Entries by Caroline Dowling

Genomic history and ecology of the geographic spread of rice (Nature Plants)

Originating in China’s Yangtze Valley ~9,000 years ago, rice (Oryza sativa) is a staple food for over half of the world’s population. While rice domestication has been well-researched, studies addressing the species’ diversification and spread post-domestication are lacking. Here, Gutaker et al. tell the “first draft of the story” of how rice was dispersed across Asia (check […]

Review: Ten years of the maize nested association mapping population: Impact, limitations, and future directions (Plant Cell)

Linking phenotype to genotype is a major obstacle in plant biology, and conventional approaches (linkage analysis, association mapping) have limitations. Here Gage et al. review the past, present, and future impacts of a maize Nested Association Mapping (NAM) population developed throughout the 2000s. Designed to capitalize on the advantages while overcoming the weaknesses of traditional […]

MYB30 negatively regulates photomorphogenesis by interacting with PIFs and phytochromes in Arabidopsis (Plant Cell)

Photomorphogenesis is the growth and development of plants in response to light. The phytochrome family of photoreceptors absorbs red and far-red light, and in Arabidopsis the most abundant phytochromes are phyA and phyB. PHYTOCHROME-INTERACTING FACTORS (PIFs) repress photomorphogenesis, and under red light, phytochromes mediate PIF degradation. Here, Yan et al. reveal MYB30 as a negative regulator […]

An RNA thermoswitch regulates daytime growth in Arabidopsis (Nature Plants)

Plants are sessile organisms and as such they must be highly responsive to environmental cues including temperature, and adjust their growth and development accordingly. Considering that mean global surface temperatures are expected to continue to rise dramatically in the 21st century, it is crucial to understand how plants respond to elevated temperatures. Here, Chung et […]

No-Genome-Required-GWAS (Nature Genetics)

Conventional approaches to connect phenotype to genotype, including genome-wide association studies (GWAS), are often limited by the quality of the species’ reference genome, and frequently neglect to detect structural variants that are common in plant genomes. Here, Voichek and Weigel present a “No-Genome-Required-GWAS” approach (summarized in this Twitter thread), which is essentially the reverse of […]

AthCNV: A map of DNA copy number variations in the Arabidopsis thaliana genome (Plant Cell)

Intraspecific phenotypic variability can be attributed to differences at the genome level such as copy number variations (CNVs). CNVs are large DNA fragments which differ in number between individuals and likely have a crucial evolutionary role. Due to the 1001 Genomes Project, over 1,000 Arabidopsis accessions have been sequenced, with to-date analyses largely focusing on single […]

Genome-phenome wide association in maize and Arabidopsis identifies a common molecular and evolutionary signature (Mol. Plant)

Genome-wide association studies (GWAS) are widely used to link natural genetic variation to trait variation, with a single or a select few correlated traits assessed. High-throughput phenotyping allows the scoring of hundreds of individuals for various traits at several time points. An undeniable consequence of quantitative genetics research is the creation of large, complex datasets […]

Gene balance predicts transcriptional responses immediately following ploidy change in Arabidopsis thaliana (Plant Cell)

Throughout evolutionary time polyploidization events have occurred frequently, increasing the gene copy number (gene dosage) of multiple angiosperms. The gene balance hypothesis proposes that there is selection on gene copy number to maintain the stoichiometric balance between dosage-sensitive genes that are involved in multimeric complexes (e.g., transcription factors). However, if a whole-genome duplication occurs the […]

Roles for CHROMATIN REMODELING 4 in Arabidopsis floral transition (Plant Cell)

The time at which flowers appear is critical for plant reproductive success. As such, the vegetative to reproductive growth transition is governed by several cues: environmental (photoperiod, temperature) and endogenous (gibberellins, age). Here, Sang et al. used an elegant forward-genetics approach to identify uncharacterized regulators of the Arabidopsis endogenous flowering time pathways. A quintuple mutant […]