To celebrate the ground-breaking achievements being made in plant genomics research, Genome Biology has published a special issue, guest edited by Mario Caccamo (The Genome Analysis Centre, Norwich, UK) and Erich Grotewold (The Ohio State University, USA), dedicated to genomics research of a distinctly green nature. For those of you who would like an overview of the topic of plant genomics, a great place to start is by checking out our guest editors’ editorial on the subject. We also have a bumper selection of Review articles to enthrall avid followers of plant research, ranging from crop genomics and biofuels to how plants interact with their biotic and abiotic environments.

Do we still need model species?
The decreasing costs of next generation sequencing technologies have allowed genome sequences to be assembled for many crop species, facilitating genetic analyses directly in crops of interest. This has raised the question of whether we still need model species. A vast amount of data has already been gained in model species, and much of this information would be difficult to replicate in crop species. So, model species can still be used to more quickly and easily study traits of interest, and the knowledge gained can then be applied to crop research. In our special issue, Philip Wigge and colleagues elegantly use Brachypodium distachyon, a model grass species, to identify the epigenetic mechanisms that mediate increased thermal sensitivity during B. distachyon grain development. Other research papers in the special issue show that Arabidopsis thaliana is still a great model species for determining how plants grow and respond to their environments.

Must-read method
The special issue includes a must-see method article for mapping in Arabidopsis thaliana, which can also be applied to other species such as rice and barley. Korbinian Schneeberger, Detlef Weigel and colleagues describe guidelines for optimizing mapping-by-sequencing experiments and include a handy new tool, called Pop-seq, to simulate mapping population parameters.

A good crop of research
The latest research in a wide range of crop species can also be viewed. Several updates are described in the field of wheat genomics, including a linkage map for a bread wheat chromosome arm, and a transcriptomic analysis of pasta wheat using an approach for homeolog separation. Structural variations in barley are uncovered, and genotyping-by-sequencing is employed in both maize and sorghum to aid identifying candidate genes controlling traits of interest. A transcriptomic and epigenetic analysis of maize parents and hybrids reveals a correlation between gene expression and histone modifications, and shows there is no significant parental bias in gene expression in hybrids.

Chocolate and wine, a perfect combination
The special issue has all bases covered with publications on both wine and chocolate. You can read more about the research on grapevine plasticity in our accompanying Research Highlight from Alisdair Fernie, and research synopses for both the wine and chocolate articles are featured in Biome.

A future for plant genomics research
We are dedicated to publishing high quality plant genomics research at Genome Biology, and you can follow all our plant genomics publications at https://genomebiology.com/tags/plants.