Improvement of resistance to maize dwarf mosaic virus mediated by transgenic RNA interference

Maize actin depolymerizing factor 1 (ZmADF1) negatively regulates pollen development

The normal development of pollen grains and the completion of double fertilization in embryos are crucial for both the sexual reproduction of angiosperms and grain production. Actin depolymerizing factor (ADF) regulates growth, development, and responses to biotic and abiotic stress by binding to actin in plants. In this study, the function of the ZmADF1 gene was validated through bioinformatic analysis, subcellular localization, overexpression in maize and Arabidopsis, and knockout via CRISPR/Cas9. The amino acid sequence of ZmADF1 exhibited high conservation and a similar tertiary structure to that of ADF homologs. Subcellular localization analysis revealed that ZmADF1 is localized mainly to the nucleus and cytoplasm. The ZmADF1 gene was specifically expressed in maize pollen, and overexpression of the ZmADF1 gene decreased the number of pollen grains in the anthers of transgenic Arabidopsis plants. The germination rate of pollen and the empty seed shell rate in the fruit pods of the overexpressing plants were significantly greater than those in the wild-type (WT) plants. In maize, the pollen viability of the knockout lines was significantly greater than that of both the WT and the overexpressing lines. Our results confirmed that the ZmADF1 gene was specifically expressed in pollen and negatively regulated pollen quantity, vigor, germination rate, and seed setting rate. This study provides insights into ADF gene function and possible pathways for improving high-yield maize breeding.

Biopesticides: a Green Approach Towards Agricultural Pests

Biopesticides are biological products or organisms which are potential candidates for eco-friendly pest management and crop protection over the chemical pesticides. The so-called biopesticides include viruses, bacteria, fungi, predators, parasites, and pheromones exhibiting a variety of modes of actions. They are less toxic, rapidly degradable, and more targeted to specific pests. However, it is noted that the formulation of biopesticides plays a crucial link between production and application, and the former dictates economy, longer shelf life, ease of application, and enhanced field efficacy. Moreover, there is an urgent need for organic farmers to gain more proficiency in using biopesticides. Even though biopesticides have more advantages, the main challenge is the marketing of biopesticides. Advances in biopesticide research and development significantly reduce the environmental damage caused by the residues of synthetic insecticides and support sustainable agriculture. Numerous products have been developed since the introduction of biopesticides, some of which have taken the lead in the agro-market after being registered and released. The types of biopesticides; their mode of action; formulation strategies; recent advancements of biopesticides focusing mainly on improvement of its action spectra, to thereby replace chemical pesticides; and finally, the future aspects of biopesticides have been discussed in this review.

RNA interference and crop protection against biotic stresses

RNA interference (RNAi) is a universal phenomenon of RNA silencing or gene silencing with broader implications in important physiological and developmental processes of most eukaryotes, including plants. Small RNA (sRNA) are the critical drivers of the RNAi machinery that ensures down-regulation of the target genes in a homology-dependent manner and includes small-interfering RNAs (siRNAs) and micro RNAs (miRNAs). Plant researchers across the globe have exploited the powerful technique of RNAi to execute targeted suppression of desired genes in important crop plants, with an intent to improve crop protection against pathogens and pests for sustainable crop production. Biotic stresses cause severe losses to the agricultural productivity leading to food insecurity for future generations. RNAi has majorly contributed towards the development of designer crops that are resilient towards the various biotic stresses such as viruses, bacteria, fungi, insect pests, and nematodes. This review summarizes the recent progress made in the RNAi-mediated strategies against these biotic stresses, along with new insights on the future directions in research involving RNAi for crop protection.

Genetic dissection of maize disease resistance and its applications in molecular breeding

Disease resistance is essential for reliable maize production. In a long-term tug-of-war between maize and its pathogenic microbes, naturally occurring resistance genes gradually accumulate and play a key role in protecting maize from various destructive diseases. Recently, significant progress has been made in deciphering the genetic basis of disease resistance in maize. Enhancing disease resistance can now be explored at the molecular level, from marker-assisted selection to genomic selection, transgenesis technique, and genome editing. In view of the continuing accumulation of cloned resistance genes and in-depth understanding of their resistance mechanisms, coupled with rapid progress of biotechnology, it is expected that the large-scale commercial application of molecular breeding of resistant maize varieties will soon become a reality.

Catch Me If You Can! RNA Silencing-Based Improvement of Antiviral Plant Immunity

Viruses are obligate parasites which cause a range of severe plant diseases that affect farm productivity around the world, resulting in immense annual losses of yield. Therefore, control of viral pathogens continues to be an agronomic and scientific challenge requiring innovative and ground-breaking strategies to meet the demands of a growing world population. Over the last decade, RNA silencing has been employed to develop plants with an improved resistance to biotic stresses based on their function to provide protection from invasion by foreign nucleic acids, such as viruses. This natural phenomenon can be exploited to control agronomically relevant plant diseases. Recent evidence argues that this biotechnological method, called host-induced gene silencing, is effective against sucking insects, nematodes, and pathogenic fungi, as well as bacteria and viruses on their plant hosts. Here, we review recent studies which reveal the enormous potential that RNA-silencing strategies hold for providing an environmentally friendly mechanism to protect crop plants from viral diseases.

Maize Dwarf Mosaic Virus: From Genome to Disease Management

Maize dwarf mosaic virus (MDMV) is a serious maize pathogen, epidemic worldwide, and one of the most common virus diseases for monocotyledonous plants, causing up to 70% loss in corn yield globally since 1960. MDMV belongs to the genus Potyvirus (Potyviridae) and was first identified in 1964 in Illinois in corn and Johnsongrass. MDMV is a single stranded positive sense RNA virus and is transmitted in a non-persistent manner by several aphid species. MDMV is amongst the most important virus diseases in maize worldwide. This review will discuss its genome, transmission, symptomatology, diagnosis and management. Particular emphasis will be given to the current state of knowledge on the diagnosis and control of MDMV, due to its importance in reducing the impact of maize dwarf mosaic disease, to produce an enhanced quality and quantity of maize.

Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding

Sugarcane is an essential crop for sugar and biofuel. Globally, its production is severely affected by sugarcane yellow leaf disease (SCYLD) caused by Sugarcane Yellow Leaf Virus (SCYLV). Many aphid vectors are involved in the spread of the disease which reduced the effectiveness of cultural and chemical management. Empirical methods of plant breeding such as introgression from wild and cultivated germplasm were not possible or at least challenging due to the absence of resistance in cultivated and wild germplasm of sugarcane. RNA interference (RNAi) transformation is an effective method to create virus-resistant varieties. Nevertheless, limited progress has been made due to lack of comprehensive research program on SCYLV based on RNAi technique. In order to show improvement and to propose future strategies for the feasibility of the RNAi technique to cope SCYLV, genome-wide consensus sequences of SCYLV were analyzed through GenBank. The coverage rates of every consensus sequence in SCYLV isolates were calculated to evaluate their practicability. Our analysis showed that single consensus sequence from SCYLV could not work well for RNAi based sugarcane breeding programs. This may be due to high mutation rate and continuous recombination within and between various viral strains. Alternative multi-target RNAi strategy is suggested to combat several strains of the viruses and to reduce the silencing escape. The multi-target small interfering RNA (siRNA) can be used together to construct RNAi plant expression plasmid, and to transform sugarcane tissues to develop new sugarcane varieties resistant to SCYLV.

A Brief History of Promoter Development for Use in Transgenic Maize Applications

Promoters regulate gene expression, and are essential biotechnology tools. Since its introduction in the mid-1990s, biotechnology has greatly enhanced maize productivity primarily through the development of insect control and herbicide tolerance traits. Additional biotechnology applications include improving seed nutrient composition, industrial protein production, therapeutic production, disease resistance, abiotic stress resistance, and yield enhancement. Biotechnology has also greatly expanded basic research into important mechanisms that govern plant growth and reproduction. Many novel promoters have been developed to facilitate this work, but only a few are widely used. Transgene optimization includes a variety of strategies some of which effect promoter structure. Recent reviews examine the state of the art with respect to transgene design for biotechnology applications. This chapter examines the use of transgene technology in maize, focusing on the way promoters are selected and used. The impact of new developments in genomic technology on promoter structure is also discussed.

Small RNA Based Genetic Engineering for Plant Viral Resistance: Application in Crop Protection

Small RNAs regulate a large set of gene expression in all plants and constitute a natural immunity against viruses. Small RNA based genetic engineering (SRGE) technology had been explored for crop protection against viruses for nearly 30 years. Viral resistance has been developed in diverse crops with SRGE technology and a few viral resistant crops have been approved for commercial release. In this review we summarized the efforts generating viral resistance with SRGE in different crops, analyzed the evolution of the technology, its efficacy in different crops for different viruses and its application status in different crops. The challenge and potential solution for application of SRGE in crop protection are also discussed.

RNAi mediated broad-spectrum transgenic resistance in Nicotiana benthamiana to chilli-infecting begomoviruses

KEY MESSAGE

Two RNAi constructs were designed targeting chilli-infecting begomoviruses and associated betasatellites. Broad-spectrum resistance was achieved against multiple begomoviruses associated with leaf curl disease of chillies in India. Chilli leaf curl disease (ChiLCD) caused by begomoviruses (family: Geminiviridae) has emerged as one of the most devastating viral diseases of chilli, especially in the Indian sub-continent. The severity of disease incidence is expanding at an alarming rate due to the emergence of new begomoviruses with greater ability to infect this crop in almost all the major chilli producing regions of India. In this study, we applied the RNA interference (RNAi) based strategies to control infection of chilli-infecting begomoviruses (CIBs). For this, we have generated transgenic Nicotiana benthamiana plants harboring two different intron hairpin RNAi constructs [designated as TR1 (AC1/AC2) and TR2 (AC1/AC2/βC1)] using conserved regions of viral genome and associated betasatellite. During our study, we observed that, two lines harboring TR1 construct (13-1 and 2-4) and one line harboring TR2 construct (5-1) have shown resistance to the most predominant Indian CIBs like Chilli leaf curl virus-Pakistan isolate Varanasi, Tomato leaf curl New Delhi virus-isolate chilli, and a newly identified begomovirus species, Chilli leaf curl Vellanad virus. Resistant lines accumulated transgene-specific siRNAs, confirming RNAi-mediated resistance against these viruses. Furthermore, these resistant lines also displayed delayed symptom appearance and milder symptoms, as compared to virus-inoculated non-transgenic plants. Average viral DNA accumulation in the resistant lines was reduced up to 90% as compared to non-transgenic plants. Thus, our study demonstrated the application of RNAi-mediated approach in providing resistance against diverse monopartite and bipartite begomoviruses associated with ChiLCD.

Transgenic resistance

Transgenic resistance to plant viruses is an important technology for control of plant virus infection, which has been demonstrated for many model systems, as well as for the most important plant viruses, in terms of the costs of crop losses to disease, and also for many other plant viruses infecting various fruits and vegetables. Different approaches have been used over the last 28 years to confer resistance, to ascertain whether particular genes or RNAs are more efficient at generating resistance, and to take advantage of advances in the biology of RNA interference to generate more efficient and environmentally safer, novel "resistance genes." The approaches used have been based on expression of various viral proteins (mostly capsid protein but also replicase proteins, movement proteins, and to a much lesser extent, other viral proteins), RNAs [sense RNAs (translatable or not), antisense RNAs, satellite RNAs, defective-interfering RNAs, hairpin RNAs, and artificial microRNAs], nonviral genes (nucleases, antiviral inhibitors, and plantibodies), and host-derived resistance genes (dominant resistance genes and recessive resistance genes), and various factors involved in host defense responses. This review examines the above range of approaches used, the viruses that were tested, and the host species that have been examined for resistance, in many cases describing differences in results that were obtained for various systems developed in the last 20 years. We hope this compilation of experiences will aid those who are seeking to use this technology to provide resistance in yet other crops, where nature has not provided such.

Transgenic sugarcane resistant to Sorghum mosaic virus based on coat protein gene silencing by RNA interference

As one of the critical diseases of sugarcane, sugarcane mosaic disease can lead to serious decline in stalk yield and sucrose content. It is mainly caused by Potyvirus sugarcane mosaic virus (SCMV) and/or Sorghum mosaic virus (SrMV), with additional differences in viral strains. RNA interference (RNAi) is a novel strategy for producing viral resistant plants. In this study, based on multiple sequence alignment conducted on genomic sequences of different strains and isolates of SrMV, the conserved region of coat protein (CP) genes was selected as the target gene and the interference sequence with size of 423 bp in length was obtained through PCR amplification. The RNAi vector pGII00-HACP with an expression cassette containing both hairpin interference sequence and cp4-epsps herbicide-tolerant gene was transferred to sugarcane cultivar ROC22 via Agrobacterium-mediated transformation. After herbicide screening, PCR molecular identification, and artificial inoculation challenge, anti-SrMV positive transgenic lines were successfully obtained. SrMV resistance rate of the transgenic lines with the interference sequence was 87.5% based on SrMV challenge by artificial inoculation. The genetically modified SrMV-resistant lines of cultivar ROC22 provide resistant germplasm for breeding lines and can also serve as resistant lines having the same genetic background for study of resistance mechanisms.

Engineered plant virus resistance

Virus diseases are among the key limiting factors that cause significant yield loss and continuously threaten crop production. Resistant cultivars coupled with pesticide application are commonly used to circumvent these threats. One of the limitations of the reliance on resistant cultivars is the inevitable breakdown of resistance due to the multitude of variable virus populations. Similarly, chemical applications to control virus transmitting insect vectors are costly to the farmers, cause adverse health and environmental consequences, and often result in the emergence of resistant vector strains. Thus, exploiting strategies that provide durable and broad-spectrum resistance over diverse environments are of paramount importance. The development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Genetic engineering offers various options for introducing transgenic virus resistance into crop plants to provide a wide range of resistance to viral pathogens. This review examines the current strategies of developing virus resistant transgenic plants.

Agrobacterium tumefaciens-mediated transformation of corn (Zea mays L.) multiple shoots

An Agrobacterium tumefaciens-mediated corn transformation method based on multiple shoot tissue cultures was developed, which is effective with a variety of corn inbred lines and standard binary vectors. Six factors that affected the success of corn transformation were tested, including A. tumefaciens strain, corn genotype, tissue culture growth stage, medium composition, co-culture temperature and surfactant treatment. Agropine-type bacteria (EHA 101 and AGL 1) were eightfold more effective than octopine-type strain for corn multi-shoot tissues transformation. The average frequency of Glucuronidase (GUS)-positive explants obtained from 14 corn genotypes ranged from 36% to 76%. L-proline (0.7 g L⁻¹) in the co-culture medium apparently improved the frequency of transformation. The newly initiated multi-shoot tissues were most responsive to Agrobacterium infection. A positive correlation was found between multi-shoot tissue susceptibility to Agrobacterium and the proportion of cells in G1 phase. Transformants were identified by reverse transcription Polymerase Chain Reaction (PCR) and by southern blot hybridization assays. The frequency of transformants was approximately 2% based on the number of multi-shoot explants co-cultivated with Agrobacterium.

Delay in virus accumulation and low virus transmission from transgenic rice plants expressing Rice tungro spherical virus RNA

Rice tungro, a devastating viral disease of rice in South and Southeast Asia, is caused by the joint infection of a DNA virus, Rice tungro bacilliform virus (RTBV) and an RNA virus Rice tungro spherical virus (RTSV). RTBV and RTSV are transmitted exclusively by the insect vector Green leafhopper (GLH). RTSV is necessary for the transmission of RTBV. To obtain transgenic resistance against RTSV, indica rice plants were transformed using DNA constructs designed to express an untranslatable sense or anti-sense RTSV RNA. Progeny of primary transformants showing low copies of the integrated transgenes and accumulating the corresponding transcripts at low levels were challenged with viruliferous GLH. Three out of four transgenic plant lines expressing untranslatable RTSV RNA in the sense orientation and two out of the four lines expressing an RTSV gene in the anti-sense orientation showed delayed buildup of RTSV RNA over time. Transmission of RTBV from the above lines was reduced significantly.

Diagnosis and control of cereal viruses in the Middle East

Middle Eastern countries are major consumers of small grain cereals. Egypt is the biggest bread wheat producer with 7.4 million tons (MT) in 2007, but at the same time, it had to import 5.9 MT. Jordan and Israel import almost all the grains they consume. Viruses are the major pathogens that impair grain production in the Middle East, infecting in some years more than 80% of the crop. They are transmitted in nonpersistent, semipersistent, and persistent manners by insects (aphids, leafhoppers, and mites), and through soil and seeds. Hence, cereal viruses have to be controlled, not only in the field but also through the collaborative efforts of the plant quarantine services inland and at the borders, involving all the Middle Eastern countries. Diagnosis of cereal viruses may include symptom observation, immunological technologies such as ELISA using polyclonal and monoclonal antibodies raised against virus coat protein expressed in bacteria, and molecular techniques such as PCR, microarrays, and deep sequencing. In this chapter, we explore the different diagnoses, typing, and detection techniques of cereal viruses available to the Middle Eastern countries. We highlight the plant quarantine service and the prevention methods. Finally, we review the breeding efforts for virus resistance, based on conventional selection and genetic engineering.