The evolutionary forces that maintain genetic variation in quantitative traits within populations remain poorly understood. One hypothesis suggests that variation is under purifying selection, resulting in an excess of low-frequency variants and a negative correlation between minor allele frequency and selection coefficients. Here, we test these predictions using the genetic loci associated with total expression variation (eQTLs) and allele-specific expression variation (aseQTLs) mapped within a single population of the plant Capsella grandiflora. In addition to finding eQTLs and aseQTLs for a large fraction of genes, we show that alleles at these loci are rarer than expected and exhibit a negative correlation between phenotypic effect size and frequency. Overall, our results show that the distribution of frequencies and effect sizes of the loci responsible for local expression variation within a single outcrossing population are consistent with the effects of purifying selection.gene expression | population genomics | association mapping G enetic variation for quantitative traits persists within populations despite the expectation that prevalent stabilizing selection will reduce genetic variance (1). One hypothesis suggests that variation is under purifying selection, resulting in an excess of low-frequency variants and a negative correlation between minor allele frequency and selection coefficients (2). Although studies of allele frequency spectra show that purifying selection on functional DNA sequences is prevalent (3-5), little is known about how the genetic variants under selection relate to phenotype, and ultimately, how phenotypic variation is maintained within populations. Association mapping can identify specific loci influencing phenotypes, providing candidates for further analysis of selection (6). In particular, mapping the local regulatory variants that affect gene expression can identify a large number of genetic loci that affect a phenotype. Additionally, mapping the genetic basis of gene expression may answer questions about the basic biology of gene regulation, for example, by testing predictions that conserved noncoding sequences ("CNSs") are constrained because they have regulatory function (7).Early eQTL studies mapped expression divergence between two lines, finding that many genes have local expression QTL (8, 9). These studies have provided insight into selection on eQTLs; for example, a correlation between recombination rate and eQTL density implied that background selection is a dominant force acting on expression variation in Caenorhabditis elegans (10), and a skew toward rare allele frequencies in promoters of genes with eQTLs suggests that purifying selection may act on expression variation (11). However, eQTL studies of populationlevel genetic variation have thus far been limited to a few study systems (12-16) and only one study, in humans, has identified a negative correlation between phenotypic effect size and frequency (15). In addition, human eQTL studies have shown that loci ex...

Elucidating the genetic basis of morphological changes in evolution remains a major challenge in biology. Repeated independent trait changes are of particular interest because they can indicate adaptation in different lineages or genetic and developmental constraints on generating morphological variation. In animals, changes to "hot spot" genes with minimal pleiotropy and large phenotypic effects underlie many cases of repeated morphological transitions. By contrast, only few such genes have been identified from plants, limiting cross-kingdom comparisons of the principles of morphological evolution. Here, we demonstrate that the REDUCED COMPLEXITY (RCO) locus underlies more than one naturally evolved change in leaf shape in the Brassicaceae. We show that the difference in leaf margin dissection between the sister species Capsella rubella and Capsella grandiflora is caused by cis-regulatory variation in the homeobox gene RCO-A, which alters its activity in the developing lobes of the leaf. Population genetic analyses in the ancestral C. grandiflora indicate that the more-active C. rubella haplotype is derived from a now rare or lost C. grandiflora haplotype via additional mutations. In Arabidopsis thaliana, the deletion of the RCO-A and RCO-B genes has contributed to its evolutionarily derived smooth leaf margin, suggesting the RCO locus as a candidate for an evolutionary hot spot. We also find that temperature-responsive expression of RCO-A can explain the phenotypic plasticity of leaf shape to ambient temperature in Capsella, suggesting a molecular basis for the well-known negative correlation between temperature and leaf margin dissection.

In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles.

Identifying quantitative trait nucleotides (QTNs), the genetic polymorphisms linked to phenotypic variation, has become a goal for many plant ecologists and evolutionary biologists in recent years. But what is the true value of this potentially expensive and labor intensive programme of research? In this review we discuss the ways by which the QTN programme can offer unique insight into the ecology and evolution of adaptation in plants. We cite recent noteworthy examples of QTN work and provide recommendations for refocusing efforts to identify and study the genes underlying ecologically important traits.

Mating system shifts recurrently drive specific changes in organ dimensions. The shift in mating system from out-breeding to selfing is one of the most frequent evolutionary transitions in flowering plants and is often associated with an organ-specific reduction in flower size. However, the evolutionary paths along which polygenic traits, such as size, evolve are poorly understood. In particular, it is unclear how natural selection can specifically modulate the size of one organ despite the pleiotropic action of most known growth regulators. Here, we demonstrate that allelic variation in the intron of a general growth regulator contributed to the specific reduction of petal size after the transition to selfing in the genus Capsella. Variation within this intron affects an organ-specific enhancer that regulates the level of STERILE APETALA (SAP) protein in the developing petals. The resulting decrease in SAP activity leads to a shortening of the cell proliferation period and reduced number of petal cells. The absence of private polymorphisms at the causal region in the selfing species suggests that the small-petal allele was captured from standing genetic variation in the ancestral out-crossing population. Petal-size variation in the current out-crossing population indicates that several smalleffect mutations have contributed to reduce petal-size. These data demonstrate how tissue-specific regulatory elements in pleiotropic genes contribute to organ-specific evolution. In addition, they provide a plausible evolutionary explanation for the rapid evolution of flower size after the out-breeding-to-selfing transition based on additive effects of segregating alleles. morphological evolution | growth control | standing variation | organ-specific evolution | intronic cis-regulatory element M ating system shifts toward self-fertilization occurred repeatedly during evolution, most likely to provide reproductive assurance and because of the transmission advantage of selfing mutations (1-3). In both plant and animal kingdoms this transition has been accompanied by a set of characteristic morphological changes in reproductive organs termed "the selfing syndrome" (4-7), implying that the mating system strongly constrains the evolution of reproductive-organ morphology. Still, it is unclear whether repeated evolution of these morphological changes is a result of positive selection, of the relaxation of purifying selection, or results from stronger genetic drift in selfing populations. In plants, the genetic basis underlying the reduction in flower size of selfing species is unclear. In particular, the observation that this reduction is often highly specific for floral organs contrasts with the pleiotropic activity of almost all known regulators of shoot-organ growth in both leaves and flowers, raising the question of how natural evolution has brought about organ-specific changes with a largely universal tool-kit. Different hypotheses have therefore been formulated to explain how such polygenic traits could be modified in a sing...