Physical access to regulatory DNA, including cis-regulatory sequences found within proximal promoters and distal enhancer elements, is a vital property of chromatin. In turn, their access is determined by nucleosome occupancy and posttranslational modification of histone proteins. A continuum of chromatin accessibility states from closed to permissive and open chromatin is a critical determinant of chromatin’s regulatory capacity in modulating gene expression. Transcription factors (TFs) can dynamically regulate local access to DNA by modulating nucleosome occupancy; in turn, the cell/tissue-specific chromatin landscape affects TF binding. Recent identification of chromatin signatures of cis-regulatory elements across angiosperms provides a strong foundation for understanding TFs and their interaction with the chromatin environment in modulating gene expression (Lu et al. 2019)…

Flowering plants have witnessed multiple cycles of whole-genome duplication (WGD) over the past 200 million years of evolution. Typically, WGD increases genome size and gene content, followed by gene loss, or fractionation, depending on functional categories. Certain classes of genes are retained as duplicates for longer periods of evolutionary time. Duplicate genes provide a potential source of genome diversity and evolution of novel traits (Panchy et al., 2016). Comparative analysis of available genome sequence data provides valuable resources to understand gene duplication and the mechanisms behind duplicate gene retention. Genes involved in macromolecular complexes such as signal transduction and transcription factors are preferentially retained as duplicates, whereas these same gene classes are underrepresented in small-scale duplications (e.g., tandem duplication, transposition)…

The measurement of the characteristics of living organisms is referred to as phenotyping (Singh et al., 2016). While the use of phenotyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genetics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent of inexpensive genotyping tools, crop functional genomics has entered the “big data” era, but efficient large-scale phenotyping is still an impediment hindering plant functional genomics…

Nearly every aspect of growth, morphogenesis, physiology, and stress response is influenced by cell/tissue-type specific gene expression. Transcription factors (TFs) recognize cis-regulatory elements and signal transcription machinery for gene regulation, and the interaction between TFs and their target genes creates spatiotemporal patterns of gene expression. Accurate functional annotation of these regulatory sites is essential for a comprehensive understanding of gene regulation in a variety of cell types and under diverse conditions…