SignificancePopulations often show “islands of divergence” in the genome. Analysis of divergence between subspecies of Antirrhinum that differ in flower color patterns shows that sharp peaks in relative divergence occur at two causal loci. The island is shaped by a combination of gene flow and multiple selective sweeps, showing how divergence and barriers between populations can arise and be maintained.

Root meristem controls The plant meristem, a small cluster of stem cells generates all of the cell types necessary for the plant’s indeterminate growth pattern. Roszak et al . use single-cell analyses to follow development from the stem cell to the enucleated cell of the phloem vasculature. In the root of the small mustard plant Arabidopsis , this process takes just over 3 days, and the developmental trajectory spans more than a dozen different cell states. A transcriptional program initially held under repressive control is released as those initial repressors dissipate. Reciprocal repression by regulators early and late in the developmental trajectory control a rapid switch in the differentiation program. —PJH

One Sentence Summary:Selection acting on an inverted duplication that generates small RNAs leads to evolution of regulatory interactions and phenotypic change. LENGTH Main Text:A convenient system for studying selection in natural populations is afforded by hybrid zones, where closely-related species or populations come into contact (1). Such a hybrid zone has been described for two subspecies of Antirrhinum majus (snapdragon), that 4 differ in flower color (2), a trait involved in pollinator attraction (3-7). Both subspecies are pollinated by bees but have alternate patterns for guiding flower entry:A.m.pseudomajus flowers are magenta, with a patch of yellow highlighting the bee entry point (Fig. 1A), whereas A.m.striatum flowers are yellow with magenta veins at the entry point (Fig. 1B). The magenta and yellow flower color intensities show sharp clines at a hybrid zone (2) where the subspecies come into contact. Production of magenta is regulated by ROSEA (ROS) and ELUTA (EL) (8-10). ROS encodes a MYB-like transcription factor that promotes anthocyanin biosynthetic gene expression in A.m.pseudomajus and exhibits a steep cline in allele frequencies at the hybrid zone (2, 9).Distribution of yellow pigment is regulated by SULF (Fig. 1B, C), which represses production of the yellow flavonoid aurone in A.m.pseudomajus ( Fig. 1D) (2, 9, 10). Here we study the molecular nature of SULF.To isolate SULF we first mapped it to an interval of ~3Mb on chromosome 4 by sequencing pools of sulf and SULF phenotypes from a segregating population ( fig. S1).In parallel, we carried out a transposon mutagenesis experiment in A. majus (SULF) and isolated a mutant, sulf-660, that was both somatically and genetically unstable ( fig. S2A and Methods). Comparing the genome sequence of sulf-660 and its revertants revealed a single insertion site, within the mapped region of SULF, specific to sulf-660. Three independent revertants had different excision footprints at this site, confirming that the transposon was responsible for the sulf phenotype ( fig. S2B). 5BLAST searches of the sequence flanking the transposon insertion site revealed regions of 74-88% nucleotide sequence identity to A.majus chalcone 4'-O-gluosyltransferase (Am4'CGT), which encodes an enzyme involved in synthesis of the yellow pigment aurone ( Fig. 2A and table S1) (11). The regions of Am4'CGT homology were organized as an inverted duplication in the A. majus SULF genome. Both the left and right arms of the duplication carried deletions relative to intact Am4'CGT, suggesting they had independently degenerated from a more complete precursor. A contiguous region of inverted homology between the left and right arms spanned a ~590 bp region (red arrows, Fig. 2A), separated by a ~600 bp spacer region, which contained the transposon insertion site of sulf-660. Phylogenetic analysis indicated that the SULF inverted repeats were likely generated from Am4'CGT recently in the evolution of the Antirrhinum lineage ( Fig. 2B and fig. S3).To determine whether the inverted duplicatio...

The capacity of organisms to tune their development in response to environmental cues is pervasive in nature. This phenotypic plasticity is particularly striking in plants, enabled by their modular and continuous development. A good example is the activation of lateral shoot branches in Arabidopsis, which develop from axillary meristems at the base of leaves. The activity and elongation of lateral shoots depends on the integration of many signals both external (e.g. light, nutrient supply) and internal (e.g. the phytohormones auxin, strigolactone and cytokinin). Here, we characterise natural variation in plasticity of shoot branching in response to nitrate supply using two diverse panels of Arabidopsis lines. We find extensive variation in nitrate sensitivity across these lines, suggesting a genetic basis for variation in branching plasticity. High plasticity is associated with extreme branching phenotypes such that lines with the most branches on high nitrate have the fewest under nitrate deficient conditions. Conversely, low plasticity is associated with a constitutively moderate level of branching. Furthermore, variation in plasticity is associated with alternative life histories with the low plasticity lines flowering significantly earlier than high plasticity lines. In Arabidopsis, branching is highly correlated with fruit yield, and thus low plasticity lines produce more fruit than high plasticity lines under nitrate deficient conditions, whereas highly plastic lines produce more fruit under high nitrate conditions. Low and high plasticity, associated with early and late flowering respectively, can therefore be interpreted alternative escape vs mitigate strategies to low N environments. The genetic architecture of these traits appears to be highly complex, with only a small proportion of the estimated genetic variance detected in association mapping.

Genetically identical plants growing in the same conditions can display heterogeneous phenotypes. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability and its underlying mechanisms. We show extensive variation in seed germination time variability between Arabidopsis accessions and use a multiparent recombinant inbred population to identify two genetic loci involved in this trait. Both loci include genes implicated in modulating abscisic acid (ABA) sensitivity. Mutually antagonistic regulation between ABA, which represses germination, and gibberellic acid (GA), which promotes germination, underlies the decision to germinate and can act as a bistable switch. A simple stochastic model of the ABA-GA network shows that modulating ABA sensitivity can generate the range of germination time distributions we observe experimentally. We validate the model by testing its predictions on the effects of exogenous hormone addition. Our work provides a foundation for understanding the mechanism and functional role of phenotypic variability in germination time.

Single cell sequencing has recently allowed the generation of exhaustive root cell atlases.However, some cell types are elusive and remain underrepresented. Here, we use a secondgeneration single cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology.As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy.Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

The mechanisms that allow cells in the plant meristem to coordinate tissue-wide maturation gradients with specialized cell networks are critical for indeterminate growth. Here, we reconstructed the protophloem developmental trajectory of 19 cells from cell birth to terminal differentiation at single cell resolution in the Arabidopsis root. We found that cellular specification is mediated near the stem cell niche by PHLOEM EARLY DOF (PEAR) transcription factors. However, the PEAR dependent differentiation program is repressed by a broad gradient of PLETHORA (PLT) transcription factors, which directly inhibit PEARs’ own direct target ALTERED PHLOEM DEVELOPMENT (APL). The dissipation of PLT gradient around 7 cells from the stem cell activates APL expression, and a subsequent transitional network that results in a “seesaw” pattern of mutual inhibition over developmental time. Together, we provide a mechanistic understanding of how morphogen-like maturation gradients interface with cell-type specific transcriptional regulators to stage cellular differentiation.

Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.