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Keepers K, Peterson K, Raduski A, Turner KM, Van Tassel D, Smith K, Harkess A, Bever JD, Brandvain Y. Disease resistance gene count increases with rainfall in Silphium integrifolium. Ecol Evol 2024; 14:e11143. [PMID: 39234161 PMCID: PMC11371658 DOI: 10.1002/ece3.11143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 09/06/2024] Open
Abstract
Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n = 99) and PacBio long-read (n = 10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant's source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.
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Affiliation(s)
- Kyle Keepers
- Department of Plant and Microbial Biology University of Minnesota St Paul Minnesota USA
| | - Kelsey Peterson
- Department of Plant and Microbial Biology University of Minnesota St Paul Minnesota USA
| | - Andrew Raduski
- Department of Plant and Microbial Biology University of Minnesota St Paul Minnesota USA
| | | | | | - Kevin Smith
- Department of Agronomy and Plant Genetics University of Minnesota St Paul Minnesota USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology Huntsville Alabama USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas USA
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology University of Minnesota St Paul Minnesota USA
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Normantovich M, Amitzur A, Offri S, Pashkovsky E, Shnaider Y, Nizan S, Yogev O, Jacob A, Taylor CG, Desbiez C, Whitham SA, Bar-Ziv A, Perl-Treves R. The melon Fom-1-Prv resistance gene pair: Correlated spatial expression and interaction with a viral protein. PLANT DIRECT 2024; 8:e565. [PMID: 38389929 PMCID: PMC10883720 DOI: 10.1002/pld3.565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/24/2024]
Abstract
The head-to-head oriented pair of melon resistance genes, Fom-1 and Prv, control resistance to Fusarium oxysporum races 0 and 2 and papaya ringspot virus (PRSV), respectively. They encode, via several RNA splice variants, TIR-NBS-LRR proteins, and Prv has a C-terminal extra domain with a second NBS homologous sequence. In other systems, paired R-proteins were shown to operate by "labor division," with one protein having an extra integrated domain that directly binds the pathogen's Avr factor, and the second protein executing the defense response. We report that the expression of the two genes in two pairs of near-isogenic lines was higher in the resistant isoline and inducible by F. oxysporum race 2 but not by PRSV. The intergenic DNA region separating the coding sequences of the two genes acted as a bi-directional promoter and drove GUS expression in transgenic melon roots and transgenic tobacco plants. Expression of both genes was strong in melon root tips, around the root vascular cylinder, and the phloem and xylem parenchyma of tobacco stems and petioles. The pattern of GUS expression suggests coordinated expression of the two genes. In agreement with the above model, Prv's extra domain was shown to interact with the cylindrical inclusion protein of PRSV both in yeast cells and in planta.
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Affiliation(s)
- Michael Normantovich
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Arie Amitzur
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Sharon Offri
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ekaterina Pashkovsky
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Yula Shnaider
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Shahar Nizan
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ohad Yogev
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Avi Jacob
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | | | | | - Steven A Whitham
- Department of Plant Pathology and Microbiology Iowa State University Ames Iowa USA
| | - Amalia Bar-Ziv
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Rafael Perl-Treves
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
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Boissot N, Chovelon V, Rittener-Ruff V, Giovinazzo N, Mistral P, Pitrat M, Charpentier M, Troadec C, Bendahmane A, Dogimont C. A highly diversified NLR cluster in melon contains homologs that confer powdery mildew and aphid resistance. HORTICULTURE RESEARCH 2024; 11:uhad256. [PMID: 38269294 PMCID: PMC10807702 DOI: 10.1093/hr/uhad256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/29/2023] [Indexed: 01/26/2024]
Abstract
Podosphaera xanthii is the main causal agent of powdery mildew (PM) on Cucurbitaceae. In Cucumis melo, the Pm-w resistance gene, which confers resistance to P. xanthii, is located on chromosome 5 in a cluster of nucleotide-binding leucine-rich repeat receptors (NLRs). We used positional cloning and transgenesis, to isolate the Pm-wWMR 29 gene encoding a coiled-coil NLR (CC-NLR). Pm-wWMR 29 conferred high level of resistance to race 1 of PM and intermediate level of resistance to race 3 of PM. Pm-wWMR 29 turned out to be a homolog of the Aphis gossypii resistance gene Vat-1PI 161375. We confirmed that Pm-wWMR 29 did not confer resistance to aphids, while Vat-1PI 161375 did not confer resistance to PM. We showed that both homologs were included in a highly diversified cluster of NLRs, the Vat cluster. Specific Vat-1PI 161375 and Pm-wWMR 29 markers were present in 10% to 13% of 678 accessions representative of wild and cultivated melon types worldwide. Phylogenic reconstruction of 34 protein homologs of Vat-1PI 161375 and Pm-wWMR 29 identified in 24 melon accessions revealed an ancestor with four R65aa-a specific motif in the LRR domain, evolved towards aphid and virus resistance, while an ancestor with five R65aa evolved towards PM resistance. The complexity of the cluster comprising the Vat/Pm-w genes and its diversity in melon suggest that Vat homologs may contribute to the recognition of a broad range of yet to be identified pests and pathogens.
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Affiliation(s)
| | | | | | | | | | | | - Myriam Charpentier
- INRAE, IPS2, 91190 Gif-sur-Yvette, France
- John Innes Centre, Department Cell & Developmental Biology, Colney Lane, Norwich NR4 7UH, UK
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4
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Li G, Tang L, He Y, Xu Y, Bendahmane A, Garcia-Mas J, Lin T, Zhao G. The haplotype-resolved T2T reference genome highlights structural variation underlying agronomic traits of melon. HORTICULTURE RESEARCH 2023; 10:uhad182. [PMID: 37885818 PMCID: PMC10599238 DOI: 10.1093/hr/uhad182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/04/2023] [Indexed: 10/28/2023]
Abstract
Melon (Cucumis melo L.) is an important vegetable crop that has an extensive history of cultivation. However, the genome of wild and semi-wild melon types that can be used for the analysis of agronomic traits is not yet available. Here we report a chromosome-level T2T genome assembly for 821 (C. melo ssp. agrestis var. acidulus), a semi-wild melon with two haplotypes of ~373 Mb and ~364 Mb, respectively. Comparative genome analysis discovered a significant number of structural variants (SVs) between melo (C. melo ssp. melo) and agrestis (C. melo ssp. agrestis) genomes, including a copy number variation located in the ToLCNDV resistance locus on chromosome 11. Genome-wide association studies detected a significant signal associated with climacteric ripening and identified one candidate gene CM_ac12g14720.1 (CmABA2), encoding a cytoplasmic short chain dehydrogenase/reductase, which controls the biosynthesis of abscisic acid. This study provides valuable genetic resources for future research on melon breeding.
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Affiliation(s)
- Guoli Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
- China Agricultural University, College of Horticulture, Beijing 100193, China
| | - Lingli Tang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453400, China
| | - Yuhua He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Yongyang Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), INRAE, CNRS, University of Paris-Saclay, University of Evry, University of Paris-Diderot, Gif sur Yvette 91192, France
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Tao Lin
- China Agricultural University, College of Horticulture, Beijing 100193, China
| | - Guangwei Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang 453400, China
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Zhang H, Chen H, Tan J, Huang S, Chen X, Dong H, Zhang R, Wang Y, Wang B, Xiao X, Hong Z, Zhang J, Hu J, Zhang M. The chromosome-scale reference genome and transcriptome analysis of Solanum torvum provides insights into resistance to root-knot nematodes. FRONTIERS IN PLANT SCIENCE 2023; 14:1210513. [PMID: 37528971 PMCID: PMC10390315 DOI: 10.3389/fpls.2023.1210513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023]
Abstract
Solanum torvum (Swartz) (2n = 24) is a wild Solanaceae plant with high economic value that is used as a rootstock in grafting for Solanaceae plants to improve the resistance to a soil-borne disease caused by root-knot nematodes (RKNs). However, the lack of a high-quality reference genome of S. torvum hinders research on the genetic basis for disease resistance and application in horticulture. Herein, we present a chromosome-level assembly of genomic sequences for S. torvum combining PacBio long reads (HiFi reads), Illumina short reads and Hi-C scaffolding technology. The assembled genome size is ~1.25 Gb with a contig N50 and scaffold N50 of 38.65 Mb and 103.02 Mb, respectively as well as a BUSCO estimate of 98%. GO enrichment and KEGG pathway analysis of the unique S. torvum genes, including NLR and ABC transporters, revealed that they were involved in disease resistance processes. RNA-seq data also confirmed that 48 NLR genes were highly expressed in roots and fibrous roots and that three homologous NLR genes (Sto0288260.1, Sto0201960.1 and Sto0265490.1) in S. torvum were significantly upregulated after RKN infection. Two ABC transporters, ABCB9 and ABCB11 were identified as the hub genes in response to RKN infection. The chromosome-scale reference genome of the S. torvum will provide insights into RKN resistance.
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Affiliation(s)
- Hongyuan Zhang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Hao Chen
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Jie Tan
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Shuping Huang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xia Chen
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Hongxia Dong
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Ru Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Benqi Wang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID, United States
| | - Junhong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jihong Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Min Zhang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
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6
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Sadon P, Corre MN, Lugan R, Boissot N. Aphid adaptation to cucurbits: sugars, cucurbitacin and phloem structure in resistant and susceptible melons. BMC PLANT BIOLOGY 2023; 23:239. [PMID: 37147560 PMCID: PMC10161555 DOI: 10.1186/s12870-023-04248-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/25/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND Aphis gossypii, a strictly phloemophagaous aphid, colonize hundreds of plant families, and a group of clones formed a cucurbit-specialised host-race. Cucurbits are unique in having evolved a specific extra-fascicular phloem (EFP), which carries defence-related metabolites such as cucurbitacin, whereas the fascicular phloem (FP) is common to all higher plants and carries primary metabolites, such as raffinose-family oligosaccharides (RFOs). Both cucurbitacins (in the EFP) and galactinol (in the FP) have been suggested to be toxic to aphids. We investigated these hypotheses in cucurbit-specialized A. gossypii fed on melon plants with or without aphid-resistance conferred by the NLR gene Vat. We selected a plant-aphid system with (i) Vat-mediated resistance not triggered, (ii) Vat-mediated resistance triggered by an aphid clone adapted to the presence of Vat resistant alleles and (iii) Vat-mediated resistance triggered by a non-adapted aphid clone. RESULTS We quantified cucurbitacin B, its glycosylated derivative, and sugars, in melon plants and aphids that fed on. The level of cucurbitacin in plants was unrelated to both aphid infestation and aphid resistance. Galactinol was present at higher quantities in plants when Vat-mediated resistance was triggered, but its presence did not correlate with aphid performance. Finally, we showed that cucurbit-specialized A. gossypii fed from the FP but could also occasionally access the EFP without sustainably feeding from it. However, the clone not adapted to Vat-mediated resistance were less able to access the FP when the Vat resistance was triggered. CONCLUSION We concluded that galactinol accumulation in resistant plants does not affect aphids, but may play a role in aphid adaptation to fasting and that Cucurbitacin in planta is not a real threat to Aphis gossypii. Moreover, the specific phloem of Cucurbits is involved neither in A. gossypii cucurbit specialisation nor in adaptation to Vat-dependent resistance.
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Affiliation(s)
- Pierre Sadon
- Génétique et Amélioration des Fruits et Légumes, National Institute for Agriculture, Food and Environment, INRAE, Domaine St-Maurice, 84143, Montfavet, Cedex, France
| | - Marie-Noëlle Corre
- Génétique et Amélioration des Fruits et Légumes, National Institute for Agriculture, Food and Environment, INRAE, Domaine St-Maurice, 84143, Montfavet, Cedex, France
| | - Raphael Lugan
- Plantes et Systèmes de cultures Horticoles, National Institute for Agriculture, Food and Environment, INRAE, Domaine St Paul, 84914, Avignon, Cedex, France
| | - Nathalie Boissot
- Génétique et Amélioration des Fruits et Légumes, National Institute for Agriculture, Food and Environment, INRAE, Domaine St-Maurice, 84143, Montfavet, Cedex, France.
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7
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Genome wide identification and evolutionary analysis of vat like NBS-LRR genes potentially associated with resistance to aphids in cotton. Genetica 2023; 151:119-131. [PMID: 36717534 DOI: 10.1007/s10709-023-00181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/24/2023] [Indexed: 02/01/2023]
Abstract
Nucleotide Binding Site - Leucine Rich Repeat (NBS-LRR) genes play a significant role in plant defense against biotic stresses and are an integral part of signal transduction pathways. Vat gene has been well reported for their role in resistance to Aphis gossypii and viruses transmitted by them. Despite their importance, Vat like NBS-LRR resistance genes have not yet been identified and studied in cotton species. This study report hundreds of orthologous Vat like NBS-LRR genes from the genomes of 18 cotton species through homology searches and the distribution of those identified genes were tend to be clustered on different chromosome. Especially, in a majority of the cases, Vat like genes were located on chromosome number 13 and they all shared two conserved NBS-LRR domains, one disease resistant domain and several repeats of LRR on the investigated cotton Vat like proteins. Gene ontology study on Vat like NBS-LRR genes revealed the molecular functions viz., ADP and protein binding. Phylogenetic analysis also revealed that Vat like sequences of two diploid species, viz., G. arboreum and G. anomalum, were closely related to the sequences of the tetraploids than all other diploids. The Vat like genes of G. aridum and G. schwendimanii were distantly related among diploids and tetraploids species. Various hormones and defense related cis-acting regulatory elements were identified from the 2 kb upstream sequences of the Vat like genes implying their defensive response towards the biotic stresses. Interestingly, G. arboreum and G. trilobum were found to have more regulatory elements than larger genomes of tetraploid cotton species. Thus, the present study provides the evidence for the evolution of Vat like genes in defense mechanisms against aphids infestation in cotton genomes and allows further characterization of candidate genes for developing aphid and aphid transmitted viruses resistant crops through cotton breeding.
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8
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Boissot N. NLRs are highly relevant resistance genes for aphid pests. CURRENT OPINION IN INSECT SCIENCE 2023; 56:101008. [PMID: 36764482 DOI: 10.1016/j.cois.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Since the 20th century, when plant resistance to aphids was available, it has been widely used by farmers and the inheritance of plant resistance has been understood for several crops. However, it is only when the plant-aphid relationship was compared with that of microbial pathogens, that aphid resistance has begun to be understood and integrated into the plant immune network. Three of the four genes identified for plant resistance to aphid encode nucleotide-binding site leucine-rich repeat receptor (NLR) proteins responsible for aphid-effector triggered immunity, and NLRs are serious candidates for aphid resistance in four other plant species. Aphids are vectors for plant viruses, and aphid-effectors triggering immunity when they pierce plant cells are expected to trigger resistance to the viruses transmitted to the plant with effectors, as has been shown for aphid resistance in melon. This dual phenotype increases the interest of NLRs in the control of aphids.
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Affiliation(s)
- Nathalie Boissot
- INRAE, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France.
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Yang M, Zhou C, Yang H, Kuang R, Liu K, Huang B, Wei Y. Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya ( Carica papaya L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1038598. [PMID: 36618670 PMCID: PMC9816866 DOI: 10.3389/fpls.2022.1038598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Colletotrichum brevisporum is an important causal pathogen of anthracnose that seriously affects the fruit quality and yield of papaya (Carica papaya L.). Although many genes and biological processes involved in anthracnose resistance have been reported in other species, the molecular mechanisms involved in the response or resistance to anthracnose in post-harvest papaya fruits remain unclear. In this study, we compared transcriptome changes in the post-harvest fruits of the anthracnose-susceptible papaya cultivar Y61 and the anthracnose-resistant cultivar G20 following C. brevisporum inoculation. More differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElnRNAs) were identified in G20 than in Y61, especially at 24 h post-inoculation (hpi), suggesting a prompt activation of defense responses in G20 in the first 24 h after C. brevisporum inoculation. These DEGs were mainly enriched in plant-pathogen interaction, phenylpropanoid biosynthesis/metabolism, and peroxisome and flavonoid biosynthesis pathways in both cultivars. However, in the first 24 hpi, the number of DEGs related to anthracnose resistance was greater in G20 than in Y61, and changes in their expression levels were faster in G20 than in Y61. We also identified a candidate anthracnose-resistant gene cluster, which consisted of 12 genes, 11 in G20 and Y61, in response to C. brevisporum inoculation. Moreover, 529 resistance gene analogs were identified in papaya genome, most of which responded to C. brevisporum inoculation and were genetically different between papaya cultivars and wild-type populations. The total expression dose of the resistance gene analogs may help papaya resist C. brevisporum infection. This study revealed the mechanisms underlying different anthracnose resistance between the anthracnose-resistant and anthracnose-susceptible cultivars based on gene expression, and identified some potential anthracnose resistance-related candidate genes/major regulatory factors. Our findings provided potential targets for developing novel genetic strategies to overcome anthracnose in papaya.
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Affiliation(s)
- Min Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chenping Zhou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hu Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruibin Kuang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Bingxiong Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuerong Wei
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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10
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Yan T, Zhou Z, Wang R, Bao D, Li S, Li A, Yu R, Wuriyanghan H. A cluster of atypical resistance genes in soybean confers broad-spectrum antiviral activity. PLANT PHYSIOLOGY 2022; 188:1277-1293. [PMID: 34730802 PMCID: PMC8825445 DOI: 10.1093/plphys/kiab507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/02/2021] [Indexed: 06/12/2023]
Abstract
Soybean mosaic virus (SMV) is a severe soybean (Glycine max) pathogen. Here we characterize a soybean SMV resistance cluster (SRC) that comprises five resistance (R) genes. SRC1 encodes a Toll/interleukin-1 receptor and nucleotide-binding site (TIR-NBS [TN]) protein, SRC4 and SRC6 encode TIR proteins with a short EF-hand domain, while SRC7 and SRC8 encode TNX proteins with a noncanonical basic secretory protein (BSP) domain at their C-termini. We mainly studied SRC7, which contains a noncanonical BSP domain and gave full resistance to SMV. SRC7 possessed broad-spectrum antiviral activity toward several plant viruses including SMV, plum pox virus, potato virus Y, and tobacco mosaic virus. The TIR domain alone was both necessary and sufficient for SRC7 immune signaling, while the NBS domain enhanced its activity. Nuclear oligomerization via the interactions of both TIR and NBS domains was essential for SRC7 function. SRC7 expression was transcriptionally inducible by SMV infection and salicylic acid (SA) treatment, and SA was required for SRC7 triggered virus resistance. SRC7 expression was posttranscriptionally regulated by miR1510a and miR2109, and the SRC7-miR1510a/miR2109 regulatory network appeared to contribute to SMV-soybean interactions in both resistant and susceptible soybean cultivars. In summary, we report a soybean R gene cluster centered by SRC7 that is regulated at both transcriptional and posttranscriptional levels, possesses a yet uncharacterized BSP domain, and has broad-spectrum antiviral activities. The SRC cluster is special as it harbors several functional R genes encoding atypical TIR-NBS-LRR (TNL) type R proteins, highlighting its importance in SMV-soybean interaction and plant immunity.
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Affiliation(s)
- Ting Yan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Zikai Zhou
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ru Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Duran Bao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Shanshan Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Aoga Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
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Monnot S, Desaint H, Mary-Huard T, Moreau L, Schurdi-Levraud V, Boissot N. Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances. Cells 2021; 10:3080. [PMID: 34831303 PMCID: PMC8625838 DOI: 10.3390/cells10113080] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023] Open
Abstract
Growing virus resistant varieties is a highly effective means to avoid yield loss due to infection by many types of virus. The challenge is to be able to detect resistance donors within plant species diversity and then quickly introduce alleles conferring resistance into elite genetic backgrounds. Until now, mainly monogenic forms of resistance with major effects have been introduced in crops. Polygenic resistance is harder to map and introduce in susceptible genetic backgrounds, but it is likely more durable. Genome wide association studies (GWAS) offer an opportunity to accelerate mapping of both monogenic and polygenic resistance, but have seldom been implemented and described in the plant-virus interaction context. Yet, all of the 48 plant-virus GWAS published so far have successfully mapped QTLs involved in plant virus resistance. In this review, we analyzed general and specific GWAS issues regarding plant virus resistance. We have identified and described several key steps throughout the GWAS pipeline, from diversity panel assembly to GWAS result analyses. Based on the 48 published articles, we analyzed the impact of each key step on the GWAS power and showcase several GWAS methods tailored to all types of viruses.
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Affiliation(s)
- Severine Monnot
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
- Bayer Crop Science, Chemin de Roque Martine, 13670 Saint-Andiol, France
| | - Henri Desaint
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, Ferme du Moulon, 91190 Gif-sur-Yvette, France
- Mathématiques et Informatique Appliquées (MIA)-Paris, INRAE, AgroParisTech, Université Paris-Saclay, 75231 Paris, France
| | - Laurence Moreau
- INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, Université Paris-Saclay, Ferme du Moulon, 91190 Gif-sur-Yvette, France
| | | | - Nathalie Boissot
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
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