Entries by Caroline Dowling

Pan-genome of wild and cultivated soybeans (Cell)

Widespread genome sequencing of individuals has revealed the high level of intraspecific variability in plant species. As such, constructing high-quality pan-genomes is a growing necessity to study dynamic plant genomes. Here, Liu et al. release the soybean pan-genome formed from sequencing 2,898 accessions, including landraces, wild, and cultivated soybeans. The authors de novo assembled 26 […]

Mutation bias shapes gene evolution in Arabidopsis thaliana (bioRxiv)

Classical evolutionary theory states that the probability of a mutation occurring is independent of fitness consequences. However, reassessment of traditional assumptions is warranted with recent discoveries showing that cytogenetic (DNA sequences and epigenetic) features can affect local mutation probabilities. Cytogenetic features have distinct states among certain gene classes which may facilitate the evolution of beneficial […]

Major impacts of widespread structural variation on gene expression and crop improvement in tomato (Cell)

Structural Variants (SVs) are large genomic deletions, insertions, and duplications with underexplored roles in determining plant phenotypes. Recognizing the extent to which SVs define quantitative trait variation was previously constrained by the fact that popular short-read sequencing technologies preferentially characterize smaller variants. However, innovative long-read technologies are facilitating extensive population-level surveys of SVs. Here, Alonge, […]

A single gene underlies the dynamic evolution of poplar sex determination (Nature Plants)

Dioecy (male and female flowers residing on distinct individuals) has independently arisen several times in angiosperms, yet the genetic basis of dioecy remains obscure. Here, Müller et al. reveal a single gene that acts as a sex-determination switch throughout the Populus genus. A negative regulator of cytokinin, the Populus ortholog of ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) initiates female development when […]

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 […]