News & Views | Published:

Genomics

The language of flowers

Nature volume 534, pages 328329 (16 June 2016) | Download Citation

The complete DNA sequences of the two wild parents of the garden petunia provide valuable genetic insights into this model plant, and will improve the optimization of other crop plants for agriculture.

The domestication of plants is often thought to apply mainly to food crops, but cultivation has also been widely used to enhance the beauty of ornamental plants. Writing in Nature Plants, Bombarely et al.1 report the genome sequences of two progenitor species of Petunia hybrida, a plant domesticated for its flowers. These genomes are a notable addition to the known sequences of members of the nightshade family (Solanaceae)2. They will enable researchers to unravel fundamental mechanisms in evolution, ecology and gene function, and will help to bring an understanding of the relationships between plant genomes closer.

Petunia is used as a model organism, but one might nonetheless wonder why the genome of a popular flower is of interest. With global consumption of floriculture products estimated to be worth around US$30 billion per year, however, much research is aimed at optimizing productivity, flower shape, colour, vase-life and fragrance. Previous studies3 have identified many of the genes that influence Petunia flower characteristics, highlighting both the evolutionary conservation and diversification of function between different ornamental varieties. Bombarely et al. now provide a powerful platform for the ornamental-flower industry to translate this information to other species, increasing the development of new commercial varieties and species in this economically important research field.

The flowers of wild petunias come in diverse shapes and colours4. Cultivated petunias are a hybrid between two wild species — the pink-flowered Petunia inflata and the white-flowered Petunia axillaris. Bombarely et al. sequenced both of these genomes, and generated transcriptomic data (which detail all the messenger RNA molecules in a cell) from three unrelated cultivated P. hybrida lines. These data provide a superb resource for analysing not only the genes that confer particular Petunia characteristics, but also the genomics of hybridity.

The authors found that most of the genes expressed in the cultivated species are from P. axillaris — 15,000, compared with only 600 from P. inflata. This is partly attributable to the use of the white background colour derived from P. axillaris as a playground for colour manipulation in the cultivated species. An alternative explanation is gene conversion, in which one parental set of genes comes to predominate. Gene conversion has long been thought to be confined to species called polyploids, in which chromosome doubling has occurred during evolution. Bombarely and colleagues suggest that gene conversion similar to that commonly seen in polyploid Solanaceae crops such as tobacco might also occur in hybrids such as Petunia that are not polyploid.

Colour and scent are crucial for attracting pollinators3,5. P. axillaris is moth-pollinated and produces volatile compounds that give its night-blooming flowers their strong scent, whereas P. inflata is bee-pollinated and has little scent. Bombarely et al. find that gene sequence alone cannot explain these differences. But the 'ecosystem' of the genome is complex, consisting of many layers of regulation that do not alter DNA sequence. The authors show that the circadian clock that regulates scent production is highly diversified in Solanaceae species, perhaps pointing to a key role for the biochemical pathways that regulate circadian rhythms in driving adaptation to different environmental niches, and thus diversification.

In terms of colour, the Petunia genomes provide a powerful resource for understanding the genomic basis of the biosynthetic pathway for pigments called anthocyanins, and for analysing how gene position and duplication can contribute to diversification of traits, influencing speciation6. Both parental species share the same core anthocyanin pathway, and, as expected, the white-flowered P. axillaris has lost some peripheral components over the course of evolution. But some of the genes encoding transcription factors that regulate the expression of anthocyanin-pathway components reside in exceptionally dynamic regions of the genome. The authors provide evidence that large and extremely rapid rearrangements in these regions were involved in diversification of the Solanaceae.

Human domestication of many Solanaceae-related ancestors has resulted in related modern crops that have similar sets of genes but highly variable characteristics. For example, petunia, aubergine, tomato, pepper, potato and tobacco are all derived from members of the Solanaceae family, and sweet potato and coffee are members of the same clade, a larger grouping called the euasterids. Each species has been bred to enhance the productivity of different organs (Fig. 1). Thanks to Bombarely and colleagues' work, the genomes of this unique cluster of closely related crops are all now available2, which allows us to investigate a major biological question — what are the genetic factors that dictate a plant's balance between vegetative, photosynthetic carbon-dioxide-fixing organs (known as the source), and the reproductive organs consumed by humans (the sink) that store chemical energy in the form of carbohydrates7?

Figure 1: A diverse family of crops.
Figure 1

Crops of the Solanaceae family have been bred to produce diverse agricultural and ornamental products, including fruits (tomatoes), flowers (petunias) and tubers (potatoes). Bombarely et al.1 report the genome sequences of two progenitor species of the domesticated Petunia, which will help researchers to dissect the genetic basis of crop productivity. Image: From left: Fotodisk/Getty; Onepony/Getty; The Garden Smallholder/Getty

Answers to this question will be useful for optimizing crop productivity across many plant species, because the balance between vegetative and reproductive development determines how much chemical energy will be converted to agricultural yield. The fact that different organs constitute sinks in solanaceous crops and their relatives could enable us to identify genes that regulate the source–sink balance beyond those that control specific sink-organ traits. Such knowledge will allow identification of evolutionary or breeder-selected sink–source innovations in one species that could then be deployed in other crops by using the plant breeder's rapidly expanding molecular toolbox8.

The rich diversity of petunias, combined with our new understanding of the genes that regulate this ornamental beauty, will facilitate a deeper understanding of the genetic language that regulates the glory of flowers. A bigger challenge, however, is to understand naturally occurring variability and diversification, and to use this knowledge to better conserve the biodiversity on which our future depends.

If we are to use genomics to unpick evolutionary relationships between solanaceous and other species, each genome must be considered in the context of the organism's characteristics and the selection pressures that it faces in the wild. A major barrier to linking genomes and traits is a lack of consensus on how to annotate qualitative and quantitative traits in a computable manner9. A step towards this goal is the database developed by the Solanaceae Genome Network (https://solgenomics.net), which presents an ontology to describe traits from different plant species in a common framework10.

The next step is to link genomes and traits in a bioinformatics framework that can associate specific DNA sequences with traits that arise at different stages of organismal development and in different environments. Finally, perhaps the greatest challenge in linking the genome to the traits that it encodes is social — persuading the scientific community to deposit its data in open-source platforms so that others can use them.

Notes

References

  1. 1.

    et al. Nature Plants (2016).

  2. 2.

    , , & PLoS ONE 6, e16717 (2011).

  3. 3.

    & Trends Plant Sci. 10, 251–256 (2005).

  4. 4.

    et al. in Petunia (eds Gerats T. & Strommer T.) 1–26 (Springer, 2009).

  5. 5.

    et al. Nature Genet. 48, 159–166 (2016).

  6. 6.

    , & Phil. Trans. R. Soc. Lond. B 365, 461–468 (2010).

  7. 7.

    , , & J. Exp. Bot. 67, 31–45 (2016).

  8. 8.

    Genome Biol. 17, 51 (2016).

  9. 9.

    et al. PLoS Biol. 13, e1002033 (2015).

  10. 10.

    et al. Nucleic Acids Res. 43, D1036–D1041 (2014).

Download references

Author information

Affiliations

  1. Sandra Knapp is in the Department of Life Sciences, Natural History Museum, London SW7 5BD, UK.

    • Sandra Knapp
  2. Dani Zamir is in the Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot, Israel.

    • Dani Zamir

Authors

  1. Search for Sandra Knapp in:

  2. Search for Dani Zamir in:

Corresponding authors

Correspondence to Sandra Knapp or Dani Zamir.

About this article

Publication history

Published

DOI

https://doi.org/10.1038/nature18445

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Newsletter Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing