Recent Posts

Co-expression networks for strawberry flower and fruit development

The diploid strawberry (Fragaria vesca) is a useful model system for understanding non-climacteric ripening and seed-to-fruit cross-tissues communication. Previously, spatial and temporal transcriptome data from the strawberry fruit and flowers was generated. Shahan and colleagues combine the transcriptome…

Aquatic fern genomes provide insight into land plant evolution and symbiosis (Nature Plants)

Land plants evolved from freshwater charophytic algae over ~450 million years ago and have since diverged into the plethora of embryophyte genera that we see today. Genomics efforts have classically focused on key angiosperm species representing experimental model systems and/or agriculturally important…

Review. Brachypodium: A monocot grass model system for plant biology (Plant Cell)

Brachypodium distachyon is an annual C3 grass that has become an important model species. Scholthof et al. review the genetic tools and resources (sequences and mutants) as well as robust protocols for transformation that have been developed for it. The presence of wild and perennial species within the…

Review: The rice genome revolution: from an ancient grain to Green Super Rice ($) (Nat. Rev. Genetics)

Rice is one of the major staple crops in the world as it is an essential component of diets and livelihoods. Populations in poor regions that are highly dependent on rice (Africa and South Asia) will increase dramatically by 2050, revealing the urgent need to find tools to prevent a future humanitarian…

Regulatory Divergence in the Stress Response of Tomato

Humans have domesticated crops for thousand of years by artificially selecting plants for numerous traits including morphology, lower toxicity or higher yield. As a result, plant domestication often altered plant fitness and resistance to stress under controlled conditions (Meyer & Purugganan 2013).…

Genes responsible for deceleration of circadian rhythms during tomato domestication (PNAS)

Domestication of crop plants is intimately linked to the modulation of the plants circadian rhythms, allowing adaptation to new agricultural environments. Deceleration of the clock has been instrumental in tomato domestication; however the underlying molecular mechanisms are not fully understood. In…

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis (Science)

The ability to participate in nitrogen-fixing root nodule symbiosis shows an interesting phylogenetic pattern, with some families showing a large number of nodulating species interspersed with non-nodulating ones, and some families showing only a few nodulating species. A current model suggests that…

Review: A guide to sequence your favorite plant genomes (App. Plant Sci)

Every year, genome assembly gets faster and cheaper. Li and Harkness provide a practical guide to today’s methods, with caveats and precautions that need to be considered at each step, even questions to ask before embarking on a sequencing project.  Topics include how to estimate genome size and complexity,…

Identification of cold tolerance genes and a functional allele that confers cold tolerance ($) (Plant Physiol.)

Xiao et al. used 1,033 rice accessions for GWAS to identify QTLs associated with cold tolerance.  In general, japonica-type varieties showed greater cold tolerance than indica types.  The authors identified many QTLs for cold tolerance at the seedling and booting (initiation of panicles) stages. They…