Soybean cultivar resistant to Mungbean Yellow Mosaic India Virus infection induces viral RNA degradation earlier than the susceptible cultivar

Achieving maximum efficiency of Mungbean yellow mosaic India virus infection in mungbean by agroinoculation

Mungbean is one of the important food legumes in the Indian-sub-continent. Yellow mosaic disease, caused by Mungbean yellow mosaic virus and Mungbean yellow mosaic India virus (MYMIV) poses a severe threat to its production. Agroinoculation has been the most preferred way to test the function of genomic components of these viruses. However, the available inoculation methods are not as efficient as whitefly transmission, thereby limiting their usage for screening and biological studies. We hereby report an efficient and reproducible agroinoculation method for achieving maximum (100%) efficiency using tandem repeat infectious agro-constructs of DNA A and DNA B of MYMIV. The present study targeted wounding of various meristematic tissues of root, shoot, parts of germinating seeds and also non-meristematic tissue of stem to test the suitable tissue types for maximum infection. Among the various tissues selected for, the inoculation on the epicotyl region showed maximum infectivity. Further, to enhance the infectivity of MYMIV, different concentrations of acetosyringone, incubation time and Agrobacterium cell density were also standardized. The incubation of wounded sprouted seeds in 1.0 OD of agroculture containing repeat construct of MYMIV for 2-4 h without acetosyringone followed by sowing in soil showed maximum infection of MYMIV within 10-12 days on the first trifoliate leaf. This standardized method is reproducible and has potential to screen germplasm lines and will be useful in mungbean biological/virological studies and breeding programmes.

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The online version contains supplementary material available at 10.1007/s13205-021-03088-w.

Comparative RNA-Seq analysis unfolds a complex regulatory network imparting yellow mosaic disease resistance in mungbean [Vigna radiata (L.) R. Wilczek]

Yellow Mosaic Disease (YMD) in mungbean [Vigna radiata (L.) R. Wilczek] is one of the most damaging diseases in Asia. In the northern part of India, the YMD is caused by Mungbean Yellow Mosaic India Virus (MYMIV), while in southern India this is caused by Mungbean Yellow Mosaic Virus (MYMV). The molecular mechanism of YMD resistance in mungbean remains largely unknown. In this study, RNA-seq analysis was conducted between a resistant (PMR-1) and a susceptible (Pusa Vishal) mungbean genotype under infected and control conditions to understand the regulatory network operating between mungbean-YMV. Overall, 76.8 million raw reads could be generated in different treatment combinations, while mapping rate per library to the reference genome varied from 86.78% to 93.35%. The resistance to MYMIV showed a very complicated gene network, which begins with the production of general PAMPs (pathogen-associated molecular patterns), then activation of various signaling cascades like kinases, jasmonic acid (JA) and brassinosteroid (BR), and finally the expression of specific genes (like PR-proteins, virus resistance and R-gene proteins) leading to resistance response. The function of WRKY, NAC and MYB transcription factors in imparting the resistance against MYMIV could be established. The string analysis also revealed the role of proteins involved in kinase, viral movement and phytoene synthase activity in imparting YMD resistance. A set of novel stress-related EST-SSRs are also identified from the RNA-Seq data which may be used to find the linked genes/QTLs with the YMD resistance. Also, 11 defence-related transcripts could be validated through quantitative real-time PCR analysis. The identified gene networks have led to an insight about the defence mechanism operating against MYMIV infection in mungbean which will be of immense use to manage the YMD resistance in mungbean.

Differential responses of Phaseolus vulgaris cultivars following mungbean yellow mosaic India virus infection

Phaseolus vulgaris, commonly known as French bean is a vital leguminous crop worldwide and India stood 1st rank in dry bean and 4th rank in green bean production worldwide (FAOSTAT 2017). However, this production is severely affected by Mungbean yellow mosaic India virus (MYMIV) infection. Hence it is very important to identify MYMIV tolerant P. vulgaris cultivars. MYMIV infection results in the production of reactive oxygen species and plant cells have evolved complex defense mechanisms at different levels to overcome the damage. Our study for the first time focused on the changes at the morphological and biochemical level, as well as on the relative quantification of MYMIV genes in nine cultivars of P. vulgaris after MYMIV infection. Highest growth and the highest accumulation of four antioxidants of cv. 'Anupam' after MYMIV infection, established that cv. 'Anupam' was less affected by MYMIV infection amongst all nine cultivars. Relative quantification studies also correlated well with these results. Additionally, there is a consistent level of photosynthetic pigments content in mock- and MYMIV-treated seedlings of cv. 'Anupam' over early infection period. Combining all the results we conclude that cv. 'Anupam' is a MYMIV tolerant cultivar.

Quantification of a legume begomovirus to evaluate soybean genotypes for resistance to yellow mosaic disease

Mungbean yellow mosaic India virus (MYMIV) infecting soybean and other legumes causes yellow mosaic disease (YMD). Evaluation of soybean genotypes for YMD resistance involves field screening at disease hot spots or in a protected environment using infectious clones or viruliferous whiteflies as sources of virus inocula. Development of efficient virus inoculation and quantification protocols to screen soybean genetic stocks against YMD is imperative for breeding resistant varieties. Binary plasmids harbouring complete, tandem dimeric genomic components DNA A and DNA B of MYMIV-soybean isolate were engineered. The infectivity of the clones was demonstrated in soybean genotypes JS335 and UPSM534 that display contrasting YMD resistance. As a follow-up, soybean germplasm lines, breeding lines, and representative cultivars that were initially screened at an YMD hot-spot were then subjected to Agrobacterium-based infection with MYMIV. Quantitative real time polymerase chain reaction (qRT-PCR) based copy number analysis of MYMIV genomic components allowed soybean genotypes to be classified into three discrete categories; resistant, moderately resistant and susceptible to the viral infection. Thus, a soybean germplasm disease screening system based on agro-infection and qRT-PCR based quantification of MYMIV was developed to facilitate breeding YMD resistant soybean. The implications of this study for obtaining YMD resistant soybean cultivars are discussed.

Linkage mapping of Mungbean yellow mosaic India virus (MYMIV) resistance gene in soybean

Mungbean Yellow Mosaic India Virus (MYMIV) is one of the most prevalent pathogen that limits soybean production in India. In this study RILs derived from JS335, dominant but MYMIV susceptible variety and PI171443, donor of MYMIV resistance gene in most of the MYMIV resistant varieties released in India and F2 population derived from SL525, a resistant variety released for northern India and NRC101, a susceptible genotype were used to study the inheritance of MYMIV resistance and map the gene responsible for MYMIV resistance. F1s were found to be completely susceptible. F_2:3 and RILs population segregated to fit a ratio of 1:2:1 and 1:1 indicating that a single recessive gene controlled resistance to MYMIV. BSA was performed using 144 polymorphic SSR markers. MYMIV resistance gene was mapped on chr 6 (LG C2) within a 3.5-cM genome region between two SSR markers GMAC7L and Satt322 whose size was estimated to be 77.115 kb (position of 12,259,594-12,336,709 bp). This is the first report on linkage mapping of MYMIV resistance gene in soybean. This will be helpful in breeding soybean varieties for resistance against MYMIV responsible for wide spread damage to soybean crop in India using Marker Assisted Selection.

Tropical food legumes: virus diseases of economic importance and their control

Diverse array of food legume crops (Fabaceae: Papilionoideae) have been adopted worldwide for their protein-rich seed. Choice of legumes and their importance vary in different parts of the world. The economically important legumes are severely affected by a range of virus diseases causing significant economic losses due to reduction in grain production, poor quality seed, and costs incurred in phytosanitation and disease control. The majority of the viruses infecting legumes are vectored by insects, and several of them are also seed transmitted, thus assuming importance in the quarantine and in the epidemiology. This review is focused on the economically important viruses of soybean, groundnut, common bean, cowpea, pigeonpea, mungbean, urdbean, chickpea, pea, faba bean, and lentil and begomovirus diseases of three minor tropical food legumes (hyacinth bean, horse gram, and lima bean). Aspects included are geographic distribution, impact on crop growth and yields, virus characteristics, diagnosis of causal viruses, disease epidemiology, and options for control. Effectiveness of selection and planting with virus-free seed, phytosanitation, manipulation of crop cultural and agronomic practices, control of virus vectors and host plant resistance, and potential of transgenic resistance for legume virus disease control are discussed.

Genome-wide SNP identification and characterization in two soybean cultivars with contrasting Mungbean Yellow Mosaic India Virus disease resistance traits

Mungbean yellow mosaic India virus (MYMIV) is a bipartite Geminivirus, which causes severe yield loss in soybean (Glycine max). Considering this, the present study was conducted to develop large-scale genome-wide single nucleotide polymorphism (SNP) markers and identify potential markers linked with known disease resistance loci for their effective use in genomics-assisted breeding to impart durable MYMIV tolerance. The whole-genome re-sequencing of MYMIV resistant cultivar 'UPSM-534' and susceptible Indian cultivar 'JS-335' was performed to identify high-quality SNPs and InDels (insertion and deletions). Approximately 234 and 255 million of 100-bp paired-end reads were generated from UPSM-534 and JS-335, respectively, which provided ~98% coverage of reference soybean genome. A total of 3083987 SNPs (1559556 in UPSM-534 and 1524431 in JS-335) and 562858 InDels (281958 in UPSM-534 and 280900 in JS-335) were identified. Of these, 1514 SNPs were found to be present in 564 candidate disease resistance genes. Among these, 829 non-synonymous and 671 synonymous SNPs were detected in 266 and 286 defence-related genes, respectively. Noteworthy, a non-synonymous SNP (in chromosome 18, named 18-1861613) at the 149th base-pair of LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE gene responsible for a G/C transversion [proline (CCC) to alanine(GCC)] was identified and validated in a set of 12 soybean cultivars. Taken together, the present study generated a large-scale genomic resource such as, SNPs and InDels at a genome-wide scale that will facilitate the dissection of various complex traits through construction of high-density linkage maps and fine mapping. In the present scenario, these markers can be effectively used to design high-density SNP arrays for their large-scale validation and high-throughput genotyping in diverse natural and mapping populations, which could accelerate genomics-assisted MYMIV disease resistance breeding in soybean.

Differential soybean gene expression during early phase of infection with Mungbean yellow mosaic India virus

Mungbean yellow mosaic India virus (MYMIV), a bipartite begomovirus, causes yellow mosaic disease to soybean. Studies related to host gene expression in response to begomovirus infection have mostly been performed with systemically infected tissues at a later period of infection. In this study, soybean gene expression analysis has been performed to understand local responses against MYMIV at an early stage of infection before appearance of detectable limit of late viral transcripts. 444 soybean transcripts belonging to eleven functional categories showed significant changes in expression level at two days after infection. MYMIV infection resulted in enhanced expression of genes associated with hypersensitive response, programmed cell death and resistance response pathways and reduced expression of genes for photosynthesis and sugar transport. Comparative expression analysis of selected transcripts in the susceptible and a resistant variety displayed differential expression of host genes involved in intercellular virus movement and long distance signaling of systemic acquired resistance.

Begomovirus research in India: a critical appraisal and the way ahead

Begomoviruses are a large group of whitefly-transmitted plant viruses containing single-stranded circular DNA encapsidated in geminate particles. They are responsible for significant yield losses in a wide variety of crops in India. Research on begomoviruses has focussed on the molecular characterization of the viruses, their phylogenetic analyses, infectivities on host plants, DNA replication, transgenic resistance, promoter analysis and development of virus-based gene silencing vectors. There have been a number of reports of satellite molecules associated with begomoviruses. This article aims to summarize the major developments in begomoviral research in India in the last approximately 15 years and identifies future areas that need more attention.

Enhanced viral intergenic region-specific short interfering RNA accumulation and DNA methylation correlates with resistance against a geminivirus

RNA silencing mediated by short-interfering RNA (siRNA) is used by plants as a defense against viruses. In the case of geminiviruses, viral DNA is targeted at the transcriptional level, while virus-derived transcripts are targeted by posttranscriptional silencing. Mungbean yellow mosaic India virus (MYMIV), a bipartite geminivirus, causes yellow mosaic disease in soybean (Glycine max). A soybean variety resistant to this disease has been identified (line PK416). To understand the molecular mechanism underlying this resistance, distribution of MYMIV-derived siRNAs along the viral genome was compared in resistant and susceptible plants, using samples obtained in the first few days following inoculation. We observed that, in the resistant soybean variety, most of the virus-derived siRNAs were complementary to the intergenic region (IR), while in the susceptible variety (line JS335), a majority of the siRNAs corresponded to coding regions of the viral genome. Most of the IR-specific siRNA molecules produced in the resistant plants were 24 nt in size. Bisulfite sequencing showed that, in the resistant plants, a higher level of methylation occurred in the IR of viral DNA.

Characterization of Geminivirus resistance in an accession of Capsicum chinense Jacq

Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV), members of the Geminiviridae family, are important pathogens of pepper (Capsicum annuum L.) and other solanaceous crops. Accession BG-3821 of C. chinense Jacq. was reported earlier as resistant to mixed infection with PepGMV and PHYVV. In this work, we characterized the Geminivirus resistance trait present in BG-3821. Segregation analysis suggested that resistance depends on two genes. Our data showed that PepGMV replication in protoplast of resistant plants is approximately 70% lower when compared with the levels observed in protoplasts from susceptible plants. Additionally, viral movement is less efficient in resistant plants. We also evaluated several characteristics commonly associated with systemic acquired resistance (SAR), which is a conserved defensive mechanism. The concentration of salicylic acid was higher in resistant plants inoculated with PepGMV than in susceptible plants. Marker genes for SAR were induced after inoculation with PepGMV in resistant leaves. Similarly, we found a higher accumulation of reactive oxygen species on resistant leaves compared with susceptible ones. A model for the mechanism acting in the Geminivirus resistance detected in BG-3821 is proposed. Finally, the importance of BG-3821 in Geminivirus resistance breeding programs is discussed.

Tomato cultivar tolerant to Tomato leaf curl New Delhi virus infection induces virus-specific short interfering RNA accumulation and defence-associated host gene expression

Tomato leaf curl New Delhi virus (ToLCNDV) infection causes significant yield loss in tomato. The availability of a conventional tolerance source against this virus is limited in tomato. To understand the molecular mechanism of virus tolerance in tomato, the abundance of viral genomic replicative intermediate molecules and virus-directed short interfering RNAs (siRNAs) by the host plant in a naturally tolerant cultivar H-88-78-1 and a susceptible cultivar Punjab Chhuhara at different time points after agroinfection was studied. We report that less abundance of viral replicative intermediate in the tolerant cultivar may have a correlation with a relatively higher accumulation of virus-specific siRNAs. To study defence-related host gene expression in response to ToLCNDV infection, the suppression subtractive hybridization technique was used. A library was prepared from tolerant cultivar H-88-78-1 between ToLCNDV-inoculated and Agrobacterium mock-inoculated plants of this cultivar at 21 days post-inoculation (dpi). A total of 106 nonredundant transcripts was identified and classified into 12 different categories according to their putative functions. By reverse Northern analysis and quantitative real-time polymerase chain reaction (qRT-PCR), we identified the differential expression pattern of 106 transcripts, 34 of which were up-regulated (>2.5-fold induction). Of these, eight transcripts showed more than four fold induction. qRT-PCR analysis was carried out to obtain comparative expression profiling of these eight transcripts between Punjab Chhuhara and H-88-78-1 on ToLCNDV infection. The expression patterns of these transcripts showed a significant increase in differential expression in the tolerant cultivar, mostly at 14 and 21 dpi, in comparison with that in the susceptible cultivar, as analysed by qRT-PCR. The probable direct and indirect relationship of siRNA accumulation and up-regulated transcripts with the ToLCNDV tolerance mechanism is discussed.