Epistasis between genes is traditionally studied with mutations that eliminate protein activity, but most natural genetic variation is in cis-regulatory DNA and influences gene expression and function quantitatively. In this study, we used natural and engineered cis-regulatory alleles in a plant stem-cell circuit to systematically evaluate epistatic relationships controlling tomato fruit size. Combining a promoter allelic series with two other loci, we collected over 30,000 phenotypic data points from 46 genotypes to quantify how allele strength transforms epistasis. We revealed a saturating dose-dependent relationship but also allele-specific idiosyncratic interactions, including between alleles driving a step change in fruit size during domestication. Our approach and findings expose an underexplored dimension of epistasis, in which cis-regulatory allelic diversity within gene regulatory networks elicits nonlinear, unpredictable interactions that shape phenotypes. Description Editor’s summary Epistasis occurs when one gene or variant modifies the phenotypic effect of another, for example, when loss of an enzyme involved in pigmentation masks another gene’s regulation of patterning. Aguirre et al. looked at a series of cis-regulatory alleles of three genes involved in meristem development, specifically examining the effect on tomato seed compartment number. They found that although some relationships between genes were dose dependent, many of these interactions had unexpected effects. These results not only add to our understanding of genetic interactions between three genes at once, but also give insight into the potentially unexpected phenotypes that can emerge from alleles engineered for agricultural purposes. —Corinne Simonti Analysis of cis-regulatory alleles reveals unpredictable interactions between genes involved in tomato fruit size.

Idiosyncratic and dose-dependent epistasis drives variation in tomato fruit size

Cytokinins are a type of mobile phytohormone that regulate plant growth, development, and environmental adaptability. The major cytokinin species include isopentenyl adenine (iP), trans-zeatin (tZ), cis-zeatin (cZ), and dihydrozeatin (DZ). The spatial distributions of different cytokinin species in different organelles, cells, tissues, and organs are primarily shaped by biosynthesis via isopentenyltransferases (IPT), cytochrome P450 monooxygenase, and 5'-ribonucleotide phosphohydrolase, and by conjugation or catabolism via glycosyltransferase or cytokinin oxidase/dehydrogenase (CKX). Cytokinins bind to histidine receptor kinases (HKs) in the endoplasmic reticulum (ER) or plasma membrane (PM) and relay signals to response regulators (RRs) in the nucleus by shuttle proteins known as histidine phosphotransfer proteins (HPs). The movements of cytokinins from sites of biosynthesis to signal perception sites usually require long-distance, intercellular, and intracellular transport. In the past decade, ATP-binding cassette (ABC) transporters, purine permeases (PUP), AZA-GUANINE RESISTANT (AZG) transporters, equilibrative nucleoside transporters (ENT), and Sugars Will Eventually be Exported Transporters (SWEET) have been characterized as involved in cytokinin transport processes. This review begins by introducing the spatial distributions of various cytokinins and the subcellular localizations of the proteins involved in cytokinin metabolism and signaling. Highlights focus on an inventory of the characterized transporters involved in cytokinin compartmentalization, including long-distance, intercellular, and intracellular transport, and the regulation of spatial distributions of cytokinins by environmental cues. Future directions for cytokinin research are also discussed. 

Spatially Distributed Cytokinins: Metabolism, Signaling, and Transport

Gene duplication is a powerful source of biological innovation giving rise to paralogous genes that undergo diverse fates. Redundancy between paralogous genes is an intriguing outcome of duplicate gene evolution, and its maintenance over evolutionary time has long been considered a paradox. Redundancy can also be dubbed 'a geneticist's nightmare': It hinders the predictability of genome editing outcomes and limits our ability to link genotypes to phenotypes. Genetic studies in yeast and plants have suggested that the ability of ancient redundant duplicates to compensate for dosage perturbations resulting from a loss of function depends on the reprogramming of gene expression, a phenomenon known as active compensation. Starting from considerations on the stoichiometric constraints that drive the evolutionary stability of redundancy, this review aims to provide insights into the mechanisms of active compensation between duplicates that could be targeted for breaking paralog dependencies - the next frontier in plant functional studies.

Tackling redundancy: genetic mechanisms underlying paralog compensation in plants.

Plants have to endure unfavorable environmental conditions due to their sessility. To adapt to environmental constraints, plants have evolved intricate balancing mechanisms to achieve optimal survival while maintaining growth and development. The APETALA2/Ethylene-Responsive element binding Factor (AP2/ERF) family of transcription factors (TFs) are unique for plants and have been shown to regulate plant tolerance by modulating the expression of downstream genes in response to stresses, such as low or high temperature, drought, excessive water, and high salinity. AP2/ERF TFs have been extensively studied in model plants Arabidopsis and rice. In this review, we discuss AP2/ERF family classification and elaborate on their functions mostly in Arabidopsis, and a few rice AP2/ERF family TFs are also discussed here. We highlight the subfamilies of Dehydration-Responsive Element-Binding proteins/Ethylene-Responsive element binding Factor (DREBs/ERFs). We summarize our current understanding of the molecular mechanisms of their actions, and the signaling and regulatory networks through which they are modulated in the coordination of stress tolerance and plant growth and development. 

AP2/ERF Transcription Factors and Their Functions in Arabidopsis Responses to Abiotic Stresses

Cytokinins (CKs) are important plant hormones that regulate a variety of biological processes implicated in plant development and stress responses. Here, we summarize the most recent advances in discovering and characterizing the membrane transporters involved in long- and short-distance translocation of CKs and their significance in CK signal activity. We highlight the discovery of PUP7 and PUP21 tonoplast-localized transporters and propose potential mechanisms for CK subcellular homeostasis. Finally, we discuss the importance of subcellular hormone transport in light of the localization of histidine kinase receptors of CKs at the endoplasmic reticulum and plasma membrane.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/nph.19001

Cytokinin activity - transport and homeostasis at the whole plant, cell, and subcellular levels.

Plant genomes are characterized by large and complex gene families that often result in similar and partially overlapping functions. This genetic redundancy severely hampers current efforts to uncover novel phenotypes, delaying basic genetic research and breeding programmes. Here we describe the development and validation of Multi-Knock, a genome-scale clustered regularly interspaced short palindromic repeat toolbox that overcomes functional redundancy in Arabidopsis by simultaneously targeting multiple gene-family members, thus identifying genetically hidden components. We computationally designed 59,129 optimal single-guide RNAs that each target two to ten genes within a family at once. Furthermore, partitioning the library into ten sublibraries directed towards a different functional group allows flexible and targeted genetic screens. From the 5,635 single-guide RNAs targeting the plant transportome, we generated over 3,500 independent Arabidopsis lines that allowed us to identify and characterize the first known cytokinin tonoplast-localized transporters in plants. With the ability to overcome functional redundancy in plants at the genome-scale level, the developed strategy can be readily deployed by scientists and breeders for basic research and to expedite breeding efforts. The study describes the development and validation of Multi-Knock, a genome-scale clustered regularly interspaced short palindromic repeat toolbox that overcomes functional redundancy in plants by simultaneously targeting multiple gene-family members, thus identifying genetically hidden components. 

/pdf/multi-knock-a-multi-targeted-genome-scale-crispr-toolbox-to-1llvxw4p.pdf

Multi-Knock—a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants

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Multi-Knock—a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants