Improved Efficiency of Zea mays Agroinoculation with Maize streak virus

Identification of the wild and cultivated hosts of wheat dwarf virus and oat dwarf virus in Iran

In the last decade two mastreviruses, Wheat dwarf virus (WDV) and Oat dwarf virus (ODV) have been reported from cereal farms in Iran. In a survey, wild and cultivated hosts of these mastreviruses were studied during 2015 to 2017. Symptomatic small grain cereal samples and weed species were collected and assayed for WDV and/or ODV infection by PCR. While WDV which was detected in 139/284 (49%) of total symptomatic samples, low incidence (2%) was recorded for ODV which was detected only in slender wild oat (Avena barbata Pott ex Link) and red brome (Bromus rubens L.). In agroinfection studies, the clone of ODV infected common oat (A. sativa) and slender wild oat (A. barbata) with the low efficiency and did not infect wheat or barley. ODV was transmitted by the leafhopper Psammotettix alienus, from agroinfected common oat to healthy seedlings. The results show that, in contrast to WDV, ODV has a low incidence and a narrow host range in gramineous plants.

Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events

Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own "lethally recombinant." Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains. Importance: Recombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.

Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing

The exploding availability of genome and EST-based sequences from grasses requires a technology that allows rapid functional analysis of the multitude of genes that these resources provide. There are several techniques available to determine a gene's function. For gene knockdown studies, silencing through RNAi is a powerful tool. Gene silencing can be accomplished through stable transformation or transient expression of a fragment of a target gene sequence. Stable transformation in rice, maize, and a few other species, although routine, remains a relatively low-throughput process. Transformation in other grass species is difficult and labor-intensive. Therefore, transient gene silencing methods including Agrobacterium-mediated and virus-induced gene silencing (VIGS) have great potential for researchers studying gene function in grasses. VIGS in grasses already has been used to determine the function of genes during pathogen challenge and plant development. It also can be used in moderate-throughput reverse genetics screens to determine gene function. However, the number of viruses modified to serve as silencing vectors in grasses is limited, and the silencing phenotype induced by these vectors is not optimal: the phenotype being transient and with moderate penetration throughout the tissue. Here, we review the most recent information available for VIGS in grasses and summarize the strengths and weaknesses in current virus-grass host systems. We describe ways to improve current virus vectors and the potential of other grass-infecting viruses for VIGS studies. This work is necessary because VIGS for the foreseeable future remains a higher throughput and more rapid system to evaluate gene function than stable transformation.

Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution

BACKGROUND

Maize streak virus -strain A (MSV-A; Genus Mastrevirus, Family Geminiviridae), the maize-adapted strain of MSV that causes maize streak disease throughout sub-Saharan Africa, probably arose between 100 and 200 years ago via homologous recombination between two MSV strains adapted to wild grasses. MSV recombination experiments and analyses of natural MSV recombination patterns have revealed that this recombination event entailed the exchange of the movement protein - coat protein gene cassette, bounded by the two genomic regions most prone to recombination in mastrevirus genomes; the first surrounding the virion-strand origin of replication, and the second around the interface between the coat protein gene and the short intergenic region. Therefore, aside from the likely adaptive advantages presented by a modular exchange of this cassette, these specific breakpoints may have been largely predetermined by the underlying mechanisms of mastrevirus recombination. To investigate this hypothesis, we constructed artificial, low-fitness, reciprocal chimaeric MSV genomes using alternating genomic segments from two MSV strains; a grass-adapted MSV-B, and a maize-adapted MSV-A. Between them, each pair of reciprocal chimaeric genomes represented all of the genetic material required to reconstruct - via recombination - the highly maize-adapted MSV-A genotype, MSV-MatA. We then co-infected a selection of differentially MSV-resistant maize genotypes with pairs of reciprocal chimaeras to determine the efficiency with which recombination would give rise to high-fitness progeny genomes resembling MSV-MatA.

RESULTS

Recombinants resembling MSV-MatA invariably arose in all of our experiments. However, the accuracy and efficiency with which the MSV-MatA genotype was recovered across all replicates of each experiment depended on the MSV susceptibility of the maize genotypes used and the precise positions - in relation to known recombination hotspots - of the breakpoints required to re-create MSV-MatA. Although the MSV-sensitive maize genotype gave rise to the greatest variety of recombinants, the measured fitness of each of these recombinants correlated with their similarity to MSV-MatA.

CONCLUSIONS

The mechanistic predispositions of different MSV genomic regions to recombination can strongly influence the accessibility of high-fitness MSV recombinants. The frequency with which the fittest recombinant MSV genomes arise also correlates directly with the escalating selection pressures imposed by increasingly MSV-resistant maize hosts.

Rapid host adaptation by extensive recombination

Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.

Agroinoculation: a simple procedure for systemic infection of plants with viruses

Plant-virus interaction studies, for long, plagued by asynchronous/failed infections, have improved since the usage of Agrobacterium as a delivery agent for viral genomes. Popularly known as "agroinoculation," this method has revolutionized plant virology studies, leading to identification of viruses as casual agents of disease, viral genome mutagenesis and recombination analyses, and virus-induced gene silencing (VIGS) applications. We present here a brief overview of the recent applications of this method and a detailed protocol for agroinoculation and VIGS used in our laboratory.

Resistance of Four Inbred Maize Lines to Inoculation with 20 Isolates of Maize streak virus from Zimbabwe

Maize streak is the most widespread and important disease of maize in sub-Saharan Africa. Maize streak virus (MSV)-resistant maize germ plasm is available in several countries, but little is known about the stability of its resistance to MSV strains that may differ from one region to another. We used four maize inbred lines (CML312, CML206, CML216, and MSR) known to differ widely for their resistance to MSV in Harare, and evaluated their resistance to 20 MSV isolates collected from the wild during 2 years at locations across Zimbabwe. Maize streak development and symptom severity were evaluated in replicated greenhouse experiments using artificial inoculation via viruliferous leafhoppers. All 20 MSV isolates induced maize streak symptoms on moderately and highly susceptible genotypes by about 1 week after inoculation (WAI). Differences among isolates for severity of early maize streak symptoms were ephemeral, and resistance was accurately differentiated by all isolates by 3 to 4 WAI. Differences in final maize streak symptom scores induced by the isolates were statistically significant, but differed only by a maximum of 7% in 1999 and 19% in 2000. Although genotype, isolate, and genotype by isolate effects for maize streak symptom scores were significant (P < 0.01), relative MSV resistance of the genotypes was consistently ranked by all 20 MSV isolates.

Transmission of Maize streak virus by vascular puncture inoculation with unit-length genomic DNA

The infectivity of cloned unit-length genomes of Maize streak virus (MSV) was tested using vascular puncture inoculation (VPI). VPI of kernels with plasmid DNA (pUC19) carrying a tandem repeat of the MSV genome produced 33+/-8% infection. Similar plasmids carrying the unit-length MSV genome were not infectious. If the MSV genome was released from the plasmid prior to VPI, 16+/-4% of plants became infected. Ligation of the free linear MSV genome did not increase infectivity. The three infective inocula produced symptoms of similar severity in maize. Bioassay of systemically infected leaves indicated the virus was equally infectious regardless of inoculum. In Southern blots of bioassay plants, no differences in MSV genome restriction endonuclease sites were observed. Thus, inoculation with the free linear or circularized MSV unit-length genome produced infections similar to those with plasmids carrying tandemly repeated genomes. The infectivity of free linear MSV unit-length genomes will facilitate molecular analysis of MSV, because cloning steps are minimized.

Mungbean yellow mosaic virus-Vi Agroinfection by Codelivery of DNA A and DNA B From One Agrobacterium Strain

Agroinfection of bipartite geminiviruses is routinely done by mixing two Agrobacterium strains that independently harbor partial tandem repeats of DNA A and DNA B. We report here an improved agroinfection method for bipartite geminiviruses that utilizes one strain of Agrobacterium that harbors DNA A and DNA B partial tandem repeats on two compatible replicons. A cointegrate vector, pGV2260∷pGV1.3A, with the partial tandem repeat of Mungbean yellow mosaic virus-Vi (MYMV-Vi) DNA A and a binary vector, pGA1.9B, with the partial tandem repeat of MYMV-Vi DNA B gave an agroinfection efficiency of 24% when harbored in two Agrobacterium strains and an efficiency of 61% when harbored in one Agrobacterium strain. A combination of binary vectors, pGA1.9A with MYMV-Vi DNA A partial tandem repeat and pGA1.9B with DNA B partial tandem repeat, gave an agroinfection efficiency of 74% when harbored in two strains. But pGA1.9A and pPZP1.9B (a partial tandem repeat of DNA B), when present in the same Agrobacterium strain, gave 100% agroinfection. Accumulation of viral DNA was shown by Southern blotting. The single-strain method using two compatible replicons consistently gave 100% agroinfection efficiency.

Biological and Genomic Sequence Characterization of Maize streak virus Isolates from Wheat

ABSTRACT Maize streak virus (MSV) is best known as the causal agent of maize streak disease. However, only a genetically uniform subset of the viruses within this diverse species is actually capable of producing severe symptoms in maize. Whereas these "maize-type" viruses all share greater than 95% sequence identity, MSV strains isolated from grasses may share as little as 79% sequence identity with the maize-type viruses. Here, we present the complete genome sequences and biological characterization of two MSV isolates from wheat that share approximately 89% sequence identity with the maize-type viruses. Clonal populations of these two isolates, named MSV-Tas and MSV-VW, were leafhopper-transmitted to Digitaria sanguinalis and a range of maize, wheat, and barley genotypes. Whereas the two viruses showed some differences in their pathogenicity in maize, they were both equally pathogenic in D. sanguinalis and the various wheat and barley genotypes tested. Phylogenetic analyses involving the genome sequences of MSV-Tas and MSV-VW, a new maize-type virus also fully sequenced in this study (MSV-VM), and all other available African streak virus sequences, indicated that MSV-Tas and MSV-VW are close relatives that together represent a distinct MSV strain. Sequence analyses revealed that MSV-VM has a recombinant genome containing MSV-Tas/VW-like sequences within its movement protein gene.