Genome size, quantitative genetics and the genomic basis for flower size evolution in Silene latifolia

DNA-Binding One Finger Transcription Factor PhDof28 Regulates Petal Size in Petunia

Petal size is a key indicator of the ornamental value of plants, such as Petunia hybrida L., which is a popular ornamental species worldwide. Our previous study identified a flower-specific expression pattern of a DNA-binding one finger (Dof)-type transcription factor (TF) PhDof28, in the semi-flowering and full-flowering stages of petunia. In this study, subcellular localization and activation assays showed that PhDof28 was localized in the cell nucleus and could undergo in vitro self-activation. The expression levels of PhDof28 tended to be significantly up-regulated at the top parts of petals during petunia flower opening. Transgenic petunia 'W115' and tobacco plants overexpressing PhDof28 showed similar larger petal phenotypes. The cell sizes at the middle and top parts of transgenic petunia petals were significantly increased, along with higher levels of endogenous indole-3-acetic acid (IAA) hormone. Interestingly, the expression levels of two TFs, PhNAC100 and PhBPEp, which were reported as negative regulators for flower development, were dramatically increased, while the accumulation of jasmonic acid (JA), which induces PhBPEp expression, was also significantly enhanced in the transgenic petals. These results indicated that PhDof28 overexpression could increase petal size by enhancing the synthesis of endogenous IAA in petunias. Moreover, a JA-related feedback regulation mechanism was potentially activated to prevent overgrowth of petals in transgenic plants. This study will not only enhance our knowledge of the Dof TF family, but also provide crucial genetic resources for future improvements of plant ornamental traits.

Genome Size and Labellum Epidermal Cell Size Are Evolutionarily Correlated With Floral Longevity in Paphiopedilum Species

Genome size is known to influence phenotypic traits in leaves and seeds. Although genome size is closely related to cellular and developmental traits across biological kingdoms, floral longevity is a floral trait with important fitness consequence, but less is known about the link between floral longevity and sizes of genomes and cells. In this study, we examined evolutionary coordination between genome size, floral longevity, and epidermal cell size in flowers and leaves in 13 Paphiopedilum species. We found that, across all the study species, the genome size was positively correlated with floral longevity but negatively associated with labellum epidermal cell size, and a negative relationship was found between floral longevity and labellum epidermal cell size. This suggested that genome size is potentially correlated with floral longevity, and genome size has an important impact on life-history trait. In addition, genome size was positively correlated with leaf epidermal cell size, which was different from the relationship in flower due to different selective pressures they experienced or different functions they performed. Therefore, genome size constraints floral longevity, and it is a strong predictor of cell size. The impact of genome size on reproduction might have more implications for the evolution of flowering plants and pollination ecology.

The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights

BACKGROUND AND AIMS

Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species.

METHODS

We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples.

KEY RESULTS

We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small.

CONCLUSIONS

We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.

The Evolution of Diverse Floral Morphologies

The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.

Expansion of the pseudo-autosomal region and ongoing recombination suppression in the Silene latifolia sex chromosomes

There are two very interesting aspects to the evolution of sex chromosomes: what happens after recombination between these chromosome pairs stops and why suppressed recombination evolves. The former question has been intensively studied in a diversity of organisms, but the latter has been studied largely theoretically. To obtain empirical data, we used codominant genic markers in genetic mapping of the dioecious plant Silene latifolia, together with comparative mapping of S. latifolia sex-linked genes in S. vulgaris (a related hermaphrodite species without sex chromosomes). We mapped 29 S. latifolia fully sex-linked genes (including 21 newly discovered from transcriptome sequencing), plus 6 genes in a recombining pseudo-autosomal region (PAR) whose genetic map length is ∼25 cM in both male and female meiosis, suggesting that the PAR may contain many genes. Our comparative mapping shows that most fully sex-linked genes in S. latifolia are located on a single S. vulgaris linkage group and were probably inherited from a single autosome of an ancestor. However, unexpectedly, our maps suggest that the S. latifolia PAR region expanded through translocation events. Some genes in these regions still recombine in S. latifolia, but some genes from both addition events are now fully sex-linked. Recombination suppression is therefore still ongoing in S. latifolia, and multiple recombination suppression events have occurred in a timescale of few million years, much shorter than the timescale of formation of the most recent evolutionary strata of mammal and bird sex chromosomes.

Control of flower size

Flowers exhibit amazing morphological diversity in many traits, including their size. In addition to interspecific flower size differences, many species maintain significant variation in flower size within and among populations. Flower size variation can contribute to reproductive isolation of species and thus has clear evolutionary consequences. In this review we integrate information on flower size variation from both evolutionary and developmental biology perspectives. We examine the role of flower size in the context of mating system evolution. In addition, we describe what is currently known about the genetic basis of flower size based on quantitative trait locus (QTL) mapping in several different plant species and molecular genetic studies in model plants, primarily Arabidopsis thaliana. Work in Arabidopsis suggests that many independent pathways regulate floral organ growth via effects on cell proliferation and/or cell expansion.

‘Junk’ DNA and phenotypic evolution inSilenesectionSiphonomorpha

One of the long-standing mysteries in genomic evolution is the observation that much of the genome is composed of repetitive DNA, resulting in inter- and intraspecific variation in nuclear DNA content. Our discovery of a negative correlation between nuclear DNA content and flower size inSilene latifoliahas been supported by our subsequent investigation of changes in DNA content as a correlated response to selection on flower size. Moreover, we have observed a similar trend across a range of related dioecious species inSilenesect.Elisanthe. Given the presence of sex chromosomes in dioeciousSilenespecies, and the tendency of sex chromosomes to accumulate repetitive DNA, it seems plausible that dioecious species undergo genomic evolution in ways that differ from what one might expect in hermaphroditic species. Specifically, we query whether the observed relationship between nuclear DNA content and flower size observed in dioeciousSileneis a peculiarity of sex chromosome evolution. In the present study we investigated nuclear DNA content and flower size variation in hermaphroditic species ofSilenesect.Siphonomorpha, as close relatives of the dioecious species studied previously. Although the nuclear DNA contents of these species were lower than those for species in sect.Elisanthe, there was still significant intra- as well as interspecific variation in nuclear DNA content. Flower size variation was found among species of sect.Siphonomorphafor petal claw and petal limb lengths, but not for calyx diameter. This last trait varies extensively in sect.Elisanthe, in part due to sex-specific selection. A negative correlation with nuclear DNA content was found across populations for petal limb length, but not for other floral dimensions. We conclude that impacts of nuclear DNA content on phenotypic evolution do manifest themselves in hermaphroditic species, so that the effects observed in sect.Elisanthe, and particularly inS. latifolia, while perhaps amplified by the genomic impacts of sex chromosomes, are not limited to dioecious taxa.

Active miniature transposons from a plant genome and its nonrecombining Y chromosome

Mechanisms involved in eroding fitness of evolving Y chromosomes have been the focus of much theoretical and empirical work. Evolving Y chromosomes are expected to accumulate transposable elements (TEs), but it is not known whether such accumulation contributes to their genetic degeneration. Among TEs, miniature inverted-repeat transposable elements are nonautonomous DNA transposons, often inserted in introns and untranslated regions of genes. Thus, if they invade Y-linked genes and selection against their insertion is ineffective, they could contribute to genetic degeneration of evolving Y chromosomes. Here, we examine the population dynamics of active MITEs in the young Y chromosomes of the plant Silene latifolia and compare their distribution with those in recombining genomic regions. To isolate active MITEs, we developed a straightforward approach on the basis of the assumption that recent transposon insertions or excisions create singleton or low-frequency size polymorphisms that can be detected in alleles from natural populations. Transposon display was then used to infer the distribution of MITE insertion frequencies. The overall frequency spectrum showed an excess of singleton and low-frequency insertions, which suggests that these elements are readily removed from recombining chromosomes. In contrast, insertions on the Y chromosomes were present at high frequencies. Their potential contribution to Y degeneration is discussed.

Gene-based modelling for rice: An opportunity to enhance the simulation of rice growth and development?

Process-based crop simulation models require employment of new knowledge for continuous improvement. To simulate growth and development of different genotypes of a given crop, most models use empirical relationships or parameters defined as genetic coefficients to represent the various cultivar characteristics. Such a loose introduction of different cultivar characteristics can result in bias within a simulation, which could potentially integrate to a high simulation error at the end of the growing season when final yield at maturity is predicted. Recent advances in genetics and biomolecular analysis provide important opportunities for incorporating genetic information into process-based models to improve the accuracy of the simulation of growth and development and ultimately the final yield. This improvement is especially important for complex applications of models. For instance, the effect of the climate change on the crop growth processes in the context of natural climatic and soil variability and a large range of crop management options (e.g., N management) make it difficult to predict the potential impact of the climate change on the crop production. Quantification of the interaction of the environmental variables with the management factors requires fine tuning of the crop models to consider differences among different genotypes. In this paper we present this concept by reviewing the available knowledge of major genes and quantitative trait loci (QTLs) for important traits of rice for improvement of rice growth modelling and further requirements. It is our aim to review the assumption of the adequacy of the available knowledge of rice genes and QTL information to be introduced into the models. Although the rice genome sequence has been completed, the development of gene-based rice models still requires additional information than is currently unavailable. We conclude that a multidiscipline research project would be able to introduce this concept for practical applications.

Linking the evolution of gender variation to floral development

BACKGROUND AND AIMS

In the present review, I have endeavoured to conduct a joint assessment of the thinking underlying the evolutionary genetics of gender polymorphism and the developmental genetics of gender determination. It is my hope, through highlighting the historical development of ideas in two related but somewhat disparate sets of scientific literature, to encourage a synthetic perspective that integrates the two.

SCOPE

An overview is provided of various theories on the evolution of sex polymorphism and examples of evidence that has been brought to bear in support of them. Current knowledge on floral development is summarized, with an emphasis on gender variation. Finally, an attempt is made to integrate the two perspectives with the hope that it will encourage future research at the interface.

CONCLUSIONS

Evolutionary models of gender evolution have, of necessity, posited genetic effects that are relatively simple in their impacts. Emerging insights from developmental genetics have demonstrated that the underlying reality is a more complex matrix of interacting factors. The study of gender variation in plants is poised for significant advance through the integration of these two perspectives. Bringing genomic tools to bear on population-level processes, we may finally develop a comprehensive perspective on the evolution of floral gender.

Genome size variation in the Artemisia arborescens complex (Asteraceae, Anthemideae) and its cultivars

Different wild Mediterranean populations of Artemisia arborescens from diverse locations representing its geographical distribution, as well as some of its well-known cultivars and some specimens cultivated as ornamentals in gardens, streets, roads and nurseries, were analysed for genome size. Other closely related species endemic to Macaronesia, Artemisia canariensis, Artemisia argentea, and Artemisia gorgonum, were also analysed, and their nuclear DNA amount has been related to the biogeography of this group of species. Additionally, 5 populations of the closely related Artemisia absinthium were analysed to establish comparisons. Measurements acquired by flow cytometry ranged from 8.29 to 11.61 pg for 2C values. Statistically significant differences of 2C nuclear DNA amounts with respect to factors such as insularity or domestication have been detected. However, quite a low intraspecific genome size variation has been found in these species. Furthermore, the study also addressed the possible hybrid origins and possible misidentifications of some of the supposed cultivars of A. arborescens.

Phenotypic impacts of repetitive DNA in flowering plants

The discovery that nuclear DNA content varies widely among species, and even within species, was unexpected because it was thought that the number of genes required for an organism should be common across taxa. We now know that the bulk of nuclear DNA content variation is caused by repetitive DNA sequences characterized according to the nature of repeat (tandem vs dispersed) or chromosomal location/mechanism of replication (pericentromeric, telomeric or subtelomeric, microsatellites, minisatellites, satellites, transposable elements, retroelements). Variation in repetitive DNA, manifested as variation in nuclear DNA content, has been shown to have broad ecological and life-history consequences. For example, large genome size appears to limit fitness in extreme environmental conditions. Within species, variation in DNA content has been coupled to growth and development, such as maturation time in crop species. In Silene latifolia, DNA content is negatively correlated with flower size, a character that, in turn, has well documented ecological significance. These intraspecific studies suggest a connection between repetitive DNA and quantitative genetic determination of continuous characters. Novel insights into mechanisms by which repetitive DNA influences phenotype will lead to models of evolutionary change that extend well beyond the conventional view of evolution by allelic substitution.

Plant genome size research: a field in focus

This Special Issue contains 18 papers arising from presentations at the Second Plant Genome Size Workshop and Discussion Meeting (hosted by the Royal Botanic Gardens, Kew, 8-12 September, 2003). This preface provides an overview of these papers, setting their key contents in the broad framework of this highly active field. It also highlights a few overarching issues with wide biological impact or interest, including (1) the need to unify terminology relating to C-value and genome size, (2) the ongoing quest for accurate gold standards for accurate plant genome size estimation, (3) how knowledge of species' DNA amounts has increased in recent years, (4) the existence, causes and significance of intraspecific variation, (5) recent progress in understanding the mechanisms and evolutionary patterns of genome size change, and (6) the impact of genome size knowledge on related biological activities such as genetic fingerprinting and quantitative genetics. The paper offers a vision of how increased knowledge and understanding of genome size will contribute to holisitic genomic studies in both plants and animals in the next decade.

When does intraspecific C-value variation become taxonomically significant?

AIMS

To examine what possible role intraspecific DNA C-value variation may play in plant taxonomy.

SCOPE

Although many of the original examples of intraspecific C-value variation have been shown to be the result of experimental variation, new examples using the appropriate standards and controls continue to be published. The evidence that intraspecific C-value variation alters phenotypes can be equivocal, and detailed studies are needed to clarify any possible relationship. However, populations within species have been shown to have varying DNA amounts that can be correlated with eco-geographic variables, suggesting that the variation is adaptive and that these may be examples of incipient speciation.

CONCLUSIONS

Where intraspecific C-value variation appears most significant for taxonomy is as an indicator of taxonomic heterogeneity, pointing to the need for a re-evaluation of the delimitation of the species in question. There is also the need to test whether intraspecific C-value variants produce fertile F(1) hybrids or not, as this would be a good indication of whether they belong in the same biological species.