Mark C. Ungerer

Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation.

The origin of new diploid species through inter-specific hybridization may be facilitated by rapid genomic reorganization. There is evidence that this process was involved in the independent origins of three annual sunflower species in the genus Helianthus. The three hybrid taxa, H. anomalus, H. deserticola and H. paradoxus, are products of ancient hybridization events between the same two parental taxa, H. annuus and H. petiolaris[1]. The hybrid species have geographically restricted ranges and occupy habitats that are abiotically extreme relative to other Helianthus species; H.

Ecological genomics: understanding gene and genome function in the natural environment

The field of ecological genomics seeks to understand the genetic mechanisms underlying responses of organisms to their natural environments. This is being achieved through the application of functional genomic approaches to identify and characterize genes with ecological and evolutionary relevance. By its very nature, ecological genomics is an interdisciplinary field. In this review, we consider the significance of this new area of study from both an ecological and genomic perspective using examples from the recent literature. We submit that by considering more fully an ecological context, researchers may gain additional insights into the underlying genetic basis of ecologically relevant phenotypic variation. Likewise, genomic approaches are beginning to offer new insights into higher-level biological phenomena that previously occupied the realm of ecological investigation only. We discuss various approaches that are likely to be useful in ecological genomic studies and offer thoughts on where this field is headed in the future.

Genetics of microenvironmental canalization in Arabidopsis thaliana

Canalization is a fundamental feature of many developmental systems, yet the genetic basis for this property remains elusive. We examine the genetic basis of microenvironmental canalization in the model plant Arabidopsis thaliana, focusing on differential developmental stability between genotypes in one fitness and four quantitative morphological traits. We measured developmental stability in genetically identical replicates of two populations of recombinant inbred (RI) lines and one population of geographically widespread accessions of A. thaliana grown in two different photoperiod-controlled environments. We were able to map quantitative trait loci associated with developmental stability. We also identified a candidate gene, ERECTA, that may contribute to microenvironmental canalization in rosette leaf number under long-day photoperiods, and analysis of mutant lines indicates that the er-105 allele results in increased canalization for this trait. ERECTA, which encodes a signaling protein, appears to act as an ecological amplifier by transducing developmental noise (e.g., microenvironmental variation) into phenotypic differentiation. We also measured genotypic selection on four plant architecture traits and find evidence for selection for both increased and decreased canalization at various traits.

Map-based cloning of quantitative trait loci: progress and prospects

Map-based cloning has been considered problematic for isolating quantitative trait loci (QTLs) due to the confounding phenotypic effects of environment and other QTLs. However, five recent studies, all in plants, have succeeded in cloning QTLs using map-based methods. We review the important features of these studies and evaluate the prospects for broader application of the techniques. Successful map-based cloning requires that QTLs represent single genes that can be isolated in near-isogenic lines, and that genotypes can be unambiguously inferred by progeny testing. In plants or animals for which map-based cloning of genes with discrete phenotypes is feasible, the modified procedures required for QTLs should not be limiting in most cases. The choice between map-based cloning and alternative methods will depend on details of the species and traits being studied.

Natural selection drives clinal life history patterns in the perennial sunflower species, Helianthus maximiliani

In plants, ecologically important life history traits often display clinal patterns of population divergence. Such patterns can provide strong evidence for spatially varying selection across environmental gradients but also may result from nonselective processes, such as genetic drift, population bottlenecks and spatially restricted gene flow. Comparison of population differentiation in quantitative traits (measured as QST) with neutral molecular markers (measured as FST) provides a useful tool for understanding the relative importance of adaptive and nonadaptive processes in the formation and maintenance of clinal variation. Here, we demonstrate the existence of geographic variation in key life history traits in the diploid perennial sunflower species Helianthus maximiliani across a broad latitudinal transect in North America. Strong population differentiation was found for days to flowering, growth rate and multiple size‐related traits. Differentiation in these traits greatly exceeds neutral predictions, as determined both by partial Mantel tests and by comparisons of global QST values with theoretical FST distributions. These findings indicate that clinal variation in these life history traits likely results from local adaptation driven by spatially heterogeneous environments.

GENETIC ARCHITECTURE OF A SELECTION RESPONSE IN ARABIDOPSIS THALIANA

Abstract Quantitative trait locus (QTL) mapping has become an established and effective method for studying the genetic architecture of complex traits. In this report, we use a QTL mapping approach in combination with data from a large selection experiment in Arabidopsis thaliana to explore a response to selection of experimental populations with differentiated genetic backgrounds. Experimental populations with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were exposed to multiple generations of fertility and viability selection. This selection resulted in phenotypic shifts in a number of life‐history and fitness‐related characters including early development time, flowering time, dry biomass, longevity, and fruit production. Quantitative trait loci were mapped for these traits and their positions were compared to previously characterized allele frequency changes in the experimental populations (Ungerer et al. 2003). Quantitative trait locus positions largely colocalized with genomic regions under strong and consistent selection in populations with differentiated genetic backgrounds, suggesting that alleles for these traits were selected similarly in differentiated genetic backgrounds. However, one QTL region exhibited a more variable response; being positively selected on one genetic background but apparently neutral in another. This study demonstrates how QTL mapping approaches can be combined with map‐based population genetic data to study how selection acts on standing genetic variation in populations.

Molecular systematics and a revised taxonomy of the onocleoid ferns (Dryopteridaceae: Onocleeae).

Nucleotide sequences of the chloroplast-encoded rbcL gene were determined for all five species of the onocleoid ferns (Dryopteridaceae tribe Onocleeae), including both varieties of Onoclea sensibilis, and for outgroup member Blechnum glandulosum. Together with GenBank sequences of three additional onocleoid accessions and four additional taxa representing the outgroup Blechnaceae, these were analyzed cladistically under the optimality criteria of maximum parsimony and maximum likelihood. Maximum parsimony yielded a single most-parsimonious tree with the three accessions of Onoclea sensibilis var. sensibilis left as an unresolved trichotomy. Maximum likelihood yielded a single set of three optimal trees whose only topological variation was in the trivial positioning of the three accessions of Onoclea sensibilis var. sensibilis relative to each other. Thus tree topologies of the onocleoid ingroup under maximum parsimony and maximum likelihood were completely congruent. Matteuccia orientalis and M. intermedia formed the basalmost ingroup clade strongly separated from the remaining taxa and sister to them. Onoclea sensibilis is strongly separated from its sister clade of Matteuccia struthiopteris plus Onocleopsis hintonii, and the two varieties of Onoclea sensibilis are well differentiated from each other. Matteuccia struthiopteris and Onocleopsis hintonii form the least strongly supported clade. Levels of sequence divergence among onocleoid taxa are compared with values from other taxa, and morphological and chromosomal data used in previous, noncladistic studies of the onocleoids are reevaluated in light of this rbcL phylogeny. Matteuccia orientalis and M. intermedia should be recognized in their own genus Pentarhizidium, and the previously recognized varieties of Onoclea sensibilis are supported at least at varietal rank and possibly at the rank of species. Molecular and morphological data bearing on the circumscriptions of Matteuccia and Onocleopsis are equivocal but perhaps most concordant with their continued recognition as monotypic genera.

Transposable Element Proliferation and Genome Expansion Are Rare in Contemporary Sunflower Hybrid Populations Despite Widespread Transcriptional Activity of LTR Retrotransposons

Hybridization is a natural phenomenon that has been linked in several organismal groups to transposable element derepression and copy number amplification. A noteworthy example involves three diploid annual sunflower species from North America that have arisen via ancient hybridization between the same two parental taxa, Helianthus annuus and H. petiolaris. The genomes of the hybrid species have undergone large-scale increases in genome size attributable to long terminal repeat (LTR) retrotransposon proliferation. The parental species that gave rise to the hybrid taxa are widely distributed, often sympatric, and contemporary hybridization between them is common. Natural H. annuus × H. petiolaris hybrid populations likely served as source populations from which the hybrid species arose and, as such, represent excellent natural experiments for examining the potential role of hybridization in transposable element derepression and proliferation in this group. In the current report, we examine multiple H. annuus × H. petiolaris hybrid populations for evidence of genome expansion, LTR retrotransposon copy number increases, and LTR retrotransposon transcriptional activity. We demonstrate that genome expansion and LTR retrotransposon proliferation are rare in contemporary hybrid populations, despite independent proliferation events that took place in the genomes of the ancient hybrid species. Interestingly, LTR retrotransposon lineages that proliferated in the hybrid species genomes remain transcriptionally active in hybrid and nonhybrid genotypes across the entire sampling area. The finding of transcriptional activity but not copy number increases in hybrid genotypes suggests that proliferation and genome expansion in contemporary hybrid populations may be mitigated by posttranscriptional mechanisms of repression.

Different scales of Ty1/copia -like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

Activation of transposable elements in species’ genomes represents an important mechanism of new mutation and of potential rapid change in genome size. Thus, it is increasingly recognized that transposable elements likely have played a significant role in shaping species’ evolution. In an earlier report, we showed that the genomes of three sunflower species of ancient hybrid origin have experienced large-scale proliferation events of sequences within the Ty3/gypsy-like superfamily of long terminal repeat (LTR) retrotransposons. In this report, we investigate whether another superfamily of LTR retrotransposon (Ty1/copia-like elements) have experienced similar derepression and proliferation events in the genomes of these sunflower hybrid taxa. We show that Ty1/copia-like elements also have undergone copy number increases following or associated with the origins of these species, although the scale of proliferation is less than that for Ty3/gypsy-like elements. Surveys of sequence heterogeneity of Ty1/copia-like elements in the genomes of the three hybrid and two parental species’ genomes reveal that a single sub-lineage of these elements exhibits characteristics of recent amplification, and likely served as the proliferative source lineage. These findings indicate that the genomic and/or environmental conditions associated with the origins of these sunflower hybrid taxa were conducive to derepression of at least two major groups of transposable elements.

The effects of mating design on introgression between chromosomally divergent sunflower species

Population genetic theory suggests that mating designs employing one or more generations of sib-crossing or selfing prior to backcrossing are more effective than backcrossing alone for moving alleles across linkage groups where effective recombination rates are low (e.g., chromosomally divergent linkages). To test this hypothesis, we analyzed the effects of chromosomal structural differences and mating designs on the frequency and genomic distribution of introgressed markers using the domesticated sunflower, Helianthus annuus, and one of its wild relatives, H. petiolaris, as the experimental system. We surveyed 170 progeny, representing the end products of three different mating designs (design I, P-F1-BC1-BC2-F2-F3; design II, P-F1-F2-BC1-BC2-F3; and design III, P-F1-F2-F3-BC1-BC2), for 197 parental RAPD markers of known genomic location. Comparison of observed patterns of introgression with expectations based on simulations of unrestricted introgression revealed that much of the genome was protected from introgression regardless of mating design or chromosomal structural differences. Although the simulations indicated that all markers should introgress into multiple individuals in each of the three mating designs, 20 of 58 (34%) markers from collinear linkage groups, and 112 of 139 (81%) markers from rearranged linkage groups did not introgress. In addition, the average size of introgressed fragments (12.2 cM) was less than half that predicted by theoretical models (26–33 cM). Both of these observations are consistent with strong selection against introgressed linkage blocks, particularly in chromosomally divergent linkages. Nonetheless, mating designs II and III, which employed one and two generations of sib-mating, respectively, prior to backcrossing, were significantly more effective at moving alleles across both collinear and rearranged linkages than mating design I, in which the backcross generations preceded sib-mating. Thus, breeding strategies that include sib-crossing, in combination with backcrossing, should significantly increase the effectiveness of gene transfer across complex genic or chromosomal sterility barriers.