Joshua A. Banta

Genome-Wide Patterns of Arabidopsis Gene Expression in Nature

Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ∼110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PCveg) correlate to temperature and precipitation occurrence in the field. The largest PCveg axes included thermoregulatory genes while the second major PCveg was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild.

Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture

Significance Species display a range of plastic phenotypes that presumably have evolved as a result of adaptation to heterogeneous environments. We asked whether the genetic mechanisms that underlie adaptation across populations also determine the response of an individual plant to environmental cues in Arabidopsis. Using an integrative root phenotyping approach, genes that underlie natural variation in root architecture across populations were shown to control plasticity responses within an individual. Together, our results uncover a genetic mechanism underlying the phenotypic plasticity of an individual and phenotypic diversity across natural variants. Phenotypic plasticity is presumed to be involved in adaptive change toward species diversification. We thus examined how candidate genes underlying natural variation across populations might also mediate plasticity within an individual. Our implementation of an integrative “plasticity space” approach revealed that the root plasticity of a single Arabidopsis accession exposed to distinct environments broadly recapitulates the natural variation “space.” Genome-wide association mapping identified the known gene PHOSPHATE 1 (PHO1) and other genes such as Root System Architecture 1 (RSA1) associated with differences in root allometry, a highly plastic trait capturing the distribution of lateral roots along the primary axis. The response of mutants in the Columbia-0 background suggests their involvement in signaling key modulators of root development including auxin, abscisic acid, and nitrate. Moreover, genotype-by-environment interactions for the PHO1 and RSA1 genes in Columbia-0 phenocopy the root allometry of other natural variants. This finding supports a role for plasticity responses in phenotypic evolution in natural environments.

Plasticity regulators modulate specific root traits in discrete nitrogen environments.

Plant development is remarkably plastic but how precisely can the plant customize its form to specific environments? When the plant adjusts its development to different environments, related traits can change in a coordinated fashion, such that two traits co-vary across many genotypes. Alternatively, traits can vary independently, such that a change in one trait has little predictive value for the change in a second trait. To characterize such “tunability” in developmental plasticity, we carried out a detailed phenotypic characterization of complex root traits among 96 accessions of the model Arabidopsis thaliana in two nitrogen environments. The results revealed a surprising level of independence in the control of traits to environment – a highly tunable form of plasticity. We mapped genetic architecture of plasticity using genome-wide association studies and further used gene expression analysis to narrow down gene candidates in mapped regions. Mutants in genes implicated by association and expression analysis showed precise defects in the predicted traits in the predicted environment, corroborating the independent control of plasticity traits. The overall results suggest that there is a pool of genetic variability in plants that controls traits in specific environments, with opportunity to tune crop plants to a given environment.

Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS.

The onset of flowering, the change from vegetative to reproductive development, is a major life history transition in flowering plants. Recent work suggests that mutations in cis-regulatory mutations should play critical roles in the evolution of this (as well as other) important adaptive traits, but thus far there has been little evidence that directly links regulatory mutations to evolutionary change at the species level. While several genes have previously been shown to affect natural variation in flowering time in Arabidopsis thaliana, most either show protein-coding changes and/or are found at low frequency (<5%). Here we identify and characterize natural variation in the cis-regulatory sequence in the transcription factor CONSTANS that underlies flowering time diversity in Arabidopsis. Mutation in this regulatory motif evolved recently and has spread to high frequency in Arabidopsis natural accessions, suggesting a role for these cis-regulatory changes in adaptive variation of flowering time.

An assessment of the molecular mechanisms contributing to tolerance to apical damage in natural populations of Arabidopsis thaliana

Herbivory imposes substantial selection pressure on plants, with the ability to regrow and maintain reproductive success a challenging but often necessary response by the plant. Despite the commonness of herbivore-induced damage, vast variation in tolerance ability exists among plants. Recent studies have suggested the role of endoreduplication (increasing ploidy within an individual) and the pentose phosphate pathway (a metabolic pathway that supports both primary and secondary metabolism) in contributing to the variation in tolerance ability among genotypes of Arabidopsis thaliana. We measured natural variation in apical meristem damage frequency, endoreduplication, and the sequence of G6PD1, an important gene in the pentose phosphate pathway, and related them to variation in tolerance of natural populations of A. thaliana over a portion of its native European range. Variation among populations in tolerance was significantly positively related to damage frequency, suggesting the potential for directional selection for tolerance ability as a product of damage frequency. We also discovered likely loss-of-function G6PD1 alleles in two populations, both of which displayed among the lowest levels of tolerance of all populations assessed. In addition, populations with the greatest increase in endopolyploidy also had the greatest ability to tolerate damage while populations with the greatest reduction in endopolyploidy had the lowest ability to tolerate damage. This study provides an assessment of variation in tolerance, damage frequency, G6PD1 sequence, and endopolyploidy in natural populations of A. thaliana, and also contributes to the growing body of research on the contributions of these specific molecular mechanisms to the tolerance response.

Quantitative epigenetics and evolution

Epigenetics refers to chemical modifications of chromatin or transcribed DNA that can influence gene activity and expression without changes in DNA sequence. The last 20 years have yielded breakthroughs in our understanding of epigenetic processes that impact many fields of biology. In this review, we discuss how epigenetics relates to quantitative genetics and evolution. We argue that epigenetics is important for quantitative genetics because: (1) quantitative genetics is increasingly being combined with genomics, and therefore we should expand our thinking to include cellular-level mechanisms that can account for phenotypic variance and heritability besides just those that are hard-coded in the DNA sequence; and (2) epigenetic mechanisms change how phenotypic variance is partitioned, and can thereby change the heritability of traits and how those traits are inherited. To explicate these points, we show that epigenetics can influence all aspects of the phenotypic variance formula: VP (total phenotypic variance) = VG (genetic variance) + VE (environmental variance) + VGxE (genotype-by-environment interaction) + 2COVGE (the genotype–environment covariance) + Vɛ (residual variance), requiring new strategies to account for different potential sources of epigenetic effects on phenotypic variance. We also demonstrate how each of the components of phenotypic variance not only can be influenced by epigenetics, but can also have evolutionary consequences. We argue that no sources of epigenetic effects on phenotypic variance can be easily cast aside in a quantitative genetic research program that seeks to understand evolutionary processes.

DNA Barcoding Permits Identification of Potential Fish Hosts of Unionid Freshwater Mussels

Abstract: Fish have an ecologically significant role in the life-history of unionid freshwater mussels, as the larvae of most species are obligate ectoparasites (glochidia) on fish hosts. Although this ecological interaction is vital to freshwater mussel conservation, there is a paucity of data on fish-host specificity for many species. A species-specific DNA barcoding dataset utilizing the mitochondrial NADH dehydrogenase subunit 1 (ND1) gene was used to identify 154 glochidia attached to wild fish collected from March through August of 2013 in the Sabine and Neches rivers in Texas, U.S.A. These data include the first report of potential hosts for two state-threatened species, Fusconaia askewi (Marsh, 1896) and Pleurobema riddellii (I. Lea, 1862), as well as potential hosts for Amblema plicata (Say, 1817), Obliquaria reflexa (Rafinesque, 1820), Plectomerus dombeyanus (Valenciennes, 1827), Potamilus purpuratus (Lamarck, 1819), Quadrula mortoni (I. Lea, 1831), Q. verrucosa (Rafinesque, 1820), and Truncilla truncata (Rafinesque, 1820). Cyprinella lutrensis appears to be the primary host for F. askewi, as 50% (54/108) of its glochidia were found on this minnow species alone. Pleurobema riddellii may be a cyprinid specialist, infesting only C. lutrensis and Pimephales vigilax. Alternatively, F. askewi may be a host generalist, as glochidia were found encysted on 17 fish species suggesting that host fish availability may not be an important factor contributing to observed population declines. The findings here will be instrumental in the future conservation of these species, through the translocation to correct habitat and developing successful propagation programs