Biology subjects

Rojas-Gutierrez, J. D.

Publications and source records attributed to Rojas-Gutierrez, J. D..

4 recordsLinked to original sources

bioRxiv2026

Environment-dependent and often antagonistic effects of dominance and epistasis on heterosis in crosses between natural populations

Genetic drift in natural populations reduces the efficacy of selection, promoting the fixation of deleterious recessive alleles with consequences for maladaptation and population persistence. Heterosis, or increased F1 fitness relative to the parental mean, has been proposed as a tool for investigating the role of drift on genetic variation in fitness, but its genetic basis and environmental dependence remain unclear in natural populations. We used heterozygous near-isogenic lines (NILs) derived from a cross between locally adapted Arabidopsis thaliana ecotypes to assess how specific genomic regions influence heterosis. Cumulative fitness, estimated as fruits per seedling, was evaluated in a greenhouse and two simulated native environments. There was strong overall heterosis in the greenhouse and one simulated environment. Non-additive effects in heterozygous NILs were highly environment- and background-dependent, varying in magnitude and sign, and no NIL had consistent effects across environments. The relative fitness of heterozygous NILs was not correlated with gene number or genomic load in the introgressed regions. Small heterozygous regions often had large effects, indicating that complementation of mildly deleterious alleles alone does not fully explain heterosis. Evidence of epistasis was also observed, including outbreeding depression in some NILs, likely due to negative additive-by-dominance interactions. Summed effects of individual heterozygous genomic regions often exceeded the fitness increase of the F1 suggesting dominance-by-dominance epistasis, but the direction of these epistatic effects depended on both genetic background and environment. Our results demonstrate that F1 fitness reflects both positive dominance and different epistatic interactions that are environment- and background-dependent.

evolutionary biology↗

bioRxiv2025

A panel of near-isogenic lines derived from locally adapted populations of a wild plant: A powerful tool for dissecting additive and non-additive effects on ecologically important traits

Identifying and estimating the effects of loci contributing to natural variation in ecologically important traits can be hampered by quantitative inheritance, dominance, epistasis, and environmentally dependent trait expression. Here we announce the availability of germplasm and sequence data for a reciprocal panel of near-isogenic lines (NILs) derived from locally adapted natural populations of Arabidopsis thaliana, for investigating the genetic basis of ecologically important traits. We created a panel of 54 NILs and performed whole genome sequencing to precisely locate introgression segments(s) in each NIL. Deep sequencing largely confirmed prior knowledge of NIL genotypes but also identified multiple novel small introgressions and regions of residual heterozygosity. To illustrate the utility of this panel, we identified genomic regions underlying ecotypic differences in flowering time in a laboratory common garden experiment. We detected strong additive effects on flowering time in multiple NILs with segments at the top of chromosome 5 implicating the floral regulator FLC, as expected based on previous quantitative trait locus studies. We also detected novel and complex contributions to ecotypic differences in flowering time, only visible in the NILs, suggesting the possibility of epistasis. Our results highlight the utility of this panel for dissecting the genetic architecture of ecologically important traits, including the future potential for fine mapping of additive effects and testing for epistasis and linkage using NILs derived from the panel. This panel can be used by any member of the research community to investigate any of a broad suite of traits for which the parents differ.

evolutionary biology↗

bioRxiv2024

Heterosis in crosses between remnant populations of a rare prairie forb: implications for restoration genetics

PremiseCalls to adopt seed sourcing strategies in biological restoration that preserve local adaptation while maximizing genetic variation (e.g., regional admixture provenancing) are increasingly common. Heterosis, the increased fitness of progeny from between-relative to within-population crosses, could provide an added benefit under such strategies, but several open questions remain. MethodsWe quantified heterosis in crosses between three small remnant populations of the rare prairie forb Silene regia. We measured early fitness components (seed number per fruit, germination, and juvenile survival) in a greenhouse. Adult fitness components (survival and reproduction) were quantified over two flowering seasons in two different environments: a field experiment simulating the initial stages of a restoration, and a greenhouse. Our approach is unique in estimating heterosis in an environment most relevant to the early stages of a restoration and in comparing heterosis under field and controlled conditions. Key ResultsThe consequences of between-population crosses for cumulative fitness in the field were strongly positive in two of the populations (281% and 50% heterosis) and nearly neutral in a third. Heterosis was generally stronger when measured under field conditions, and stage specific patterns of heterosis varied among populations. ConclusionsRegional admixture provenancing in restorations should be beneficial for this species. We advocate for more research on heterosis in rare species, particularly in restorations. We also provide a cautionary note on how to calculate and report results for heterosis studies.

evolutionary biology↗

bioRxiv2023

Inbreeding depression, heterosis, and outbreeding depression in the cleistogamous perennial Ruellia humilis

What maintains mixed mating is an evolutionary enigma. Cleistogamy, the production of both potentially outcrossing chasmogamous, and obligately selfing cleistogamous flowers on the same individual plant, is an excellent system to study the costs of selfing. Inbreeding depression can prevent the evolution of greater selfing within populations, and heterosis in crosses between populations may further tip the balance in favor of outcrossing. Few empirical estimates of inbreeding depression and heterosis in the same system exist for cleistogamous species. We investigate the potential costs of selfing by quantifying inbreeding depression and heterosis in three populations of the cleistogamous perennial Ruellia humilis Nutt (Acanthaceae). We performed hand-pollinations to self, and outcross within and between populations, and measured seed number, germination, total flower production, and estimated cumulative fitness for the resulting progeny in a greenhouse experiment. We found moderate inbreeding depression for cumulative fitness (<30%) in two populations, but outbreeding depression for crosses within a third population (-26%). For between population crosses, there was weak to modest heterosis (11-47%) in two of the population combinations, but modest to strong outbreeding (-21 to -71%) depression in the other four combinations. Neither inbreeding depression nor heterosis was of sufficient magnitude to explain the continued production of CH flowers given the relative energetic advantage of CL flowers previously estimated for these populations. Outbreeding depression either within or between populations makes the maintenance of chasmogamous flowers even harder to explain. More information is needed on the genetic basis of cleistogamy in order to resolve this conundrum.

evolutionary biology↗