves, and inflorescences underpins essential physiological functions such as light capture, assimilate partitioning, flowering, and ultimately, yield. In cassava (Manihot esculenta), architectural traits such us plant height, branching level, and plant shape are agronomically important yet remain underexploited in breeding. Here, a large-scale analysis was conducted using phenotypic and genomic data from more than 14,000 cassava accessions evaluated across 34 field locations in Nigeria between 2010 and 2021, encompassing the national breeding programs of the National Root Crops Research Institute and the International Institute of Tropical Agriculture. The study aimed to dissect the genetic architecture, environmental stability, and breeding relevance of four key traits: plant full height, height to first branching, the branching level number (BranchlevelNum) and plant shape. Phenotypic analyses across breeding stages revealed consistent variation in plant height, branching height, and branching intensity, reflecting the cumulative effects of selection and evaluation across environments. Broad-sense heritability estimates ranged from 0.41 to 0.72, with BranchlevelNum and Cylindrical shape exhibiting strong genetic control and weak correlations with yield components, indicating their suitability for independent improvement. Genome-wide association analyses identified significant loci associated with BranchlevelNum, including a major region on chromosome 2 and an additional locus on chromosome 13, collectively explaining approximately 11% of the phenotypic variance. Candidate genes within these regions included regulators of meristem activity and hormone-related pathways, supporting a developmental basis for branching variation. Genomic prediction accuracy for BranchlevelNum reached 0.44, comparable to values reported for key agronomic traits in cassava. These results demonstrate that branching-related architectural traits are genetically tractable, largely independent of yield, and amenable to genomic selection. The findings support the integration of BranchlevelNum and plant shape into ideotype-driven breeding frameworks aimed at improving flowering efficiency, canopy structure, and field performance in cassava. Author SummaryCassava is a major food crop, and its plant shape plays an important role in how easily it can be grown, harvested, and improved through breeding. Traits such as plant height, branching, and canopy form affect flowering, seed production, and field management, yet they have received much less attention than yield or disease resistance. In this study, we examined plant architecture using field and genetic data from more than 14,000 cassava plants grown across Nigeria over twelve years. We focused on key traits describing plant height, branching level, and overall plant shape. We found that branching level is strongly controlled by genetics, remains stable across environments, and can be predicted accurately using genomic data. We also identified specific regions of the cassava genome linked to branching behavior. Our findings show that plant architecture can be improved using modern breeding tools without compromising yield. Incorporating branching traits into breeding programs can help develop cassava varieties that flower more reliably and perform better in farmers fields.

genetics↗

bioRxiv2026

Simplifying Systems Genetics with QTLretrievR: An R Package for Molecular QTL Identification

MotivationOver the past two decades, integrating "-omics" scale molecular profiling with genetic mapping in diverse populations--termed "systems genetics"--has proven powerful for linking complex disease phenotypes to genetic variants and their regulatory effects. However, these combined genomic and genetic analyses remain computationally intensive and often inaccessible to researchers without a strong computational background, a problem compounded in studies with multiple tissues or thousands of molecular -omics phenotypes. ResultsWe developed QTLretrievR, an R package designed to simplify and streamline the identification and downstream analysis of molecular quantitative trait loci in genetically diverse populations. QTLretrievR builds on widely used R packages such as r/qtl2 for quantitative trait locus mapping and r/intermediate for mediation analysis, and incorporates substantial parallelization features to improve computational efficiency. Benchmarking demonstrates that QTLretrievR can reproduce results from previous quantitative trait locus studies while significantly reducing the time required for quantitative trait locus peak detection and downstream analyses. Additionally, QTL-retrievR includes plotting functions to visualize results of the included downstream analyses. AvailabilitySource code is available at https://github.com/deweyhannah/QTLretrievR. ContactSteven Munger, steven.munger@jax.org

genetics↗

bioRxiv2026

Genetic influences on food liking and food preference patterns in young adults: a genome-wide association study

Genetic variation contributes to individual differences in food liking and dietary behaviour. Genome-wide association studies (GWAS) have identified genetic variants associated with these traits, but most evidence comes from middle-aged and older populations. Young adulthood is a key life stage during which long-term dietary habits develop, yet the genetic basis of food liking during this period remains largely unexplored. We conducted GWAS of 97 food-liking traits and two derived principal components (PCs) in 2,784 young adults (aged 25) from the Avon Longitudinal Study of Parents and Children. The PCs captured broader plant-based/seafood (PC1) and meat-based (PC2) food preference patterns. GWAS identified 16 genome-wide significant associations across 14 individual food-liking traits and one food preference pattern (PC1). Cross-trait analyses showed that several variants were associated liking for multiple foods. For example, the lentil-associated variant rs76659918 was associated with PC1 and with liking for avocado, honey, plain yogurt, chilli peppers, aubergines, and black olives, whereas burger- and steak-associated variants were linked to multiple meat-based foods and PC2. Exploratory analyses showed that TAS2R38 bitter-sensitive alleles were associated with lower liking for Brussels sprouts, with limited evidence for associations with other traits. Comparison with food liking GWAS from the UK Biobank (aged 37-73) showed limited replication, with robust evidence only for the grapefruit juice-associated variant rs2264192. This study identifies genetic variants associated with food liking in young adulthood and suggests that genetic influences operate at both the level of individual foods and broader food preference patterns.

genetics↗

bioRxiv2026

Isoform-Resolved Genetic Architecture of Epilepsy and SUDEP Reveals Divergent Brain and Heart Channelopathy Signatures

Sudden unexpected death in epilepsy (SUDEP) is the most devastating complication of epilepsy, yet the molecular features distinguishing individuals at risk remain poorly defined. Although epilepsy and SUDEP share substantial genetic overlap, fatal outcomes may arise when shared risk genes are differentially deployed across neuronal and cardiac systems. Here, we identify tissue- and isoform-level regulation as a key determinant of divergence between epilepsy and SUDEP risk. We performed a large-scale integrated analysis of genetic variants reported in epilepsy and SUDEP across 419 sequencing-based studies encompassing 35,659 individuals, and quantified gene-level burden using a Bayesian Poisson-Gamma rate ratio framework. This analysis revealed preferential enrichment of genes related to cardiac electrophysiology and contractile function in SUDEP, whereas epilepsy was dominated by genes involved in neuronal excitability and synaptic signaling. To determine how shared genetic loci are deployed across tissues, we integrated GTEx-based tissue expression profiles with long-read single-cell transcriptomic datasets from human heart and brain to resolve isoform-level expression patterns. These analyses revealed pronounced tissue-specific transcript architectures. Cardiac-associated genes, including HCN4, KCNH2, KCNE1, MYH6, MYO18B, and ATP1A2, showed heart-restricted isoform expression, whereas neuronal genes such as ADGRV1, CACNA1A, GRIN2B, HCN1, HCN2, KCNA1, SCN1A, SCN2A, and SCN8A. Importantly, several shared genes exhibited tissue-partitioned isoform expression, with distinct transcript repertoires in heart and brain, particularly across pathways related to ion transport, signaling, metabolism, and structural organization. Consistent patterns were observed in iPSC-derived cardiomyocytes and neurons, indicating that lineage-dependent deployment of shared genes is preserved in controlled systems. Together, these findings suggest that tissue-specific isoform regulation provides a mechanistic basis linking shared epilepsy genetics to SUDEP susceptibility, whereby the same genetic loci contribute to neuronal dysfunction in epilepsy and to cardiac vulnerability in SUDEP. This positions SUDEP as a neuro-cardiac interface disorder shaped by isoform-level regulatory divergence.

genetics↗

bioRxiv2026

Optimizing phenotype scale improves genetic analyses in large-scale biobanks

Large-scale biobanks have enabled increasingly complicated genetic analyses across thousands of phenotypes. However, studies rarely consider the appropriate phenotype measurement scale, a problem that can drastically affect inferences on genetic architecture. Here, we introduce SIQReg, a practical solution to this classical problem, which learns a data-driven phenotype scale by minimizing heterogeneity across phenotype quantiles. Applied to complex traits in UK Biobank, SIQReg rejects the default scale for 24/25 traits. Generally, SIQReg scales lie between default and logarithmic, indicating that default-scale traits are neither purely additive nor purely multiplicative. We show that SIQReg improves both non-additive and additive genetic analyses. SIQReg eliminates most non-additive genetic signals (such as 97% of vQTL and 76% of quantile-dependent TWAS genes), indicating they may be statistical artifacts, while preserving biologically plausible non-additive signals. Simultaneously, SIQReg improves power to detect additive signals, increasing GWAS loci, TWAS genes, and PGS prediction accuracy by 11%, 13%, and 10%, respectively, and identifies 50% more high-risk individuals. These gains replicate across ancestry groups. Our results establish SIQReg as a principled approach to phenotype scale transformation that improves genetic analyses of complex traits.

genetics↗

bioRxiv2026

Pharmacological stress exposes hidden allelic background effects in genetic interaction screen normalisation

Synthetic Genetic Array (SGA) analysis comprises the high-throughput crossing of a query deletion strain against a genome-wide deletion library to score fitness interactions in thousands of double mutants. SGAs have produced comprehensive genetic interaction maps in yeasts and have emerged as a leading platform for pharmacogenomics: mapping genetic modifiers of drug response, identifying synthetic lethal targets and illuminating mechanisms of drug action and resistance. We have previously demonstrated that in fission yeast, the ade6 mutant is functionally neutral relative to the parental library and can serve as a standard negative control for SGA screens. Here, while we confirm our previous observation, we show that this neutrality fails under pharmacological stress. Using Torin1, an ATP-competitive TOR kinase inhibitor, we demonstrate that the ade6 SGA fitness profile diverges from that of the parental library in a dose-dependent and genomically widespread manner. At 2 M Torin1 only 12.2% of scored genes exceed a 1.5-fold fitness difference between backgrounds; at 3 M this proportion rises to 43.2% -a 3.5-fold increase driven by qualitative reorganisation of the genetic interaction landscape rather than simple scaling of pre-existing differences. Gene ontology analysis of divergent genes implicates autophagy, iron starvation responses, central carbon metabolism, and vesicle trafficking, consistent with TOR-regulated nutrient adaptation being differentially affected by the ade6-M210/M216 point mutations in the library versus the ade6 null in the SGA control. Our results have implications in fission yeast and beyond and we propose solutions towards reliable retrieval of genetic interactions.

genetics↗

bioRxiv2026

Genetic Modeling of Dyadic Behavioral Traits: Implications for Estimation and Interpretation of Variance Components

Studying the genomic control of dyadic social interactions is gaining traction in animal genetics. However, genetic modeling of social interactions poses several challenges, one of which is whether social interactions should be treated as dyadic traits or as aggregated traits at the individual level. In this study, we systematically compared two approaches: dyadic models using dyadic traits and marginal models using marginally aggregated traits and we derived the algebraic relationships between their variance components. In the application, we used a published dataset on post-mixing aggression in pigs, including both directed and undirected aggression records collected during the 9-hour period after mixing among 797 finishing pigs in 59 social groups, as an example to show how model choice can affect variance estimation. Results showed that dyadic models can estimate genetic effects and permanent environmental effects by exploiting repeated dyadic interaction records, thereby enabling a more complete understanding of the sources of variation underlying social interactions. In contrast, marginal models can bias the estimation and interpretation of genetic components, as the aggregated genetic variance may be confounded with other variance components due to the aggregation of dyadic traits. Marginal models may also lead to overestimation of social group and residual variance. These results can provide useful guidance for choosing appropriate modeling strategies for social interaction traits.

genetics↗

bioRxiv2026

Genetic analysis of maize seedling root traits under chilling highlights their importance for early field development

Characterizing the genetic basis of root system architecture and its role in early plant development is essential for developing maize varieties with improved nutrient uptake, enhanced early vigour, and higher yield potential in temperate regions. Landraces represent an invaluable source of allelic diversity that can be leveraged to enrich the genetic basis of modern breeding material. In this study, we used a high throughput phenotyping platform to characterize genetic variation for seedling root traits under chilling conditions relevant for early plant establishment in a large doubled haploid (DH) library derived from two European maize landraces. We dissected the quantitative genetic architecture of twelve seedling root traits using a haplotype-based genome-wide association study, identifying large-effect haplotypes specific to the individual landraces as well as numerous small-effect haplotypes present in both landraces. We validated the effects of four QTL in a biparental population, demonstrating their stability across genetic backgrounds. We found highly significant correlations between haplotype effects on seedling root traits evaluated in the phenotyping platform and early plant height evaluated in multi environment field trials, demonstrating the relevance of seedling root architecture for early plant establishment. In particular, haplotypes associated with seminal and lateral root length were the major determinants of early plant height under field conditions. Several of the haplotypes increasing seedling root length were absent from a broad panel of flint breeding lines, highlighting their potential as targets for introgression to improve early plant establishment under temperate growing conditions. Key messageSeedling root QTL discovered in a high throughput phenotyping platform under chilling conditions influence early plant development in the field.

genetics↗

bioRxiv2026

Revising the genetic and epigenetic architecture of in vitro regeneration capacity in natural Arabidopsis thaliana populations

Plant regeneration is a dynamic developmental process that spans from cell dedifferentiation to organ reconstruction in response to inductive cues, such as wounding stress and hormonal signals. Although this capacity varies widely both between and within species, a comprehensive understanding of the genetic and epigenetic bases of this variation remains incomplete. To address this issue, we revisited published datasets on natural variation in in vitro regeneration capacity in Arabidopsis thaliana. Using quantitative genetic approaches, including meta-analyses of genome-wide association studies (GWAS) and multi-locus models, we dissected the genetic architecture underlying regeneration traits. Our results showed that shoot regeneration capacity is primarily explained by allelic variation in the cis-regulatory region of WUSCHEL (WUS), a key regulator of shoot meristem formation. Notably, these polymorphisms are also associated with epigenetic variants of the DNA transposon ATDNA2T9C, which is located within the regulatory region. Furthermore, allelic variation in ARABIDOPSIS RESPONSE REGULATOR 2 (ARR2), a positive regulator of cytokinin signaling, is associated with callus formation and greening traits and may promote shoot formation through genetic interactions with WUS alleles. Although in vitro regeneration is controlled by complex, multilayered gene regulatory networks, our results suggest that, in A. thaliana, natural variation in regeneration capacity is largely shaped by a small number of major-effect modifiers together with epigenetic variation and genetic interactions, despite the substantial heterogeneity observed among natural populations.

genetics↗

bioRxiv2026

Primitive GLMY Homology: An Algebraic Topology Approach for the Quantitative Characterization of Graph Pangenomes toward Population Genetic Analysis

A central task in population genetics is to identify genetic diversity in a population containing a number of individuals. In recent years, with the development of the third generation sequencing (TGS) technology, pan-genome research has become a hot topic. Although graphical representation has been a popular way to represent the pangenome, few works have attempted to describe it in a more mathematical way. In this paper, we used 79 high-quality assembly data of third-generation sequencing in yeast (includingSaccharomyces cerevisiae and Saccharomyces paradoxus) to construct the graph pangenome, and introduced the Primitive GLMY (Grigoryan-Lin-Muranov-Yau) Homology in algebraic topology to quantitatively represent the pan-genome. We further made an intriguing attempt to conduct a population genetic analysis of this resulting dataset from the topological features of the graph pangenome. We found that there was good agreement between the obtained results and the biological context. We believe this study has developed a method for population genetic analysis of the genetic diversity of genome structural variation.

genetics↗

bioRxiv2026

Population Genetic Structure of Ariolimax columbianus around Corvallis, Oregon, USA

Urbanization has been previously shown to affect evolution of plants and animals by restricting gene flow, increasing genetic drift, and causing divergent selection between rural and urban populations, however, the effect of urbanization on terrestrial gastropod evolution has only been minimally researched. Most research on terrestrial gastropods primarily focusing on invasive pest species, and little attention is given to native species like Ariolimax columbianus (Pacific banana slug). There is no current published research on the phylogeography of A. columbianus. In this study, surface epithelial cells from 66 Ariolimax columbianus individuals were collected from 11 locations around Corvallis, Oregon, and one site in northern California. These samples were amplified and sequenced at two loci: cytochrome oxidase 1 (CO1) and the internal transcribed spacer 2 (ITS-2). This data was used to generate maximum-likelihood phylogenetic trees to better understand the population genetics of these local native gastropods. The CO1 phylogenetic analysis showed two major haplotypes around the city of Corvallis - northwestern and southern, while the ITS-2 phylogenetic analysis showed three general haplotypes around the city - northern, western, and southern. The results in this study show the presence of genetic breaks between many of these populations, possibly due to a combination of factors including anthropogenic fragmentation, natural barriers, and the low active dispersal ability of A. columbianus. However, the extent that each of those factors has on disrupting gene flow and explaining patterns of genetic variation in this species requires further research. The present study acts as a foundation for the development of future research on banana slug phylogenetics and population genetic structure.

genetics↗

bioRxiv2026

Genetic mapping of a spontaneous short-grain mutation reveals a novel loss-of-function allele of SRS3 in rice

Spontaneous mutations are a rare but important source of novel genetic variation, yet their detection and characterization within active breeding programs are seldom documented at gene-level resolution. Grain size and shape are key determinants of rice quality, yield, and market classification. Here, we report the discovery and genetic characterization of a spontaneous short-grain (SG) mutation arising in the long-grain wild-type (WT) advanced breeding line RU2002174 from the LSU AgCenter Rice Breeding Program. The SG phenotype was first observed in 2019 and segregated in subsequent generations as a single recessive gene across both indica and japonica genetic backgrounds. Genetic mapping localized the mutation to a 41.6 kb interval on chromosome 5. Whole-genome sequencing identified a single candidate causal variant: a G[->]T transversion in exon 4 of SRS3 (Os05g06280), introducing a premature stop codon and resulting in a truncated protein. This allele was absent from representative U.S. breeding germplasm and the IRRI 3K SNP database, demonstrating that it represents a novel spontaneous loss-of-function allele of a previously characterized grain-size gene. These findings document the real-time emergence of functional genetic variation in elite rice germplasm and highlight the importance of monitoring off-types during seed increase and purification in breeding programs. They also provide additional insight into the role of kinesin-mediated cell elongation in determining rice grain architecture.

genetics↗

bioRxiv2026

Genetic Diversity and Population Structure of Maize Doubled Haploid Lines from Drought and Low Nitrogen Tolerant Populations

Understanding the genetic diversity and population structure of breeding materials is essential for developing stress-resilient cultivars. In tropical maize, where drought and low soil nitrogen (low N) severely limit productivity, continuous development of tolerant varieties remains a priority. This study assessed the genetic diversity and population structure of 250 doubled haploid lines (DHLs) derived from five drought- and low N-tolerant tropical populations. Genotyping was performed using mid-density DArTseq markers, yielding 3,305 high-quality SNPs for analysis. Results revealed a moderate level of diversity among the DHLs, with an average genetic distance of 0.39, a polymorphism information content (PIC) of 0.33, and a minor allele frequency (MAF) of 0.29. These values reflect substantial allelic variation, important for identifying complementary parental combinations in hybrid development. Discriminant analysis of principal components (DAPC) grouped the DHLs into five distinct clusters, largely corresponding to their source populations, although some admixture was observed. This indicates that while the genetic backgrounds of the source populations were mostly retained, recombination introduced useful variation. Overall, the clear population structure and high diversity observed among these DHLs provide a strong genetic foundation for future maize improvement. These lines represent valuable resources for heterotic group formation, hybrid development, and recurrent selection schemes aimed at enhancing drought and low nitrogen tolerance in tropical maize.

genetics↗

bioRxiv2026

Genetics of Cocaine Consumption and Preference in Drosophila melanogaster

Cocaine Use Disorder (CUD) poses a significant public health and socioeconomic challenge. Determining the genetic basis of predisposition for development of CUD is challenging in human populations but can be studied in Drosophila. We assessed cocaine consumption and cocaine preference of 74,875 flies from 598 sequenced, wild-derived, inbred lines from the expanded Drosophila melanogaster Genetic Reference Panel (DGRP3). We found significant genetic variation, sexual dimorphism, and genetic variation in sexual dimorphism for these traits. Whereas most lines showed cocaine avoidance, ~10% of the lines showed innate cocaine preference in at least one sex. Genome-wide association analyses for cocaine consumption, preference, and micro-environmental variance of these traits identified 2,155 polymorphisms in/near 866 genes that were enriched for Gene Ontology terms associated with neurogenesis, development, and behavior. Many of the associated genes had human orthologs with known associations with CUD and other substance use disorders as well as psychiatric and behavioral traits. We confirmed causal associations with cocaine preference for three polymorphisms with large effect sizes by assessing their effects in DGRP3 lines not included in the initial association analyses. Pairwise associations between these polymorphisms exhibited suppressing epistasis. These polymorphisms are in genes with human orthologs that fulfill essential functions in the nervous system, including the glucose transporter SLC2A8; KCNC2, a subunit of the voltage gated potassium channel; and CHRNA7, a nicotinic cholinergic receptor subunit. Thus, studies on Drosophila can provide insights into the genetic and neural mechanisms of CUD.

genetics↗

bioRxiv2026

Unmasking genetic load: Genomic inbreeding drives growth depression in captive critically endangered Chinese Bahaba (Bahaba taipingensis)

Chinese bahaba (Bahaba taipingensis) is a critically endangered marine fish that has been commercially extinct in the wild. Conservation-oriented captive breeding has become an effective strategy for rescuing such endangered species, but concerns about inbreeding depression often remain. Here, after merely two generations of closed breeding from 18 wild founders, Chinese bahaba exhibited severe growth depression, with body length and weight diverging by more than three-fold. To further investigate the early genomic consequences of captive breeding, we analyzed whole-genome sequences from 348 F2 individuals together with 19 wild individuals from the same marine region. While genome-wide genetic diversity was overall preserved, closed breeding rapidly partitioned the F2 population into eight distinct genetic lineages. A significant elevation in genomic inbreeding was observed to facilitate the homozygous exposure of recessive deleterious mutations, which was strongly correlated with growth decline. An integrative framework combining GWAS, gene-level burden test, and ROH hotspots was applied to dissect the genetic architecture underlying growth decline, which converged predominantly on skeletal scaffolding and immune regulation. This was evidenced by candidate genes related to skeleton development and homeostasis (e.g. fam20b, c-fos, trpv5, and il23r), the GH/IGF axis (e.g. socs1a), and immune/inflammatory pathways (e.g. il23r, nlrp7, cd163, il12rb2), as well as calcium ion transport pathway. Together, our findings provide novel insights into the genomic consequences and genetic architecture of growth decline under captive conditions in Chinese bahaba, and offer critical guidance for genetic management in captive conservation programs of endangered species.

genetics↗

bioRxiv2026

BATOseq-PE: A public batoid DNA library with the first molecular insights into the cryptic diversity, genetic health, and management of Peruvian marine rays

Batoids (rays, skates, and relatives) are among the most threatened cartilaginous fishes globally, yet the molecular diversity of Peruvian taxa remains poorly evaluated. Furthermore, regional barcode sequences for high-conservation-priority taxa, such as sawfish, manta, and devil rays, are often restricted to private records, hindering essential phylogeographic and population structure assessments. To bridge this gap, we developed BATOseq-PE, the first public genetic reference library for Peruvian marine batoids, covering 14 species sequenced in vitro from local specimens, complemented by a novel in silico assembled mitogenome for Notoraja martinezi. This open-access repository contributes 73 novel COI barcodes, providing robust taxonomic resolution across 15 molecular operational taxonomic units (MOTUs) and Barcode Index Numbers (BINs). Notably, we provide the first Peruvian public records for high-priority species such as Mobula munkiana, Mobula thurstoni, Myliobatis peruviana, Rostroraja velezi, and the first global public barcodes for N. martinezi and Zapteryx xyster. By coupling BATOseq-PE with global datasets, we conducted the first multi-taxa screening for delimitation and phylogeographic assessments on Peruvian batoids, revealing a cryptic lineage within R. velezi and genetic connectivity patterns suggesting female philopatry in Mobula mobular. Finally, by integrating nucleotide diversity into a Genetic Diversity Risk Indicator (GDRI) alongside ecological and fishery data, we identified an alarming trend where heavy fishing pressure overlaps with extinction risk and depleted genetic diversity, allowing us to suggest data-driven, tailored management strategies. BATOseq-PE represents a valuable resource to accelerate taxonomic and population assessments, ultimately fostering ray conservation through the integration of genetic frameworks into fishery management.

genetics↗

bioRxiv2026

Genetic diversity of endangered Acropora spp. corals in Bonaire: implications for restoration and gene banking

Species restoration is a valuable tool to combat biodiversity loss. However, maintaining genetic diversity in species restoration is challenging, particularly for species that can reproduce asexually, such as plants and corals, because a seemingly diverse collection of individuals could be composed of many clones of a few genotypes. Caribbean elkhorn and staghorn corals (Acropora palmata, A. cervicornis) are critically endangered reef-building corals that are a major target for restoration. To better understand the genetic diversity of an Acropora spp. restoration program and interpret local population genetic structure, we conducted microsatellite genotyping on the gene banks of 35 A. palmata lineages and 25 A. cervicornis lineages maintained by Reef Renewal Foundation Bonaire (RRFB) in the Caribbean Netherlands. We found that RRFB had high genotypic richness for A. palmata (0.971) and A. cervicornis (1.0) and estimated that they captured 88.9% and 74.7% of Bonaires microsatellite asymptotic allelic diversity, respectively. Compared to populations of Acropora spp. studied in other locations across the Caribbean, A. palmata in Bonaire had relatively low expected heterozygosity, while A. cervicornis was greater than approximately half of other populations. Across Bonaire and for both coral species, we did not find evidence for genetic structuring among spatially separated subpopulations, indicating that both species are likely well-connected around the island. Together, these results demonstrate the effectiveness of RRFBs strategies to capture high genetic diversity and can be used to inform future initiatives on coral sexual breeding and assisted gene flow beyond Bonaire.

genetics↗

bioRxiv2026

GxE and changes to the genetic architecture of flowering time in an overwintering environment

Characterizing how the expression of genetic variation changes across environments is essential for understanding evolution in complex environments, the evolution of phenotypic plasticity, and the genetic architecture of adaptation. We investigated how the phenotypic distribution, large-effect loci, and polygenetic architecture of flowering time in Arabidopsis thaliana changes when grown in an ecologically realistic environment compared to standard chamber conditions. We grew 479 A. thaliana accessions in an overwintering common garden that have previously been phenotyped in growth chambers by the 1001 Genomes Project (2016). Our findings suggest there is extensive GxE for flowering time between the overwintering common garden and the growth chamber environments. None of the large effect loci that we identified using a multivariate Genome Wide Association Study (GWAS) were shared across growth conditions. We find evidence of allelic differential sensitivity, conditional neutrality, and antagonistic pleiotropy contributing to GxE for flowering time between growth conditions. Our results also suggest that the effects of genetic variation across multiple flowering time regulatory pathways is revealed when grown in a more ecologically realistic environment. The effect sizes for the most significant 1% of SNPs are moderately correlated between the outdoor and growth chamber conditions which indicates a partially shared genetic basis. Overall, our findings highlight how making inferences about the genetic basis and evolution of complex traits may be dependent on conducting experiments in ecologically realistic environments.

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