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Koeda S, Mori N, Horiuchi R, Watanabe C, Nagano AJ, Shiragane H. PepYLCIV and PepYLCAV resistance gene Pepy-2 encodes DFDGD-Class RNA-dependent RNA polymerase in Capsicum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2437-2452. [PMID: 35652932 DOI: 10.1007/s00122-022-04125-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
A begomovirus resistance gene Pepy-2 encoding the DFDGD-Class RNA-dependent RNA polymerase 3a was identified in pepper (C. annuum) through the forward and reverse genetic analyses. In several countries throughout the world, the whitefly-transmitted begomovirus causes massive yield losses in pepper (Capsicum spp.) production. Although introgression of the genetic resistance against begomovirus to commercial cultivars is strongly required, the recently discovered recessive resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, is the only begomovirus resistance gene identified in Capsicum so far. In this study, we fine-mapped another begomovirus resistance gene from PG1-1 (C. annuum), which is resistant to pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV), to further speed up the marker-assisted breeding of begomovirus resistance in peppers. A single dominant locus, Pepy-2, conferring resistance against PepYLCIV in PG1-1 was identified on chromosome 7 by screening recombinants from the F2 and F3 segregating populations derived from a cross between PG1-1 and begomovirus susceptible SCM334. In the target region spanning 722 kb, a strong candidate gene, the RNA-dependent RNA polymerase 3a (CaRDR3a), was identified. The whole-genome and transcriptome sequences of PG1-1 and SCM334 revealed a single Guanine (G) deletion in CaRDR3a first exon, causing a frameshift resulting in loss-of-function in SCM334. In addition, multiple loss-of-function alleles of CaRDR3a were identified in the reference sequences of C. annuum, C. chinense, and C. baccatum in the public database. Furthermore, virus-induced gene silencing of CaRDR3a in PG1-1 resulted in the loss of resistance against PepYLCIV. PG1-1 and the DNA marker developed in this study will be useful to breeders using Pepy-2 in their breeding programs.
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Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
| | - Namiko Mori
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Ryo Horiuchi
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Chiho Watanabe
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Atsushi J Nagano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
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Koeda S, Onouchi M, Mori N, Pohan NS, Nagano AJ, Kesumawati E. A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2947-2964. [PMID: 34081151 DOI: 10.1007/s00122-021-03870-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/24/2021] [Indexed: 05/25/2023]
Abstract
A begomovirus resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, was identified in pepper (C. annuum) through map-based cloning and functional characterization. Pepper yellow leaf curl disease caused by begomoviruses seriously affects pepper (Capsicum spp.) production in a number of regions around the world. Ty genes of tomato, which confer resistance to the tomato yellow leaf curl virus, are the only begomovirus resistance genes cloned to date. In this study, we focused on the identification of begomovirus resistance genes in Capsicum annuum. BaPep-5 was identified as a novel source of resistance against pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV). A single recessive locus, which we named as pepper yellow leaf curl disease virus resistance 1 (pepy-1), responsible for PepYLCAV resistance in BaPep-5 was identified on chromosome 5 in an F2 population derived from a cross between BaPep-5 and the begomovirus susceptible accession BaPep-4. In the target region spanning 34 kb, a single candidate gene, the messenger RNA surveillance factor Pelota, was identified. Whole-genome resequencing of BaPep-4 and BaPep-5 and comparison of their genomic DNA sequences revealed a single nucleotide polymorphism (A to G) located at the splice site of the 9th intron of CaPelota in BaPep-5, which caused the insertion of the 9th intron into the transcript, resulting in the addition of 28 amino acids to CaPelota protein without causing a frameshift. Virus-induced gene silencing of CaPelota in the begomovirus susceptible pepper No.218 resulted in the gain of resistance against PepYLCIV, a phenotype consistent with BaPep-5. The DNA marker developed in this study will greatly facilitate marker-assisted breeding of begomovirus resistance in peppers.
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Affiliation(s)
- Sota Koeda
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
| | - Mika Onouchi
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Namiko Mori
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Nadya Syafira Pohan
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Atsushi J Nagano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
| | - Elly Kesumawati
- Faculty of Agriculture, Syiah Kuala University, Banda Aceh, Aceh , 23111, Indonesia
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Gas Chromatography-Mass Spectrometry Analysis of Compounds Emitted by Pepper Yellow Leaf Curl Virus-Infected Chili Plants: A Preliminary Study. SEPARATIONS 2021. [DOI: 10.3390/separations8090136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pepper yellow leaf curl virus (PYLCV) is a threat to chili plants and can significantly reduce yields. This study aimed as a pilot project to detect PYLCV by analyzing compounds emitted by chili plants using gas chromatography-mass spectrometry (GC-MS). The samples investigated in this research were PYLCV-infected and PYLCV-undetected chili plants taken from commercial chili fields. The infection status was validated by using a polymerase chain reaction (PCR) test. A headspace technique was used to extract the volatile organic compounds emitted by plants. The analysis of GC-MS results began with pre-processing, analyzing sample compound variability with a boxplot analysis, and sample classification by using a multivariate technique. Unsupervised multivariate technique principal component analysis (PCA) was performed to discover whether GC-MS could identify PYLCV-infected or not. The results showed that PYLCV-infected and PYLCV-undetected chili plants could be differentiated, with a total percent variance of the first three principal components reaching 91.32%, and successfully discriminated between PYLCV-infected and PYLCV-undetected chili plants. However, more comprehensive studies are needed to find the potential biomarkers of the infected plants.
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Crespo-Bellido A, Hoyer JS, Dubey D, Jeannot RB, Duffy S. Interspecies Recombination Has Driven the Macroevolution of Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0054121. [PMID: 34106000 PMCID: PMC8354330 DOI: 10.1128/jvi.00541-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Begomoviruses (family Geminiviridae, genus Begomovirus) significantly hamper crop production and threaten food security around the world. The frequent emergence of new begomovirus genotypes is facilitated by high mutation frequencies and the propensity to recombine and reassort. Homologous recombination has been especially implicated in the emergence of novel cassava mosaic begomovirus (CMB) genotypes, which cause cassava mosaic disease (CMD). Cassava (Manihot esculenta) is a staple food crop throughout Africa and an important industrial crop in Asia, two continents where production is severely constrained by CMD. The CMD species complex is comprised of 11 bipartite begomovirus species with ample distribution throughout Africa and the Indian subcontinent. While recombination is regarded as a frequent occurrence for CMBs, a revised, systematic assessment of recombination and its impact on CMB phylogeny is currently lacking. We assembled data sets of all publicly available, full-length DNA-A (n = 880) and DNA-B (n = 369) nucleotide sequences from the 11 recognized CMB species. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the CMB sequences. Six out of the 11 species descended from unique interspecies recombination events. Estimates of recombination and mutation rates revealed that all species experience mutation more frequently than recombination, but measures of population divergence indicate that recombination is largely responsible for the genetic differences between species. Our results support that recombination has significantly impacted the CMB phylogeny and has driven speciation in the CMD species complex. IMPORTANCE Cassava mosaic disease (CMD) is a significant threat to cassava production throughout Africa and Asia. CMD is caused by a complex comprised of 11 recognized virus species exhibiting accelerated rates of evolution, driven by high frequencies of mutation and genetic exchange. Here, we present a systematic analysis of the contribution of genetic exchange to cassava mosaic virus species-level diversity. Most of these species emerged as a result of genetic exchange. This is the first study to report the significant impact of genetic exchange on speciation in a group of viruses.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Divya Dubey
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Ronica B. Jeannot
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
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Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Kutnjak D. Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front Microbiol 2021; 12:671925. [PMID: 34093492 PMCID: PMC8175903 DOI: 10.3389/fmicb.2021.671925] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.
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Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,School for Viticulture and Enology, University of Nova Gorica, Nova Gorica, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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Koeda S, Fujiwara I, Oka Y, Kesumawati E, Zakaria S, Kanzaki S. Ty-2 and Ty-3a Conferred Resistance are Insufficient Against Tomato Yellow Leaf Curl Kanchanaburi Virus from Southeast Asia in Single or Mixed Infections of Tomato. PLANT DISEASE 2020; 104:3221-3229. [PMID: 33044916 DOI: 10.1094/pdis-03-20-0613-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV), a monopartite begomovirus that originated in the eastern Mediterranean, has spread worldwide, becoming a serious threat to tomato (Solanum lycopersicum L.) production. Southeast Asia is considered one of the hotspots for begomovirus diversity, and a wide variety of local begomovirus species distinct from TYLCV have been identified. In this study, the protection effect of introgressions of single TYLCV Ty resistance genes, Ty-2 and Ty-3a, in tomato was examined against inoculations of the bipartite begomoviruses Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) and Pepper yellow leaf curl Indonesia virus (PepYLCIV) isolated from Indonesia. Our findings suggest that Ty-2 in the heterozygous state was found to be ineffective against PepYLCIV and TYLCKaV, whereas Ty-3a in the heterozygous state was effective against PepYLCIV and partially effective against TYLCKaV. Quantification of viral DNAs showed correlation between symptom expression and viral DNA accumulation. Moreover, mixed infections of TYLCKaV and PepYLCIV caused notably severe symptoms in tomato plants harboring Ty-3a. In cases of mixed infection, quantifying viral DNAs showed a relatively high accumulation of PepYLCIV, indicating that Ty-3a loses its effectiveness against PepYLCIV when TYLCKaV is also present. This study demonstrates the lack of effectiveness of Ty resistance genes against single and mixed infections of distinct local begomoviruses from Southeast Asia.
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Affiliation(s)
- Sota Koeda
- Faculty of Agriculture, Kindai University, 3327-204 Nara, Japan
| | - Ikuya Fujiwara
- Graduate School of Agriculture, Kindai University, 3327-204 Nara, Japan
| | - Yuki Oka
- Faculty of Agriculture, Kindai University, 3327-204 Nara, Japan
| | - Elly Kesumawati
- Faculty of Agriculture, Syiah Kuala University, 23111 Banda Aceh, Aceh, Indonesia
| | - Sabaruddin Zakaria
- Faculty of Agriculture, Syiah Kuala University, 23111 Banda Aceh, Aceh, Indonesia
| | - Shinya Kanzaki
- Faculty of Agriculture, Kindai University, 3327-204 Nara, Japan
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Koeda S, Homma K, Kamitani M, Nagano AJ, Taniguchi M, Pohan N, Kesumawati E. Pepper vein yellows virus 9: a novel polerovirus isolated from chili pepper in Indonesia. Arch Virol 2020; 165:3017-3021. [PMID: 33037939 DOI: 10.1007/s00705-020-04838-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/06/2020] [Indexed: 11/28/2022]
Abstract
In 2017, a leaf sample from a single chili pepper (Capsicum annuum) plant exhibiting yellowing was collected from Aceh province, Indonesia. Total RNA was extracted from this sample, and RNA-Seq analysis was conducted. Putative infecting viruses were detected by mapping the obtained reads to the full-length viral genome sequences available in the GenBank database (7457 sequences) and the de novo-assembled contigs. RNA-Seq analysis detected polerovirus, begomovirus, and amalgavirus sequences, and the polerovirus-like sequences showed strong similarity to those of previously reported pepper vein yellows viruses (PeVYVs). The complete viral genome sequence obtained by RT-PCR had a length of 6023 nt, had the typical genome organization of a polerovirus and showed a high degree of sequence similarity to PeVYV-2 from Israel. Moreover, the predicted amino acid sequence of the P0 protein of the Indonesian isolate was 85.1% to 88.8% identical to those of other PeVYVs. In accordance with the polerovirus species demarcation criteria, this isolate should be assigned to a new polerovirus species, and we propose the name "pepper vein yellows virus 9" (PeVYV-9) for this virus.
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Affiliation(s)
- Sota Koeda
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
| | - Kanami Homma
- Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Mari Kamitani
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Marina Taniguchi
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Nadya Pohan
- Faculty of Agriculture, Syiah Kuala University, Darussalam, Banda Aceh, 23111, Indonesia
| | - Elly Kesumawati
- Faculty of Agriculture, Syiah Kuala University, Darussalam, Banda Aceh, 23111, Indonesia
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