Biology subjects

Moyers, B. T.

Publications and source records attributed to Moyers, B. T..

5 recordsLinked to original sources

bioRxiv2026

LEAPING A CONSERVATION GENETICS GAP: COMBINING POPULATION GENETICS AND SOCIAL NETWORK ANALYSIS FOR LUPINUS PERENNIS RESTORATION

Genomic data can assist conservation planning, but implementation of genetic-based recommendations is rare. Closing this "conservation genetics gap" is crucial for restoration and translocation decisions, particularly for highly fragmented ecosystems like pine barrens. We first analyze the conservation genetics gap in pine barren management organizations using a survey. We then analyze whole-genome data to characterize population structure and diversity in the pine barren keystone plant Lupinus perennis. We find little genetic difference among L. perennis populations in the Northeast United States. While populations show signs of isolation by distance (rho = 0.785, p = 0.001), we find no correlation between population size and heterozygosity (Estimate = 0.003, p = 0.357) or inbreeding (Estimate = 0.028, p = 0.416). We also find no effect of seed source population on forecasted effective population size in restoration simulations. These findings and our recommendation that managers consider non-local seed provenancing for L. perennis restorations in the Northeast have been integrated into SWAP policy in two states. We generally recommend practitioners record seed provenance, save genetic material for future testing, and incorporate fitness metrics into restoration monitoring. To effectively close the conservation genetics gap, researchers providing conservation recommendations must consult with practitioners before designing experiments.

genomics↗

bioRxiv2025

Pleiotropy and facilitation of local adaptation in the silverleaf sunflower Helianthus argophyllus

Local adaptation drives changes in population phenotypes that confer survival or increased reproduction in certain environments. Local adaptation may be hindered or facilitated by pleiotropy, which is the control of multiple traits by a single genetic locus. In this study, we explored the connections between pleiotropy and local adaptation in the Texas endemic silverleaf sunflower, Helianthus argophyllus. Populations of H. argopyllus exhibit a bimodal life history strategy, consisting of tall, late-flowering forms and short, early-flowering forms that occur in close geographic proximity. The expression of life history traits within H. argophyllus populations is linked to local adaptation and controlled by a highly pleiotropic locus. Still, we do not know how local adaptation and pleiotropy interact at the transcriptomic level. We identified putatively locally adapted genes using whole RNA sequencing data and two selection outlier approaches. We assessed transcriptomic pleiotropy by evaluating whether allelic variants within genes control the expression of other genes (an eQTL approach) and gene co-expression network connectivity. Our results show that candidate locally adaptive genes identified by both methods are enriched for eQTL loci. Candidate genes identified through associations with environmental variables exhibit modular expression and have significantly lower network connectivity than non-adapted genes. In contrast, candidate genes identified only by controlling for population structure have significantly higher network connectivity. Our results suggest that the role of pleiotropy in local adaptation, at least at the transcriptomic level, depends on the function of the specific loci under selection. Author SummaryThis study investigates how genes contribute to local adaptation in Helianthus argophyllus, a sunflower species with distinct ecotypes. Using transcriptomic data and two methods involving environmental association and population structure analysis, we found that adaptive genes can be categorized into two types: pleiotropic "hub" genes, which affect multiple traits, and modular genes, which affect fewer, more specific traits. Environment-associated genes tended to be modular, while population-structure-associated genes were more pleiotropic. These patterns support a dynamic model of adaptation, where pleiotropy is beneficial early in adaptation and modularity becomes increasingly crucial as populations refine their traits. The findings provide new insights into how gene network architecture influences evolutionary responses to environmental change, particularly in diverging populations, such as those of H. argophyllus.

evolutionary biology↗

bioRxiv2022

Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought

Crop adaptation is required to sustainably increase the rate of yield gains to meet projected future needs under the challenging conditions of climate change and competition for resources. Future adaptation will likely need to harness both highly polygenic traits and genotype-by-environment interactions (GxE), the study of which is aided by complex recombinant populations. We used the diverse Oryza sativa Global Multiparent Advanced Generation InterCross (MAGIC) population to study the genetic architecture and contributions of seedling emergence, establishment, and development to yield components under dry-direct seeding and seedling stage drought across three growing seasons. Dry-direct seeding is an establishment practice that has the potential to reduce methane emissions, water use, and labor demands for rice farmers, but increases the possibility of early-season drought conditions. We found substantial evidence for large roles of environmental variation and GxE in controlling trait variation. Maintenance of shoot growth during seedling stage drought was positively correlated with crown root number and both directly and indirectly influenced agronomic traits. Other than the major green revolution locus sd1, most allelic effects were conditionally neutral (affecting trait values in some environments but not others) and most alleles had their strongest effect in an environmental extreme. This discovery is both a challenge and a potential opportunity: with variable genetic architecture, selection in any one environment may not result in stable trait gains across environments. However, conditionally neutral GxE is a potential route to sustainable yield stability through allele pyramiding.

genetics↗

bioRxiv2020

Scanning the rice Global MAGIC population for dynamic genetic control of seed traits under vegetative drought.

Grain size and weight are important yield components in rice (Oryza sativa L.). There is still uncertainty about the genetic control of these traits under drought stress, the most pressing emerging issue in many rice cultivation areas. To address this lack of knowledge, we investigated the genetic architecture of seed size, shape, and weight using the rice Global Multi-parent Advanced Generation Intercross (MAGIC) population, grown under well-watered and vegetative drought conditions. We measured variation in seed size and shape with a new high-throughput phenotyping method based on a desktop scanner and the open-source package Plant Computer Vision (PlantCV). Besides being affordable, rapid, and accurate, our method captured the phenotypic divergence between drought and well-watered samples, expressed as 12 different traits that include traditional size metrics and new grain shape measures. Overall, under water deficit, the MAGIC lines produced smaller and shorter seeds. We identified ten MAGIC lines with traits that make them good candidates for the release of rice cultivars with high yield potential under vegetative drought stress. We ran a marker-trait association analysis for the measured seed-related traits. Most of the identified marker-trait associations showed strong genotype-by-environment interactions (GxE), with most allele effects being conditionally neutral. These results suggest dynamic genetic control of seed size, shape, and weight under vegetative drought stress in rice, highlighting the importance of understanding the contribution of GxE interactions on trait variation to develop resilient and high-yielding rice varieties. Our study confirms that combining low-cost and high-throughput phenotyping strategies with a diverse genetic material suited for multi-environmental trial provides solutions for adapting rice cultivation to current and future environmental adversities.

plant biology↗

bioRxiv2017

Genetic costs of domestication and improvement

The cost of domestication hypothesis posits that the process of domesticating wild species can result in an increase in the number, frequency, and/or proportion of deleterious genetic variants that are fixed or segregating in the genomes of domesticated species. This cost may limit the efficacy of selection and thus reduce genetic gains in breeding programs for these species. Understanding when and how deleterious mutations accumulate can also provide insight into fundamental questions about the interplay of demography and selection. Here we describe the evolutionary processes that may contribute to deleterious variation accrued during domestication and improvement, and review the available evidence for the cost of domestication in animal and plant genomes. We identify gaps and explore opportunities in this emerging field, and finally offer suggestions for researchers and breeders interested in understanding or avoiding the consequences of an increased number or frequency of deleterious variants in domesticated species.

evolutionary biology↗