Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis

Targeting Induced Local Lesions in Genomes (TILLING): advances and opportunities for fast tracking crop breeding

The intensification of food production via conventional crop breeding alone is inadequate to cater for global hunger. The development of precise and expeditious high throughput reverse genetics approaches has hugely benefited modern plant breeding programs. Targeting Induced Local Lesions in Genomes (TILLING) is one such reverse genetics approach which employs chemical/physical mutagenesis to create new genetic sources and identifies superior/novel alleles. Owing to technical limitations and sectional applicability of the original TILLING protocol, it has been timely modified. Successions include: EcoTILLING, Double stranded EcoTILLING (DEcoTILLING), Self-EcoTILLING, Individualized TILLING (iTILLING), Deletion-TILLING (De-TILLING), PolyTILLING, and VeggieTILLING. This has widened its application to a variety of crops and needs. They can characterize mutations in coding as well as non-coding regions and can overcome complexities associated with the large genomes. Combining next generation sequencing tools with the existing TILLING protocols has enabled screening of huge germplasm collections and mutant populations for the target genes. In silico TILLING platforms have transformed TILLING into an exciting breeding approach. The present review outlines these multifarious TILLING modifications for precise mutation detection and their application in advance breeding programmes together with relevant case studies. Appropriate use of these protocols will open up new avenues for crop improvement in the twenty first century.

Biological macromolecules mediated by environmental signals affect flowering regulation in plants: A comprehensive review

Flowering time is a crucial developmental stage in the life cycle of plants, as it determines the reproductive success and overall fitness of the organism. The precise regulation of flowering time is influenced by various internal and external factors, including genetic, environmental, and hormonal cues. This review provided a comprehensive overview of the molecular mechanisms and regulatory pathways of biological macromolecules (e.g. proteins and phytohormone) and environmental factors (e.g. light and temperature) involved in the control of flowering time in plants. We discussed the key proteins and signaling pathways that govern the transition from vegetative growth to reproductive development, highlighting the intricate interplay between genetic networks, environmental cues, and phytohormone signaling. Additionally, we explored the impact of flowering time regulation on plant adaptation, crop productivity, and agricultural practices. Moreover, we summarized the similarities and differences of flowering mechanisms between annual and perennial plants. Understanding the mechanisms underlying flowering time control is not only essential for fundamental plant biology research but also holds great potential for crop improvement and sustainable agriculture.

A word of caution: T-DNA-associated mutagenesis in plant reproduction research

T-DNA transformation is prevalent in Arabidopsis research and has expanded to a broad range of crops and model plants. While major progress has been made in optimizing the Agrobacterium-mediated transformation process for various species, a variety of pitfalls associated with the T-DNA insertion may lead to the misinterpretation of T-DNA mutant analysis. Indeed, secondary mutagenesis either on the integration site or elsewhere in the genome, together with epigenetic interactions between T-DNA inserts or frequent genomic rearrangements, can be tricky to differentiate from the effect of the knockout of the gene of interest. These are mainly the case for genomic rearrangements that become balanced in filial generations without consequential phenotypical defects, which may be confusing particularly for studies that aim to investigate fertility and gametogenesis. As a cautionary note to the plant research community studying gametogenesis, we here report an overview of the consequences of T-DNA-induced secondary mutagenesis with emphasis on the genomic imbalance on gametogenesis. Additionally, we present a simple guideline to evaluate the T-DNA-mutagenized transgenic lines to decrease the risk of faulty analysis with minimal experimental effort.

Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is a very important food legume and needs improved drought tolerance for higher seed production in dry environments. The aim of this study was to determine diversity and genetic polymorphism in zinc finger knuckle genes with CCHC domains and their functional analysis for practical improvement of chickpea breeding. Two CaZF-CCHC genes, Ca04468 and Ca07571, were identified as potentially important candidates associated with plant responses to drought and dehydration. To study these genes, various methods were used including Sanger sequencing, DArT (Diversity array technology) and molecular markers for plant genotyping, gene expression analysis using RT-qPCR, and associations with seed-related traits in chickpea plants grown in field trials. These genes were studied for genetic polymorphism among a set of chickpea accessions, and one SNP was selected for further study from four identified SNPs between the promoter regions of each of the two genes. Molecular markers were developed for the SNP and verified using the ASQ and CAPS methods. Genotyping of parents and selected breeding lines from two hybrid populations, and SNP positions on chromosomes with haplotype identification, were confirmed using DArT microarray analysis. Differential expression profiles were identified in the parents and the hybrid populations under gradual drought and rapid dehydration. The SNP-based genotypes were differentially associated with seed weight per plant but not with 100 seed weight. The two developed and verified SNP molecular markers for both genes, Ca04468 and Ca07571, respectively, could be used for marker-assisted selection in novel chickpea cultivars with improved tolerance to drought and dehydration.

Advancements in genetic techniques and functional genomics for enhancing crop traits and agricultural sustainability

Genetic variability is essential for the development of new crop varieties with economically beneficial traits. The traits can be inherited from wild relatives or induced through mutagenesis. Novel genetic elements can then be identified and new gene functions can be predicted. In this study, forward and reverse genetics approaches were described, in addition to their applications in modern crop improvement programs and functional genomics. By using heritable phenotypes and linked genetic markers, forward genetics searches for genes by using traditional genetic mapping and allele frequency estimation. Despite recent advances in sequencing technology, omics and computation, genetic redundancy remains a major challenge in forward genetics. By analyzing close-related genes, we will be able to dissect their functional redundancy and predict possible traits and gene activity patterns. In addition to these predictions, sophisticated reverse gene editing tools can be used to verify them, including TILLING, targeted insertional mutagenesis, gene silencing, gene targeting and genome editing. By using gene knock-down, knock-up and knock-out strategies, these tools are able to detect genetic changes in cells. In addition, epigenome analysis and editing enable the development of novel traits in existing crop cultivars without affecting their genetic makeup by increasing epiallelic variants. Our understanding of gene functions and molecular dynamics of various biological phenomena has been revised by all of these findings. The study also identifies novel genetic targets in crop species to improve yields and stress tolerances through conventional and non-conventional methods. In this article, genetic techniques and functional genomics are specifically discussed and assessed for their potential in crop improvement.

Plant genome information facilitates plant functional genomics

MAIN CONCLUSION

In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

Plant biochemical genetics in the multiomics era

Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.

Physical mapping of the wheat genes in low-recombination regions: radiation hybrid mapping of the C-locus

KEY MESSAGE

This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located on proximal parts of wheat chromosomes that show highly reduced recombination. Mapping wheat genes, in the centromeric and pericentromeric regions (~ 2/3rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination. Using an example of compact spike locus (C-locus), this study provides an approach to precisely map wheat genes in the pericentromeric and centromeric regions that house ~ 30% of wheat genes. In club-wheat, spike compactness is controlled by the dominant C-locus, but previous efforts have failed to localize it, on a particular arm of chromosome 2D. We integrated radiation hybrid (RH) and high-resolution genetic mapping to locate C-locus on the short arm of chromosome 2D. Flanking markers of the C-locus span a physical distance of 11.0 Mb (231.0-242 Mb interval) and contain only 11 high-confidence annotated genes. This work demonstrates the value of this integrated strategy in mapping dominant genes in the low-recombination regions of the wheat genome. A comparison of the mapping resolutions of the RH and genetic maps using common anchored markers indicated that the RH map provides ~ 9 times better resolution that the genetic map even with much smaller population size. This study provides a broadly applicable approach to fine map wheat genes in regions of suppressed recombination.

Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis

INTRODUCTION

Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions.

METHODS

The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes.

RESULTS

Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier.

DISCUSSION

The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.

Predicting Gene Regulatory Interactions Using Natural Genetic Variation

Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype-phenotype map. Although GWAS are usually used to assess simple univariate associations between genetic markers and traits of interest, it is also possible to infer the underlying genetic architecture and to predict gene regulatory interactions. In this chapter, we describe the latest methods and tools to perform GWAS by calculating permutation-based significance thresholds. For this purpose, we first provide guidelines on univariate GWAS analyses that are extended in the second part of this chapter to more complex models that enable the inference of gene regulatory networks and how these networks vary.

A single amino acid transporter controls the uptake of priming-inducing beta-amino acids and the associated tradeoff between induced resistance and plant growth

Selected β-amino acids, such as β-aminobutyric acid (BABA) and R-β-homoserine (RBH), can prime plants for resistance against a broad spectrum of diseases. Here, we describe a genome-wide screen of fully annotated Arabidopsis thaliana T-DNA insertion lines for impaired in RBH-induced immunity (iri) mutants against the downy mildew pathogen Hyaloperonospora arabidopsidis, yielding 104 lines that were partially affected and four lines that were completely impaired in RBH-induced resistance (IR). We confirmed the iri1-1 mutant phenotype with an independent T-DNA insertion line in the same gene, encoding the high-affinity amino acid transporter LYSINE HISTIDINE TRANSPORTER 1 (LHT1). Uptake experiments with yeast cells expressing LHT1 and mass spectrometry-based quantification of RBH and BABA in leaves of lht1 mutant and LHT1 overexpression lines revealed that LHT1 acts as the main transporter for cellular uptake and systemic distribution of RBH and BABA. Subsequent characterization of lht1 mutant and LHT1 overexpression lines for IR and growth responses revealed that the levels of LHT1-mediated uptake determine the tradeoff between IR and plant growth by RBH and BABA.

CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean

Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods often allow the identification of candidate causal genes. To provide true experimental evidence of a gene's function, reverse genetics techniques are highly valuable. Site-directed mutagenesis through transfer DNA (T-DNA) delivery is an efficient reverse screen method in plant functional analysis. Precise modification of targeted crop genome sequences is possible through the stable and/or transient delivery of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) reagents. Currently, CRISPR/Cas9 is the most powerful reverse genetics approach for fast and precise functional analysis of candidate genes/mutations of interest. Rapid and large-scale analyses of CRISPR/Cas-induced mutagenesis is achievable through Agrobacterium rhizogenes-mediated hairy root transformation. The combination of A. rhizogenes hairy root-CRISPR/Cas provides an extraordinary platform for rapid, precise, easy, and cost-effective "in root" functional analysis of genes of interest in legume plants, including soybean. Both hairy root transformation and CRISPR/Cas9 techniques have their own complexities and considerations. Here, we discuss recent advancements in soybean hairy root transformation and CRISPR/Cas9 techniques. We highlight the critical factors required to enhance mutation induction and hairy root transformation, including the new generation of reporter genes, methods of Agrobacterium infection, accurate gRNA design strategies, Cas9 variants, gene regulatory elements of gRNAs and Cas9 nuclease cassettes and their configuration in the final binary vector to study genes involved in root-related traits in soybean.

RPS5A Promoter-Driven Cas9 Produces Heritable Virus-Induced Genome Editing in Nicotiana attenuata

The virus-induced genome editing (VIGE) system aims to induce targeted mutations in seeds without requiring any tissue culture. Here, we show that tobacco rattle virus (TRV) harboring guide RNA (gRNA) edits germ cells in a wild tobacco, Nicotiana attenuata, that expresses Streptococcus pyogenes Cas9 (SpCas9). We first generated N. attenuata transgenic plants expressing SpCas9 under the control of 35S promoter and infected rosette leaves with TRV carrying gRNA. Gene-edited seeds were not found in the progeny of the infected N. attenuata. Next, the N. attenuata ribosomal protein S5 A (RPS5A) promoter fused to SpCas9 was employed to induce the heritable gene editing with TRV. The RPS5A promoter-driven SpCas9 successfully produced monoallelic mutations at three target genes in N. attenuata seeds with TRV-delivered guide RNA. These monoallelic mutations were found in 2%-6% seeds among M1 progenies. This editing method provides an alternative way to increase the heritable editing efficacy of VIGE.

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes

A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into 'co-essential' pathways, but this approach has been limited by ubiquitous false positives. In the present study, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. This atlas recapitulates diverse pathways and protein complexes, and predicts the functions of 108 uncharacterized genes. Validating top predictions, we show that TMEM189 encodes plasmanylethanolamine desaturase, a key enzyme for plasmalogen synthesis. We also show that C15orf57 encodes a protein that binds the AP2 complex, localizes to clathrin-coated pits and enables efficient transferrin uptake. Finally, we provide an interactive webtool for the community to explore our results, which establish co-essentiality profiling as a powerful resource for biological pathway identification and discovery of new gene functions.

Combining quantitative trait locus and co-expression analysis allowed identification of new candidates for oil accumulation in rapeseed

In crops there are quantitative trait loci (QTLs) in which some of the causal quantitative trait genes (QTGs) have not been functionally characterized even in the model plant Arabidopsis. We propose an approach to delineate QTGs in rapeseed by coordinating expression of genes located within QTLs and known orthologs related to traits from Arabidopsis. Using this method in developing siliques 15 d after pollination in 71 lines of rapeseed, we established an acyl-lipid metabolism co-expression network with 21 modules composed of 270 known acyl-lipid genes and 3503 new genes. The core module harbored 76 known genes involved in fatty acid and triacylglycerol biosynthesis and 671 new genes involved in sucrose transport, carbon metabolism, amino acid metabolism, seed storage protein processes, seed maturation, and phytohormone metabolism. Moreover, the core module closely associated with the modules of photosynthesis and carbon metabolism. From the co-expression network, we selected 12 hub genes to identify their putative Arabidopsis orthologs. These putative orthologs were functionally analysed using Arabidopsis knockout and overexpression lines. Four knockout mutants exhibited lower seed oil content, while the seed oil content in 10 overexpression lines was significantly increased. Therefore, combining gene co-expression network analysis and QTL mapping, this study provides new insights into the detection of QTGs and into acyl-lipid metabolism in rapeseed.

CRISPR/Cas9-Based Genome Editing Toolbox for Arabidopsis thaliana

CRISPR/Cas9 system has emerged as a powerful genome engineering tool to study gene function and improve plant traits. Genome editing is achieved at a specific genome sequence by Cas9 endonuclease to generate double standard breaks (DSBs) directed by short guide RNAs (sgRNAs). The DSB is repaired by error-prone nonhomologous end joining (NHEJ) or error-free homology-directed repair (HDR) pathways, resulting in gene mutation or sequence replacement, respectively. These cellular DSB repair pathways can be exploited to knock out or replace genes. Also, cytidine or adenine base editors (CBEs or ABEs) fused to catalytically dead Cas9 (dCas9) or nickase Cas9 (nCas9) are used to perform precise base editing without generating DSBs. In this chapter, we describe a detailed procedure to carry out single/multiple gene mutations and precise base editing in the Arabidopsis genome by using CRISPR/Cas9-based system. Specifically, the steps of target gene selection, sgRNA design, vector construction, transformation, and analysis of transgenic lines are described. The protocol is potentially adaptable to perform genome editing in other plant species such as rice.

Identification and characterization of unconventional membrane protein trafficking regulators in Arabidopsis: A genetic approach

Proper trafficking and subcellular localization of membrane proteins are essential for plant growth and development. The plant endomembrane system contains several membrane-bound organelles with distinct functions including the endoplasmic reticulum (ER), Golgi apparatus, trans-Golgi network (TGN) or early endosome, prevacuolar compartment (PVC) or multivesicular body (MVB) and vacuole. Multiple approaches have been successfully used to identify and study the regulators and components important for signal transduction, growth and development, as well as membrane trafficking in the endomembrane system in plants. These include the homologous characterization of the counterparts in mammals or yeast employing both reverse genetic as well as the forward genetic screen approaches. However, the deletion or mutation of membrane trafficking related proteins usually leads to seedling lethality due to their essential roles in plant development and organelle biogenesis. To overcome the limitation of lethal phenotype of the target proteins, we used DEX-inducible RNAi knock-down lines to study their function in plants. More recently, we developed and used both RNAi knock-down and T-DNA insertional lines as starting materials to screen for mutations that could suppress and rescue the lethal phenotype, or a suppressor screening. Further characterization of the newly identified suppressor mutants has resulted in the identification of novel negative regulators in mediating membrane trafficking and organelle biogenesis in plants. In this review, we summarize the current approaches in studying protein trafficking in the endomembrane system. We then describe three examples of suppressor screening with distinct starting materials (i.e. FREE1, MON1, and SH3P2 that are regulators of MVB, vacuole, and autophagosomes, respectively) to discuss the rationale, procedures, advantages and disadvantages, and possible outcomes of such a suppressor screening. We finally propose that these novel screening approaches will lead to the identification of new unconventional players in regulating protein trafficking and organelle biogenesis in plants and discuss their impact on plant cell biology research.

Diversity of genetic lesions characterizes new Arabidopsis flavonoid pigment mutant alleles from T-DNA collections

The visual phenotypes afforded by flavonoid pigments have provided invaluable tools for modern genetics. Many Arabidopsis transparent testa (tt) mutants lacking the characteristic proanthocyanidin (PA) seed coat pigmentation and often failing to accumulate anthocyanins in vegetative tissues have been characterized. These mutants have significantly contributed to our understanding of flavonoid biosynthesis, regulation, and transport. A comprehensive screening for tt mutants in available large T-DNA collection lines resulted in the identification of 16 independent lines lacking PAs and anthocyanins, or with seed coat pigmentation clearly distinct from wild type. Segregation analyses and the characterization of second alleles in the genes disrupted by the indexed T-DNA insertions demonstrated that all the lines contained at least one additional mutation responsible for the tt phenotypes. Using a combination of RNA-Seq and whole genome re-sequencing and confirmed through complementation, we show here that these mutations correspond to novel alleles of ttg1 (two alleles), tt3 (two alleles), tt5 (two alleles), ban (two alleles), tt1 (two alleles), and tt8 (six alleles), which harbored additional T-DNA insertions, indels, missense mutations, and large genomic deletion. Several of the identified alleles offer interesting perspectives on flavonoid biosynthesis and regulation.

Plant Membrane Transport Research in the Post-genomic Era

Membrane transport processes are indispensable for many aspects of plant physiology including mineral nutrition, solute storage, cell metabolism, cell signaling, osmoregulation, cell growth, and stress responses. Completion of genome sequencing in diverse plant species and the development of multiple genomic tools have marked a new era in understanding plant membrane transport at the mechanistic level. Genes coding for a galaxy of pumps, channels, and carriers that facilitate various membrane transport processes have been identified while multiple approaches are developed to dissect the physiological roles as well as to define the transport capacities of these transport systems. Furthermore, signaling networks dictating the membrane transport processes are established to fully understand the regulatory mechanisms. Here, we review recent research progress in the discovery and characterization of the components in plant membrane transport that take advantage of plant genomic resources and other experimental tools. We also provide our perspectives for future studies in the field.

A novel Arabidopsis pathosystem reveals cooperation of multiple hormonal response-pathways in host resistance against the global crop destroyer Macrophomina phaseolina

Dubbed as a "global destroyer of crops", the soil-borne fungus Macrophomina phaseolina (Mp) infects more than 500 plant species including many economically important cash crops. Host defenses against infection by this pathogen are poorly understood. We established interactions between Mp and Arabidopsis thaliana (Arabidopsis) as a model system to quantitatively assess host factors affecting the outcome of Mp infections. Using agar plate-based infection assays with different Arabidopsis genotypes, we found signaling mechanisms dependent on the plant hormones ethylene, jasmonic acid and salicylic acid to control host defense against this pathogen. By profiling host transcripts in Mp-infected roots of the wild-type Arabidopsis accession Col-0 and ein2/jar1, an ethylene/jasmonic acid-signaling deficient mutant that exhibits enhanced susceptibility to this pathogen, we identified hundreds of genes potentially contributing to a diverse array of defense responses, which seem coordinated by complex interplay between multiple hormonal response-pathways. Our results establish Mp/Arabidopsis interactions as a useful model pathosystem, allowing for application of the vast genomics-related resources of this versatile model plant to the systematic investigation of previously understudied host defenses against a major crop plant pathogen.

A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing

BACKGROUND

Nitrogen dioxide (NO₂) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death.

RESULTS

Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO₂ fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO₂ whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO₂. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO₂-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation.

CONCLUSIONS

The presented NO₂ dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.

Improvement of multiplex semi-nested PCR system for screening of rare mutations by high-throughput sequencing

The CRISPR/Cas9 system is an efficient gene-editing method, but it is difficult to obtain mutants for some specific species and special genome structures. A previously reported multiplexed, semi-nested PCR target-enrichment approach, which does not rely on transgenic technology, has been shown to be an effective and affordable strategy for the discovery of rare mutations in a large sodium azide-induced rice population. However, this strategy has the potential for further optimization. Here, we describe an improved multiplex semi-nested PCR target-enrichment strategy with simplified processing procedures, reduced false-positive rates and increased mutation detection frequency (1 mutation/73 Kb).

Distributed phenomics with the unPAK project reveals the effects of mutations

Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.

Analysis of Drought Tolerance and Associated Traits in Upland Cotton at the Seedling Stage

(1) Background: Upland cotton (Gossypium hirsutum L.) is the most important natural fiber worldwide, and it is extensively planted and plentifully used in the textile industry. Major cotton planting regions are frequently affected by abiotic stress, especially drought stress. Drought resistance is a complex, quantitative trait. A genome-wide association study (GWAS) constitutes an efficient method for dissecting the genetic architecture of complex traits. In this study, the drought resistance of a population of 316 upland cotton accessions was studied via GWAS. (2) Methods: GWAS methodology was employed to identify relationships between molecular markers or candidate genes and phenotypes of interest. (3) Results: A total of 8, 3, and 6 SNPs were associated with the euphylla wilting score (EWS), cotyledon wilting score (CWS), and leaf temperature (LT), respectively, based on a general linear model and a factored spectrally transformed linear mixed model. For these traits, 7 QTLs were found, of which 2 each were located on chromosomes A05, A11, and D03, and of which 1 was located on chromosome A01. Importantly, in the candidate regions WRKY70, GhCIPK6, SnRK2.6, and NET1A, which are involved in the response to abscisic acid (ABA), the mitogen-activated protein kinase (MAPK) signaling pathway and the calcium transduction pathway were identified in upland cotton at the seedling stage under drought stress according to annotation information and linkage disequilibrium (LD) block analysis. Moreover, RNA sequencing analysis showed that WRKY70, GhCIPK6, SnRK2.6, and NET1A were induced by drought stress, and the expression of these genes was significantly different between normal and drought stress conditions. (4) Conclusions: The present study should provide some genomic resources for drought resistance in upland cotton. Moreover, the germplasm of the different phenotypes, the detected SNPs and, the potential candidate genes will be helpful for molecular marker-assisted breeding studies about increased drought resistance in upland cotton.

CRISPR/Cas9 in plants: at play in the genome and at work for crop improvement

The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system uses single-guide RNAs for genome editing, making it a simple, robust, powerful tool for targeted gene mutagenesis, knockout and knock-in/replacement, as well as transcriptional regulation. Here, we review the working principles, components and potential modifications of CRISPR/Cas9 for efficient single and multiplex gene editing in plants. We also describe recent work that has used CRISPR/Cas9 to improve economically important traits in crop plants. Although the apparent ease of CRISPR/Cas9-mediated editing may make it appear as though scientists are merely playing with plant genomes, the combined power of CRISPR/Cas9 has enabled vital research to be completed in the battle toward optimization and adaptation of crop species, permitting crucial advances to be achieved in crop improvement.

The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants

Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.

Rapid and user-friendly open-source CRISPR/Cas9 system for single- or multi-site editing of tomato genome

CRISPR/Cas9-induced genome editing is a powerful tool for studying gene function in a variety of organisms, including plants. Using multi-sgRNAs to target one or more genes is helpful to improve the efficacy of gene editing and facilitate multi-gene editing. Here, we describe a CRISPR/Cas9 system which can be conveniently developed as a CRISPR kit. SgRNA expression cassettes can be rapidly generated by one-step PCR using our CRISPR kit. In our kit, there are two binary vectors pHNCas9 and pHNCas9HT. The binary vector pHNCas9 was constructed to allow to assemble up to eight sgRNA expression cassettes by one-step Golden Gate cloning. Another binary vector pHNCas9HT can be used to generate a large number of single target constructs by directly transforming ligation reactions products into A. tumefaciens without several procedures, such as PCR and plasmid extraction. The two binary vectors are designed according to the principles of standard BioBrick assembly to be used as an open-source tool. For example, we used BioBrick as a visual T-DNA tag. We also developed a primer design aid to complement the system. With this primer design aid, researchers can rapidly obtain primers and GC content, and sgRNA sequence of target site. Our CRISPR/Cas9 system can perform single- and multi-site editing and multiple gene editing to produce various types of mutations in tomato. This rapid and user-friendly CRISPR/Cas9 system for tomato can be potentially used for mutagenesis of important crop species for genetic improvement and is suitable for research into the function of genes.

A Highly Efficient Cell Division-Specific CRISPR/Cas9 System Generates Homozygous Mutants for Multiple Genes in Arabidopsis

The CRISPR/Cas9 system has been widely used for targeted genome editing in numerous plant species. In Arabidopsis, constitutive promoters usually result in a low efficiency of heritable mutation in the T1 generation. In this work, CRISPR/Cas9 gene editing efficiencies using different promoters to drive Cas9 expression were evaluated. Expression of Cas9 under the constitutive CaMV 35S promoter resulted in a 2.3% mutation rate in T1 plants and failed to produce homozygous mutations in the T1 and T2 generations. In contrast, expression of Cas9 under two cell division-specific promoters, YAO and CDC45, produced mutation rates of 80.9% to 100% in the T1 generation with nonchimeric mutations in the T1 (4.4–10%) and T2 (32.5–46.1%) generations. The pCDC45 promoter was used to modify a previously reported multiplex CRISPR/Cas9 system, replacing the original constitutive ubiquitin promoter. The multi-pCDC45-Cas9 system produced higher mutation efficiencies than the multi-pUBQ-Cas9 system in the T1 generation (60.17% vs. 43.71%) as well as higher efficiency of heritable mutations (11.30% vs. 4.31%). Sextuple T2 homozygous mutants were identified from a construct targeting seven individual loci. Our results demonstrate the advantage of using cell division promoters for CRISPR/Cas9 gene editing applications in Arabidopsis, especially in multiplex applications.

Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea

Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.

Genetic Analysis of Chloroplast Biogenesis, and Function and Mutant Collections

Since the time DNA was discovered as the code of life, genetic analysis has greatly advanced our understanding of the relation between genotype and phenotype and associated molecular mechanisms in various organisms including plants and algae. Forward genetics from phenotype to genotype has identified causal genes of interesting phenotypes induced by chemical, ionizing-radiation, or DNA insertional mutagenesis. Meanwhile, reverse genetics from genotype to phenotype has revealed physiological and molecular roles of known gene sequences. During the past dozen years, many molecular genetic tools have been developed to investigate gene functions quickly and efficiently. In this chapter, we introduce several approaches of forward and reverse genetics, including random chemical and DNA insertional mutagenesis, activation tagging, RNA interference, and gene overexpression and induction systems, with some examples of genetic studies of chloroplast biology mainly in Arabidopsis thaliana. We also briefly describe methods for chemical and DNA insertion mutagenesis and how to obtain sequence-tagged mutants from public collections. With greatly improved DNA sequencing and genome-editing technologies, model organisms as well as diverse species can be used for molecular biology. Genetic analysis can play an increasingly important role in elucidating chloroplast biogenesis and functions.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

Strategies and tools to improve crop productivity by targeting photosynthesis

Crop productivity needs to substantially increase to meet global food and feed demand for a rapidly growing world population. Agricultural technology developers are pursuing a variety of approaches based on both traditional technologies such as genetic improvement, pest control and mechanization as well as new technologies such as genomics, gene manipulation and environmental modelling to develop crops that are capable of meeting growing demand. Photosynthesis is a key biochemical process that, many suggest, is not yet optimized for industrial agriculture or the modern global environment. We are interested in identifying control points in maize photoassimilation that are amenable to gene manipulation to improve overall productivity. Our approach encompasses: developing and using novel gene discovery techniques, translating our discoveries into traits and evaluating each trait in a stepwise manner that reflects a modern production environment. Our aim is to provide step change advancement in overall crop productivity and deliver this new technology into the hands of growers.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.

Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized Sorghum

The accurate detection of induced mutations is critical for both forward and reverse genetics studies. Experimental chemical mutagenesis induces relatively few single base changes per individual. In a complex eukaryotic genome, false positive detection of mutations can occur at or above this mutagenesis rate. We demonstrate here, using a population of ethyl methanesulfonate (EMS)-treated Sorghum bicolor BTx623 individuals, that using replication to detect false positive-induced variants in next-generation sequencing (NGS) data permits higher throughput variant detection with greater accuracy. We used a lower sequence coverage depth (average of 7×) from 586 independently mutagenized individuals and detected 5,399,493 homozygous single nucleotide polymorphisms (SNPs). Of these, 76% originated from only 57,872 genomic positions prone to false positive variant calling. These positions are characterized by high copy number paralogs where the error-prone SNP positions are at copies containing a variant at the SNP position. The ability of short stretches of homology to generate these error-prone positions suggests that incompletely assembled or poorly mapped repeated sequences are one driver of these error-prone positions. Removal of these false positives left 1,275,872 homozygous and 477,531 heterozygous EMS-induced SNPs, which, congruent with the mutagenic mechanism of EMS, were >98% G:C to A:T transitions. Through this analysis, we generated a collection of sequence indexed mutants of sorghum. This collection contains 4035 high-impact homozygous mutations in 3637 genes and 56,514 homozygous missense mutations in 23,227 genes. Each line contains, on average, 2177 annotated homozygous SNPs per genome, including seven likely gene knockouts and 96 missense mutations. The number of mutations in a transcript was linearly correlated with the transcript length and also the G+C count, but not with the GC/AT ratio. Analysis of the detected mutagenized positions identified CG-rich patches, and flanking sequences strongly influenced EMS-induced mutation rates. This method for detecting false positive-induced mutations is generally applicable to any organism, is independent of the choice of in silico variant-calling algorithm, and is most valuable when the true mutation rate is likely to be low, such as in laboratory-induced mutations or somatic mutation detection in medicine.

Generation of EMS-Mutagenized Populations of Arabidopsis thaliana for Polyamine Genetics

In the recent years, genetic engineering of polyamine biosynthetic genes has provided evidence for their involvement in plant stress responses and different aspects of plant development. Such approaches are being complemented with the use of reverse genetics, in which mutants affected on a particular trait, tightly associated with polyamines, are isolated and the causal genes mapped. Reverse genetics enables the identification of novel genes in the polyamine pathway, which may be involved in downstream signaling, transport, homeostasis, or perception. Here, we describe a basic protocol for the generation of ethyl methanesulfonate (EMS) mutagenized populations of Arabidopsis thaliana for its use in reverse genetics applied to polyamines.

The Application of a Meiocyte-Specific CRISPR/Cas9 (MSC) System and a Suicide-MSC System in Generating Inheritable and Stable Mutations in Arabidopsis

The CRISPR/Cas9 system has been widely used for generating targeted mutations in various species. In Arabidopsis, it largely relies on the edited cells where the Cas9 protein performs its activity to obtain heritable and stable mutated lines. Here, we designed an improved CRISPR/Cas9 system, named as the MSC (meiocyte-specific CRISPR/Cas9) system, in which the Cas9 expression is driven by an experimentally approved meiocyte-specific promoter (AtDMC1 promoter). Two endogenous genes, including vegetative gene AtDET2 and reproductive gene AtDMC1, were targeted. We obtained heterozygous T1 plants for targeted genes with high efficiency (64%). In the T2 generation, the homozygous plants were abundant with high efficiency (37%). Analysis of Sanger sequencing results of T2 generation revealed that heritable gene mutations were high (52%). Moreover, we showed that the MSC system could sufficiently delete a middle size DNA fragment (∼500 bp) between two cleavage sites with a high rate (64.15%) in the T1 plants, providing direct evidence for making complete knock-out or certain domain-depletion mutations. In addition, we further made a suicide-MSC system, which can edit the targeted endogenous gene and the exogenous Cas9 gene simultaneously, not only successfully avoiding the further destroy of alleles brought in by molecular complementary or genic allelic test, but also maintaining the stable mutated alleles for functional studies. In short, the two systems provide new approaches to generate mutations for gene functional studies.

Morphological phenotyping and genetic analyses of a new chemical-mutagenized population of tobacco (Nicotiana tabacum L.)

MAIN CONCLUSION

A novel tobacco mutant library was constructed, screened, and characterized as a crucial genetic resource for functional genomics and applied research. A comprehensive mutant library is a fundamental resource for investigating gene functions, especially after the completion of genome sequencing. A new tobacco mutant population induced by ethyl methane sulfonate mutagenesis was developed for functional genomics applications. We isolated 1607 mutant lines and 8610 mutant plants with altered morphological phenotypes from 5513 independent M2 families that consisted of 69,531 M2 plants. The 2196 mutations of abnormal phenotypes in the M2 putative mutants were classified into four groups with 17 major categories and 51 subcategories. More than 60% of the abnormal phenotypes observed fell within the five major categories including plant height, leaf shape, leaf surface, leaf color, and flowering time. The 465 M2 mutants exhibited multiple phenotypes, and 1054 of the 2196 mutations were pleiotropic. Verification of the phenotypes in advanced generations indicated that 70.63% of the M3 lines, 84.87% of the M4 lines, and 95.75% of the M5 lines could transmit original mutant phenotypes of the corresponding M2, M3, and M4 mutant plants. Along with the increased generation of mutants, the ratios of lines inheriting OMPs increased and lines with emerging novel mutant phenotypes decreased. Genetic analyses of 18 stably heritable mutants showed that two mutants were double recessive, five were monogenic recessive, eight presented monogenic dominant inheritance, and three presented semi-dominant inheritance. The pleiotropy pattern, saturability evaluation, research prospects of genome, and phenome of the mutant populations were also discussed. Simultaneously, this novel mutant library provided a fundamental resource for investigating gene functions in tobacco.

Chemical genetics and strigolactone perception

Strigolactones (SLs) are a collection of related small molecules that act as hormones in plant growth and development. Intriguingly, SLs also act as ecological communicators between plants and mycorrhizal fungi and between host plants and a collection of parasitic plant species. In the case of mycorrhizal fungi, SLs exude into the soil from host roots to attract fungal hyphae for a beneficial interaction. In the case of parasitic plants, however, root-exuded SLs cause dormant parasitic plant seeds to germinate, thereby allowing the resulting seedling to infect the host and withdraw nutrients. Because a laboratory-friendly model does not exist for parasitic plants, researchers are currently using information gleaned from model plants like Arabidopsis in combination with the chemical probes developed through chemical genetics to understand SL perception of parasitic plants. This work first shows that understanding SL signaling is useful in developing chemical probes that perturb SL perception. Second, it indicates that the chemical space available to probe SL signaling in both model and parasitic plants is sizeable. Because these parasitic pests represent a major concern for food insecurity in the developing world, there is great need for chemical approaches to uncover novel lead compounds that perturb parasitic plant infections.

Chemical Genetic Dissection of Membrane Trafficking

The plant endomembrane system is an extensively connected functional unit for exchanging material between compartments. Secretory and endocytic pathways allow dynamic trafficking of proteins, lipids, and other molecules, regulating a myriad of biological processes. Chemical genetics-the use of compounds to perturb biological processes in a fast, tunable, and transient manner-provides elegant tools for investigating this system. Here, we review how chemical genetics has helped to elucidate different aspects of membrane trafficking. We discuss different strategies for uncovering the modes of action of such compounds and their use in unraveling membrane trafficking regulators. We also discuss how the bioactive chemicals that are currently used as probes to interrogate endomembrane trafficking were discovered and analyze the results regarding membrane trafficking and pathway crosstalk. The integration of different expertises and the rational implementation of chemical genetic strategies will improve the identification of molecular mechanisms that drive intracellular trafficking and our understanding of how trafficking interfaces with plant physiology and development.

Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics

In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies. Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level. Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product. We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants.

Mutagenesis and TILLING to Dissect Gene Function in Plants

Mutagenesis can be random or targeted and occur by nature or artificially by humans. However, the bulk of mutagenesis employed in plants are random and caused by physical agents such as x-ray and gamma-ray or chemicals such as ethyl-methane sulfonate (EMS). Researchers are interested in first identifying these mutations and/or polymorphisms in the genome followed by investigating their effects in the plant function as well as their application in crop improvement. The high-throughput technique called TILLING (Targeting Induced Local Lesion IN Genomes) has been already established and become popular for identifying candidate mutant individuals harboring mutations in the gene of interest. TILLING is a non-transgenic and reverse genetics method of identifying a single nucleotide changes. The procedure of TILLING comprises traditional mutagenesis using optimum type and concentration of mutagen, development of a non-chimeric population, DNA extraction and pooling, mutation detection as well as validation of results. In general, TILLING has proved to be robust in identifying useful mutant lines in diverse economically important crops of the world. The main goal of the current mini-review is to show the significance role played by mutagenesis and TILLING in the discovery of DNA lesions which are to be used in the improvement of crops for the trait of interest.

Genome wide association study (GWAS) for grain yield in rice cultivated under water deficit

The identification of rice drought tolerant materials is crucial for the development of best performing cultivars for the upland cultivation system. This study aimed to identify markers and candidate genes associated with drought tolerance by Genome Wide Association Study analysis, in order to develop tools for use in rice breeding programs. This analysis was made with 175 upland rice accessions (Oryza sativa), evaluated in experiments with and without water restriction, and 150,325 SNPs. Thirteen SNP markers associated with yield under drought conditions were identified. Through stepwise regression analysis, eight SNP markers were selected and validated in silico, and when tested by PCR, two out of the eight SNP markers were able to identify a group of rice genotypes with higher productivity under drought. These results are encouraging for deriving markers for the routine analysis of marker assisted selection. From the drought experiment, including the genes inherited in linkage blocks, 50 genes were identified, from which 30 were annotated, and 10 were previously related to drought and/or abiotic stress tolerance, such as the transcription factors WRKY and Apetala2, and protein kinases.

Glycan-binding F-box protein from Arabidopsis thaliana protects plants from Pseudomonas syringae infection

BACKGROUND

A small group of F-box proteins consisting of a conserved F-box domain linked to a domain homologous to the glycan-binding protein has been identified within the genome of Arabidopsis thaliana. Previously, the so-called F-box-Nictaba protein, encoded by the gene At2g02360, was shown to be a functional lectin which binds N-acetyllactosamine structures. Here, we present a detailed qRT-PCR expression analysis of F-box-Nictaba in Arabidopsis plants upon different stresses and hormone treatments.

RESULTS

Expression of the F-box-Nictaba gene was enhanced after plant treatment with salicylic acid and after plant infection with the virulent Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000). β-glucuronidase histochemical staining of transgenic Arabidopsis plants displayed preferential activity of the At2g02360 promoter in trichomes present on young rosette leaves. qRT-PCR analyses confirmed high expression of F-box-Nictaba in leaf trichomes. A. thaliana plants overexpressing the gene showed less disease symptoms after Pst DC3000 infection with reduced bacterial colonization compared to infected wild type and F-box-Nictaba knock-out plants.

CONCLUSIONS

Our data show that the Arabidopsis F-box-Nictaba gene is a stress-inducible gene responsive to SA, bacterial infection and heat stress, and is involved in salicylic acid related plant defense responses. This knowledge enriched our understanding of the physiological importance of F-box-Nictaba, and can be used to create plants with better performance in changing environmental conditions.

Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques

Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.

A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis

The recently developed CRISPR/Cas9 system is a promising technology for targeted genome editing in a variety of species including plants. However, the first generation systems were designed to target one or two gene loci at a time. We designed a new multiplex CRISPR/Cas9 system that allows the co-expression of six sgRNA modules in one binary vector using a simple (three steps) cloning strategy in Arabidopsis. The transcription of the sgRNA modules is under the control of three different RNA Polymerase III-dependent promoters. We tested the efficiency of the new multiplex system by targeting six of the fourteen PYL families of ABA receptor genes in a single transformation experiment. One line with mutations in all six targeted PYLs was identified from 15 T1 plants. The mutagenesis frequency for the six individual PYL targets in the T1 lines ranged from 13 to 93 %. In the presence of ABA, the transgenic line identified as containing mutations in all six PYL genes produced the highest germination rate in the T2 progeny (37 %). Among these germinated seedlings, half of the analyzed plants (15/30) were homozygous mutants for at least four targeted genes and two plants (6.7 %) contained homozygous mutations in five of the targeted PYLs and the other targeted PYL had biallelic mutations. Homozygous sextuple mutants were identified in the T3 progeny and characterized together with previously described triple and sextuple PYL mutants. We anticipate that the application of this multiplex CRISPR/Cas9 system will strongly facilitate functional analysis of genes pathways and families.

50 years of Arabidopsis research: highlights and future directions

922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.

Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis

The Streptococcus-derived CRISPR/Cas9 system is being widely used to perform targeted gene modifications in plants. This customized endonuclease system has two components, the single-guide RNA (sgRNA) for target DNA recognition and the CRISPR-associated protein 9 (Cas9) for DNA cleavage. Ubiquitously expressed CRISPR/Cas9 systems (UC) generate targeted gene modifications with high efficiency but only those produced in reproductive cells are transmitted to the next generation. We report the design and characterization of a germ-line-specific Cas9 system (GSC) for Arabidopsis gene modification in male gametocytes, constructed using a SPOROCYTELESS (SPL) genomic expression cassette. Four loci in two endogenous genes were targeted by both systems for comparative analysis. Mutations generated by the GSC system were rare in T1 plants but were abundant (30%) in the T2 generation. The vast majority (70%) of the T2 mutant population generated using the UC system were chimeras while the newly developed GSC system produced only 29% chimeras, with 70% of the T2 mutants being heterozygous. Analysis of two loci in the T2 population showed that the abundance of heritable gene mutations was 37% higher in the GSC system compared to the UC system and the level of polymorphism of the mutations was also dramatically increased with the GSC system. Two additional systems based on germ-line-specific promoters (pDD45-GT and pLAT52-GT) were also tested, and one of them was capable of generating heritable homozygous T1 mutant plants. Our results suggest that future application of the described GSC system will facilitate the screening for targeted gene modifications, especially lethal mutations in the T2 population.

Suppressor Screens in Arabidopsis

Genetic screens have proven to be a useful tool in the dissection of biological processes in plants. Specifically, suppressor screens have been widely used to study signal transduction pathways. Here we provide a detailed protocol for ethyl methanesulfonate (EMS) mutagenesis used in our suppressor screens in Arabidopsis and discuss the basic principles behind suppressor screen design and downstream analyses.

Strategies for altering plant traits using virus-induced gene silencing technologies

The rapid progress in genome sequencing and transcriptome analysis in model and crop plants has made possible the identification of a vast number of genes potentially associated with economically important complex traits. The ultimate goal is to assign functions to these genes by using forward and reverse genetic screens. Plant viruses have been developed for virus-induced gene silencing (VIGS) to generate rapid gene knockdown phenotypes in numerous plant species. To fulfill its potential for high-throughput phenomics, it is of prime importance to ensure that parameters conditioning the VIGS response, i.e., plant-virus interactions and associated loss-of-function screens, are "fit for purpose" and optimized to unequivocally conclude the role of a gene of interest in relation to a given trait. This chapter will review and discuss the different strategies used for the development of VIGS-based phenomics in model and crop species.