Biology subjects

Fiscus, C. J.

Publications and source records attributed to Fiscus, C. J..

5 recordsLinked to original sources

bioRxiv2024

Quantifying evolution of SNPs that affect RNA secondary structure in Arabidopsis thaliana genes

Single-stranded RNA molecules can form intramolecular bonds between nucleotides to create secondary structures. These structures can have phenotypic effects, meaning mutations that alter secondary structure may be subject to natural selection. Here we examined the population genetics of these mutations within Arabidopsis thaliana genes. We began by identifying derived SNPs with the potential to alter secondary structures within coding regions, using a combination of computational prediction and empirical data analysis. We identified 8,469 such polymorphisms, representing a small portion ([~]0.024%) of sites within transcribed genes. We examined nucleotide diversity and allele frequencies of these "pair-changing mutations" (pcM) in 1,001 A. thaliana genomes. The pcM SNPs at synonymous sites had an 13.4% reduction in nucleotide diversity relative to non-pcM SNPs at synonymous sites and were found at lower allele frequencies. We used demographic modeling to estimate selection coefficients, finding selection against pcMs in 5 and 3 untranslated regions. Previous work has shown that some pcMs affect gene expression in a temperature-dependent matter. We explored associations on a genome-wide scale, finding pcMs exist at higher population frequencies in colder environments, as do non-PCM alleles. Derived pcM mutations have a small but significant relationship to transcript abundance, however; alleles containing pcMs had an average reduction in expression of 137.4 normalized counts compared to genes with conserved ancestral secondary structure (mean expression = 3215.7 normalized counts). Overall, we document selection against derived pcMs in UTRs but with limited evidence for selection against derived pcMs at synonymous sites.

genomics↗

bioRxiv2024

Climate, population size, and dispersal influences mutational load across the landscape in Vitis arizonica

The interplay between genetics and the environment determines a populations ability to survive. Plants, being immobile, are particularly vulnerable to environmental shifts and must adapt to their local environment or face extinction. While considerable efforts have been devoted to identifying adaptive genetic variation and to model its relationship with climate, the role of deleterious variation has been largely overlooked. To address this gap, we studied the landscape genomics of Vitis arizonica, a grape species endemic to the American Southwest and a crop wild relative of the domesticated grapevine. We estimated mutational load, a component of genetic load, in 162 individuals sampled across the present species range and built temporal species distribution models (SDMs) to project the historical, present, and future distributions of V. arizonica to infer species range dynamics. Mutational load was highest for individuals at an inferred leading edge of range expansion. Using random forest regression (RF) models, we examined the relationship between mutational load and climatic variation. The RF models, which we transformed by a weighting method to account for correlated predictors, identified climatic variables, historical dispersion distances, and heterozygosity as high-ranking features. Our findings show that mutational load can be predicted and identifies features that contribute to load. These results provide a foundation for integrating mutational load into broader efforts to understand species adaptation and maladaptation in the face of climate change. SIGNIFICANCE STATEMENTThe accumulation of deleterious genetic variation (i.e., genetic load) in a genome can reduce organismal fitness and hinder adaptation to local conditions. While the genetic mechanisms contributing to genetic load have been well-studied, its interaction with environmental variation is less understood. Here we explored the relationship between climatic variation, species range, and genetic load in Vitis arizonica, a wild grape species native to the American Southwest. We identified associations between climatic variation and genetic load and built a machine learning model to predict genetic load under future climate scenarios. Our findings suggest that the species range will expand and that genetic load will slightly increase at the population level by the end of the century. This work enhances our understanding of the environmental factors influencing genetic load.

evolutionary biology↗

bioRxiv2023

The pattern of genetic variability in a core collection of 2,021 cowpea accessions

Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the worlds largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations origining in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA cowpea core collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.

genetics↗

bioRxiv2023

Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley

Direct observation is central to our understanding of the process of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. Here, we observe genetic and phenotypic evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 with tens of thousands of unique genotypes and has been adapted to local conditions in Davis, CA, USA for 58 generations. We find that natural selection has massively reduced genetic diversity leading to a single clonal lineage constituting most of the population by generation F50. Selection favored alleles originating from similar climates to that of Davis, and targeted genes regulating reproductive development, including some of the most well-characterized barley diversification loci, Vrs1, HvCEN, and Ppd-H1. We chronicle the dynamic evolution of reproductive timing in the population and uncover how parallel molecular pathways are targeted by stabilizing selection to optimize this trait. Our findings point to selection as the predominant force shaping genomic variation in one of the worlds oldest ongoing biological experiments. One-Sentence SummaryWholesale genetic restructuring of an experimental population is a consequence of rapid environmental adaptation.

genetics↗

bioRxiv2021

A KARRIKIN INSENSITIVE2 paralog in lettuce mediates highly sensitive germination responses to karrikinolide

Karrikins (KARs) are chemicals in smoke that can enhance germination of many plants. Lactuca sativa cv. Grand Rapids (lettuce), germinates in the presence of nanomolar karrikinolide (KAR1). We found that lettuce is much less responsive to KAR2 or a mixture of synthetic strigolactone analogs, rac-GR24. We investigated the molecular basis of selective and sensitive KAR1 perception in lettuce. The lettuce genome contains two copies of KARRIKIN INSENSITIVE2 (KAI2), a receptor that is required for KAR responses in Arabidopsis thaliana. LsKAI2b is more highly expressed than LsKAI2a in dry achenes and during early stages of seed imbibition. Through cross-species complementation assays in Arabidopsis we found that LsKAI2b confers robust responses to KAR1, but LsKAI2a does not. Therefore, LsKAI2b likely mediates KAR1 responses in lettuce. We compared homology models of the ligand-binding pockets of KAI2 proteins from lettuce and a fire follower, Emmenanthe penduliflora. This identified pocket residues 96, 124, 139, and 161 as candidates that influence the ligand-specificity of KAI2. Further support for the significance of these residues was found through a broader comparison of pocket residue conservation among 324 asterid KAI2 proteins. We tested the effects of substitutions at these four positions in Arabidopsis thaliana KAI2 and found that a broad array of responses to KAR1, KAR2, and rac-GR24 could be achieved.

plant biology↗