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Biology subjects

Ramirez-Corona, B.

Publications and source records attributed to Ramirez-Corona, B..

2 recordsLinked to original sources

Sensitivity to photoperiod is a complex trait in Camelina sativa

Day neutrality, or insensitivity to photoperiod (day length), is an important domestication trait in many crop species. Although the oilseed crop Camelina sativa has been cultivated since the Neolithic era, day-neutral accessions have yet to be described. We sought to leverage genetic diversity in existing germplasms to identify C. sativa accessions with low photoperiod sensitivity for future engineering of this trait. We quantified variation in the photoperiod response across 161 accessions of C. sativa by measuring hypocotyl length of four-day-old seedlings grown in long-day and short-day conditions, finding wide variation in photoperiod response. Similarly, soil-grown adult plants from selected accessions showed variation in photoperiod response in several traits; however, photoperiod responses in seedling and adult traits were not correlated, suggesting complex mechanistic underpinnings. Although RNA-seq experiments of the reference accession Licalla identified several differentially regulated Arabidopsis syntelogs involved in photoperiod response, including COL2, FT, LHY and WOX4, expression of these genes in the accessions did not correlate with differences in their photoperiod sensitivity. Taken together, we show that all tested accessions show some degree of photoperiod response, and that this trait is likely complex, involving several and separable seedling and adult traits. Significance StatementDay neutrality (photoperiod insensitivity) is a common trait in domesticated crops; however, the ancient oilseed crop Camelina sativa has remained photoperiod-sensitive, which likely limits seed yields. Here, we show that photoperiod sensitivity is conserved across many C. sativa cultivars, albeit to different degrees, and we establish that photoperiod sensitivity is a complex trait, which will require genetic engineering to achieve day neutrality.

plant biology↗

The regulatory potential of transposable elements in maize

The genomes of flowering plants consist largely of transposable elements (TEs), some of which modulate gene regulation and function. However, the repetitive nature of TEs and difficulty of mapping individual TEs by short-read-sequencing have hindered our understanding of their regulatory potential. We demonstrate that long-read chromatin fiber sequencing (Fiber-seq) comprehensively identifies accessible chromatin regions (ACRs) and CpG methylation across the maize genome. We uncover stereotypical ACR patterns at young TEs that degenerate with evolutionary age, resulting in TE-enhancers preferentially marked by a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility. We show that TE ACRs are co-opted as gene promoters and that ACR-containing TEs can facilitate gene amplification. Lastly, we uncover a pervasive epigenetic signature - hypo-5mCpG methylation and diffuse chromatin accessibility - directing TEs to specific loci, including the loci that sparked McClintocks discovery of TEs.

genomics↗