Efficient simultaneous mutagenesis of multiple genes in specific plant tissues by multiplex CRISPR

Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective

Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.

Endosperm cell death promoted by NAC transcription factors facilitates embryo invasion in Arabidopsis

In flowering plants, two fertilization products develop within the limited space of the seed: the embryo and the surrounding nutritive endosperm. The final size of the endosperm is modulated by the degree of embryo growth. In Arabidopsis thaliana, the endosperm expands rapidly after fertilization, but later gets invaded by the embryo that occupies most of the seed volume at maturity, surrounded by a single remaining aleurone-like endosperm layer.1,2,3,4 Embryo invasion is facilitated by the endosperm-expressed bHLH-type transcription factor ZHOUPI, which promotes weakening of endosperm cell walls.5,6 Endosperm elimination in zou mutants is delayed, and embryo growth is severely affected; the endosperm finally collapses around the dwarf embryo, causing the shriveled appearance of mature zou seeds.5,6,7 However, whether ZHOUPI facilitates mechanical endosperm destruction by the invading embryo or whether an active programmed cell death (PCD) process causes endosperm elimination has been subject to debate.2,8 Here we show that developmental PCD controlled by multiple NAC transcription factors in the embryo-adjacent endosperm promotes gradual endosperm elimination. Misexpressing the NAC transcription factor KIRA1 in the entire endosperm caused total endosperm elimination, generating aleurone-less mature seeds. Conversely, dominant and recessive higher-order NAC mutants led to delayed endosperm elimination and impaired cell corpse clearance. Promoting PCD in the zhoupi mutant partially rescued its embryo growth defects, while the endosperm in a zhoupi nac higher-order mutant persisted until seed desiccation. These data suggest that a combination of cell wall weakening and PCD jointly facilitates embryo invasion by an active auto-elimination of endosperm cells.

Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species

Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.

Signaling events for photomorphogenic root development

A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.

The translatability of genetic networks from model to crop species: lessons from the past and perspectives for the future

Comparative analyses of growth-regulatory mechanisms between Arabidopsis and maize revealed that even when the gene space is conserved, the translation of knowledge from model species to crops is not trivial. Based on these insights, we formulate future opportunities to improve the interpretation of curiosity-driven research towards crop improvement.

Virus-Induced Gene Editing and Its Applications in Plants

CRISPR/Cas-based genome editing technologies, which allow the precise manipulation of plant genomes, have revolutionized plant science and enabled the creation of germplasms with beneficial traits. In order to apply these technologies, CRISPR/Cas reagents must be delivered into plant cells; however, this is limited by tissue culture challenges. Recently, viral vectors have been used to deliver CRISPR/Cas reagents into plant cells. Virus-induced genome editing (VIGE) has emerged as a powerful method with several advantages, including high editing efficiency and a simplified process for generating gene-edited DNA-free plants. Here, we briefly describe CRISPR/Cas-based genome editing. We then focus on VIGE systems and the types of viruses used currently for CRISPR/Cas9 cassette delivery and genome editing. We also highlight recent applications of and advances in VIGE in plants. Finally, we discuss the challenges and potential for VIGE in plants.

Ectopic Expression of the Rice Grain-Size-Affecting Gene GS5 in Maize Affects Kernel Size by Regulating Endosperm Starch Synthesis

Maize is one of the most important food crops, and maize kernel is one of the important components of maize yield. Studies have shown that the rice grain-size affecting gene GS5 increases the thousand-kernel weight by positively regulating the rice grain width and grain grouting rate. In this study, based on the GS5 transgenic maize obtained through transgenic technology with specific expression in the endosperm, molecular assays were performed on the transformed plants. Southern blotting results showed that the GS5 gene was integrated into the maize genome in a low copy number, and RT-PCR analysis showed that the exogenous GS5 gene was normally and highly expressed in maize. The agronomic traits of two successive generations showed that certain lines were significantly improved in yield-related traits, and the most significant changes were observed in the OE-34 line, where the kernel width increased significantly by 8.99% and 10.96%, the 100-kernel weight increased by 14.10% and 10.82%, and the ear weight increased by 13.96% and 15.71%, respectively; however, no significant differences were observed in the plant height, ear height, kernel length, kernel row number, or kernel number. In addition, the overexpression of the GS5 gene increased the grain grouting rate and affected starch synthesis in the rice grains. The kernels’ starch content in OE-25, OE-34, and OE-57 increased by 10.30%, 7.39%, and 6.39%, respectively. Scanning electron microscopy was performed to observe changes in the starch granule size, and the starch granule diameter of the transgenic line(s) was significantly reduced. RT-PCR was performed to detect the expression levels of related genes in starch synthesis, and the expression of these genes was generally upregulated. It was speculated that the exogenous GS5 gene changed the size of the starch granules by regulating the expression of related genes in the starch synthesis pathway, thus increasing the starch content. The trans-GS5 gene was able to be stably expressed in the hybrids with the genetic backgrounds of the four materials, with significant increases in the kernel width, 100-kernel weight, and ear weight. In this study, the maize kernel size was significantly increased through the endosperm-specific expression of the rice GS5 gene, and good material for the functional analysis of the GS5 gene was created, which was of great importance in theory and application.

Zinc Finger-Homeodomain and Mini Zinc Finger proteins are key players in plant growth and responses to environmental stresses

The ZINC FINGER-HOMEODOMAIN (ZHD) protein family is a plant-specific family of transcription factors containing two conserved motifs: a non-canonical C5H3 zinc finger domain (ZF) and a DNA-binding homeodomain (HD). The MINI ZINC FINGER (MIF) proteins belong to this family, but were possibly derived from the ZHDs by losing the HD. Information regarding the function of ZHD and MIF proteins is scarce. However, different studies have shown that ZHD/MIF proteins play important roles not only in plant growth and development, but also in response to environmental stresses, including drought and pathogen attack. Here we review recent advances relative to ZHD/MIF functions in multiple species, to provide new insights into the diverse roles of these transcription factors in plants. Their mechanism of action in relation to their ability to interact with other proteins and DNA is also discussed. We then propose directions for future studies to understand better their important roles and pinpoint strategies for potential applications in crop improvement.

Spatiotemporal Regulation of CRISPR/Cas9 Enables Efficient, Precise, and Heritable Edits in Plant Genomes

CRISPR/Cas-mediated editing has revolutionized crop engineering. Due to the broad scope and potential of this technology, many studies have been carried out in the past decade towards optimizing genome editing constructs. Clearly, the choice of the promoter used to drive gRNA and Cas9 expression is critical to achieving high editing efficiency, precision, and heritability. While some important considerations for choosing a promoter include the number and nature of targets, host organism, mode of transformation and goal of the experiment, spatiotemporal regulation of Cas9 expression using tissue-specific or inducible promoters enables higher heritability and efficiency of targeted mutagenesis with reduced off-target effects. In this review, we discuss specific studies that highlight the prospects and trade-offs associated with the choice of promoters on genome editing and emphasize the need for inductive exploration and discovery to further advance this area of research in crop plants.

Conditional and tissue-specific approaches to dissect essential mechanisms in plant development

Reverse genetics approaches are routinely used to investigate gene function. However, mutations, especially in critical genes, can lead to pleiotropic effects as severe as lethality, thus limiting functional studies in specific contexts. Approaches that allow for modifications of genes or gene products in a specific spatial or temporal setting can overcome these limitations. The advent of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technologies has not only revolutionized targeted genome modification in plants but also enabled new possibilities for inducible and tissue-specific manipulation of gene functions at the DNA and RNA levels. In addition, novel approaches for the direct manipulation of target proteins have been introduced in plant systems. Here, we review the current development in tissue-specific and conditional manipulation approaches at the DNA, RNA, and protein levels.

Cellular and molecular bases of lateral root initiation and morphogenesis

Lateral root development is essential for the establishment of the plant root system. Lateral root initiation is a multistep process that impacts early primordium morphogenesis and is linked to the formation of a morphogenetic field of pericycle founder cells. Gradual recruitment of founder cells builds this morphogenetic field in an auxin-dependent manner. The complex process of lateral root primordium morphogenesis includes several subprocesses, which are presented in this review. The underlying cellular and molecular mechanisms of these subprocesses are examined.

BioCCP.jl: collecting coupons in combinatorial biotechnology

SUMMARY

In combinatorial biotechnology, it is crucial for screening experiments to sufficiently cover the design space. In the BioCCP.jl package (Julia), we provide functions for minimum sample size determination based on the mathematical framework coined the Coupon Collector Problem.

AVAILABILITY AND IMPLEMENTATION

BioCCP.jl, including source code, documentation and Pluto notebooks, is available at https://github.com/kirstvh/BioCCP.jl.

Protoplast Preparation and Fluorescence-Activated Cell Sorting for the Evaluation of Targeted Mutagenesis in Plant Cells

Fluorescence-activated cell sorting (FACS) allows for the enrichment of specific plant cell populations after protoplasting. In this book chapter, we describe the transformation and protoplasting of an Arabidopsis thaliana cell suspension culture (PSB-D, derived from MM2d) that can be used for the evaluation of CRISPR vectors in a subpopulation of cells. We also describe the protoplasting of Arabidopsis thaliana cells from the roots and stomatal lineage for the evaluation of tissue-specific gene editing. These protocols allow us to rapidly and accurately quantify various CRISPR systems in plant cells.