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Niu J, Zhao J, Guo Q, Zhang H, Yue A, Zhao J, Yin C, Wang M, Du W. WGCNA Reveals Hub Genes and Key Gene Regulatory Pathways of the Response of Soybean to Infection by Soybean mosaic virus. Genes (Basel) 2024; 15:566. [PMID: 38790195 PMCID: PMC11120672 DOI: 10.3390/genes15050566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Soybean mosaic virus (SMV) is one of the main pathogens that can negatively affect soybean production and quality. To study the gene regulatory network of soybeans in response to SMV SC15, the resistant line X149 and susceptible line X97 were subjected to transcriptome analysis at 0, 2, 8, 12, 24, and 48 h post-inoculation (hpi). Differential expression analysis revealed that 10,190 differentially expressed genes (DEGs) responded to SC15 infection. Weighted gene co-expression network analysis (WGCNA) was performed to identify highly related resistance gene modules; in total, eight modules, including 2256 DEGs, were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of 2256 DEGs revealed that the genes significantly clustered into resistance-related pathways, such as the plant-pathogen interaction pathway, mitogen-activated protein kinases (MAPK) signaling pathway, and plant hormone signal transduction pathway. Among these pathways, we found that the flg22, Ca2+, hydrogen peroxide (H2O2), and abscisic acid (ABA) regulatory pathways were fully covered by 36 DEGs. Among the 36 DEGs, the gene Glyma.01G225100 (protein phosphatase 2C, PP2C) in the ABA regulatory pathway, the gene Glyma.16G031900 (WRKY transcription factor 22, WRKY22) in Ca2+ and H2O2 regulatory pathways, and the gene Glyma.04G175300 (calcium-dependent protein kinase, CDPK) in Ca2+ regulatory pathways were highly connected hub genes. These results indicate that the resistance of X149 to SC15 may depend on the positive regulation of flg22, Ca2+, H2O2, and ABA regulatory pathways. Our study further showed that superoxide dismutase (SOD) activity, H2O2 content, and catalase (CAT) and peroxidase (POD) activities were significantly up-regulated in the resistant line X149 compared with those in 0 hpi. This finding indicates that the H2O2 regulatory pathway might be dependent on flg22- and Ca2+-pathway-induced ROS generation. In addition, two hub genes, Glyma.07G190100 (encoding F-box protein) and Glyma.12G185400 (encoding calmodulin-like proteins, CMLs), were also identified and they could positively regulate X149 resistance. This study provides pathways for further investigation of SMV resistance mechanisms in soybean.
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Affiliation(s)
- Jingping Niu
- College of Life Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China;
| | - Jing Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Qian Guo
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Hanyue Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Aiqin Yue
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Jinzhong Zhao
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (C.Y.)
| | - Congcong Yin
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (C.Y.)
| | - Min Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
| | - Weijun Du
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030801, China; (J.Z.); (Q.G.); (H.Z.); (A.Y.); (M.W.)
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Jha UC, Nayyar H, Chattopadhyay A, Beena R, Lone AA, Naik YD, Thudi M, Prasad PVV, Gupta S, Dixit GP, Siddique KHM. Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration. FRONTIERS IN PLANT SCIENCE 2023; 14:1183505. [PMID: 37229109 PMCID: PMC10204772 DOI: 10.3389/fpls.2023.1183505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023]
Abstract
Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Anirudha Chattopadhyay
- Department of Plant Pathology, Pulse Research Station, S.D. Agricultural University SK Nagar, SK Nagar, Gujarat, India
| | - Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University (KAU), Thiruvananthapuram, Kerala, India
| | - Ajaz A. Lone
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST)-Kashmir, Srinagar, India
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | | | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Girish Prasad Dixit
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Kadambot H. M. Siddique
- The University of Western Australia (UWA) Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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Du H, Fang C, Li Y, Kong F, Liu B. Understandings and future challenges in soybean functional genomics and molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:468-495. [PMID: 36511121 DOI: 10.1111/jipb.13433] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
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Affiliation(s)
- Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yaru Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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Usovsky M, Chen P, Li D, Wang A, Shi A, Zheng C, Shakiba E, Lee D, Canella Vieira C, Lee YC, Wu C, Cervantez I, Dong D. Decades of Genetic Research on Soybean mosaic virus Resistance in Soybean. Viruses 2022; 14:1122. [PMID: 35746594 PMCID: PMC9230979 DOI: 10.3390/v14061122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023] Open
Abstract
This review summarizes the history and current state of the known genetic basis for soybean resistance to Soybean mosaic virus (SMV), and examines how the integration of molecular markers has been utilized in breeding for crop improvement. SVM causes yield loss and seed quality reduction in soybean based on the SMV strain and the host genotype. Understanding the molecular underpinnings of SMV-soybean interactions and the genes conferring resistance to SMV has been a focus of intense research interest for decades. Soybean reactions are classified into three main responses: resistant, necrotic, or susceptible. Significant progress has been achieved that has greatly increased the understanding of soybean germplasm diversity, differential reactions to SMV strains, genotype-strain interactions, genes/alleles conferring specific reactions, and interactions among resistance genes and alleles. Many studies that aimed to uncover the physical position of resistance genes have been published in recent decades, collectively proposing different candidate genes. The studies on SMV resistance loci revealed that the resistance genes are mainly distributed on three chromosomes. Resistance has been pyramided in various combinations for durable resistance to SMV strains. The causative genes are still elusive despite early successes in identifying resistance alleles in soybean; however, a gene at the Rsv4 locus has been well validated.
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Affiliation(s)
- Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65201, USA;
| | - Pengyin Chen
- Delta Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO 63873, USA; (D.L.); (C.C.V.); (Y.C.L.)
| | - Dexiao Li
- College of Agronomy, Northwest University of Agriculture, Jiangling, Xianyang 712100, China;
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada;
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA;
| | | | - Ehsan Shakiba
- Rice Research and Extension Center, Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Stuttgart, AR 72160, USA;
| | - Dongho Lee
- Delta Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO 63873, USA; (D.L.); (C.C.V.); (Y.C.L.)
| | - Caio Canella Vieira
- Delta Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO 63873, USA; (D.L.); (C.C.V.); (Y.C.L.)
| | - Yi Chen Lee
- Delta Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO 63873, USA; (D.L.); (C.C.V.); (Y.C.L.)
| | - Chengjun Wu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Innan Cervantez
- Bayer CropScience, Global Soybean Breeding, 1781 Gavin Road, Marion, AR 72364, USA;
| | - Dekun Dong
- Soybean Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
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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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Ferreira EGC, Marcelino-Guimarães FC. Mapping Major Disease Resistance Genes in Soybean by Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:313-340. [PMID: 35641772 DOI: 10.1007/978-1-0716-2237-7_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soybean is one of the most valuable agricultural crops in the world. Besides, this legume is constantly attacked by a wide range of pathogens (fungi, bacteria, viruses, and nematodes) compromising yield and increasing production costs. One of the major disease management strategies is the genetic resistance provided by single genes and quantitative trait loci (QTL). Identifying the genomic regions underlying the resistance against these pathogens on soybean is one of the first steps performed by molecular breeders. In the past, genetic mapping studies have been widely used to discover these genomic regions. However, over the last decade, advances in next-generation sequencing technologies and their subsequent cost decreasing led to the development of cost-effective approaches to high-throughput genotyping. Thus, genome-wide association studies applying thousands of SNPs in large sets composed of diverse soybean accessions have been successfully done. In this chapter, a comprehensive review of the majority of GWAS for soybean diseases published since this approach was developed is provided. Important diseases caused by Heterodera glycines, Phytophthora sojae, and Sclerotinia sclerotiorum have been the focus of the several GWAS. However, other bacterial and fungi diseases also have been targets of GWAS. As such, this GWAS summary can serve as a guide for future studies of these diseases. The protocol begins by describing several considerations about the pathogens and bringing different procedures of molecular characterization of them. Advice to choose the best isolate/race to maximize the discovery of multiple R genes or to directly map an effective R gene is provided. A summary of protocols, methods, and tools to phenotyping the soybean panel is given to several diseases. We also give details of options of DNA extraction protocols and genotyping methods, and we describe parameters of SNP quality to soybean data. Websites and their online tools to obtain genotypic and phenotypic data for thousands of soybean accessions are highlighted. Finally, we report several tricks and tips in Subheading 4, especially related to composing the soybean panel as well as generating and analyzing the phenotype data. We hope this protocol will be helpful to achieve GWAS success in identifying resistance genes on soybean.
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Liu XT, Wu XY, Wu WP, Wu M, Chen JQ, Wang B. A bean common mosaic virus-resistance gene in the soybean variant V94-5152 was mapped to the Rsv4 locus conferring resistance to soybean mosaic virus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2367-2377. [PMID: 33997918 DOI: 10.1007/s00122-021-03829-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE In the soybean variant V94-5152, a BCMV-resistance gene was mapped near to the region of SMV-resistance Rsv4 locus, raising a possibility that V94-5152 may rely on Rsv4 locus to resist against both SMV and BCMV. Both Soybean mosaic virus (SMV) and Bean common mosaic virus (BCMV) can induce soybean mosaic diseases, but few studies have explored soybean resistance against BCMV so far. In this study, V94-5152, a soybean variant resistant to BCMV and SMV, was crossed with a susceptible cultivar, Williams 82 to map the resistance gene. By inoculating 292 F2 individuals with a BCMV isolate HZZB011, a segregation ratio of 3 resistant: 1 susceptible was observed, suggesting that V94-5152 possesses a single-dominant resistance gene against BCMV-HZZB011. Bulk segregation analysis (BSA) then revealed that the resistance gene is closely linked to BARCSOYSSR_02_0617, a simple sequence repeat (SSR) marker on chromosome 2. Genotyping neighboring SSR markers among the 292 F2 individuals enabled us to draw a genetic linkage map, which indicated that the BCMV-resistance gene is located 0.2 cM downstream of BARCSOYSSR_02_0617. Amplification and sequencing ten candidate genes (Glyma02g121300 to Glyma02g122200) around this marker then revealed four genes containing nonsynonymous changes or indels. Also, this location is near to the recently cloned SMV-resistance Rsv4 locus from the cultivar Peking. By obtaining ten more sequences of Rsv4 locus from cultivated and wild soybean materials, we further investigated the variation and evolutionary patterns of this virus-resistance locus. It was evident that positive selections had been acting on this locus, with one critical amino acid change (R55P) shared by all resistance soybeans tested.
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Affiliation(s)
- Xue-Ting Liu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Xiao-Yi Wu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Wen-Ping Wu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Mian Wu
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
| | - Jian-Qun Chen
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
| | - Bin Wang
- School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
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Zhao X, Jing Y, Luo Z, Gao S, Teng W, Zhan Y, Qiu L, Zheng H, Li W, Han Y. GmST1, which encodes a sulfotransferase, confers resistance to soybean mosaic virus strains G2 and G3. PLANT, CELL & ENVIRONMENT 2021; 44:2777-2792. [PMID: 33866595 DOI: 10.1111/pce.14066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/23/2021] [Accepted: 04/07/2021] [Indexed: 05/27/2023]
Abstract
Soybean mosaic virus (SMV) is one of the most widespread and devastating viral diseases worldwide. The genetic architecture of qualitative resistance to SMV in soybean remains unclear. Here, the Rsvg2 locus was identified as underlying soybean resistance to SMV by genome-wide association and linkage analyses. Fine mapping results showed that soybean resistance to SMV strains G2 and G3 was controlled by a single dominant gene, GmST1, on chromosome 13, encoding a sulfotransferase (SOT). A key variation at position 506 in the coding region of GmST1 associated with the structure of the encoded SOT and changed SOT activity levels between RSVG2-S and RSVG2-R alleles. In RSVG2-S allele carrier "Hefeng25", the overexpression of GmST1 carrying the RSVG2-R allele from the SMV-resistant line "Dongnong93-046" conferred resistance to SMV strains G2 and G3. Compared to Hefeng25, the accumulation of SMV was decreased in transgenic plants carrying the RSVG2-R allele. SMV infection differentiated both the accumulation of jasmonates and expression patterns of genes involved in jasmonic acid (JA) signalling, biosynthesis and catabolism in RSVG2-R and RSVG2-S allele carriers. This characterization of GmST1 suggests a new scenario explaining soybean resistance to SMV.
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Affiliation(s)
- Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Yan Jing
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Zhenghui Luo
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Sainan Gao
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
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Soler-Garzón A, McClean PE, Miklas PN. Genome-Wide Association Mapping of bc-1 and bc-u Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to Bean Common Mosaic Necrosis Virus in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:699569. [PMID: 34267774 PMCID: PMC8277298 DOI: 10.3389/fpls.2021.699569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 05/17/2023]
Abstract
Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean (Phaseolus vulgaris L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million single-nucleotide polymorphisms (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for bc-1. These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (Glycine max). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for bc-u. bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for bc-1 and bc-u and new markers for I and bc-3 genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F3 families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele bc-1 for the Bc-1 locus, and differential expression of the allele is based on presence vs. absence of bc-u; (ii) bc-1 exhibits dominance and incomplete dominance; (iii) bc-1 alone confers resistance to NL-8; (iv) bc-u was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol bc-u d to reflect this change; (v) bc-u d alone delays susceptible symptoms, and when combined with bc-1 enhanced resistance to NL-3; and (vi) bc-u d is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean.
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Affiliation(s)
- Alvaro Soler-Garzón
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Prosser, WA, United States
- *Correspondence: Phillip N. Miklas, , orcid.org/0000-0002-6636-454X
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Zhang P, Du H, Wang J, Pu Y, Yang C, Yan R, Yang H, Cheng H, Yu D. Multiplex CRISPR/Cas9-mediated metabolic engineering increases soya bean isoflavone content and resistance to soya bean mosaic virus. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1384-1395. [PMID: 31769589 PMCID: PMC7206993 DOI: 10.1111/pbi.13302] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 11/18/2019] [Indexed: 05/18/2023]
Abstract
Isoflavonoids, which include a variety of secondary metabolites, are derived from the phenylpropanoid pathway and are distributed predominantly in leguminous plants. These compounds play a critical role in plant-environment interactions and are beneficial to human health. Isoflavone synthase (IFS) is a key enzyme in isoflavonoid synthesis and shares a common substrate with flavanone-3-hydroxylase (F3H) and flavone synthase II (FNS II). In this study, CRISPR/Cas9-mediated multiplex gene-editing technology was employed to simultaneously target GmF3H1, GmF3H2 and GmFNSII-1 in soya bean hairy roots and plants. Various mutation types and frequencies were observed in hairy roots. Higher mutation efficiencies were found in the T0 transgenic plants, with a triple gene mutation efficiency of 44.44%, and these results of targeted mutagenesis were stably inherited in the progeny. Metabolomic analysis of T0 triple-mutants leaves revealed significant improvement in isoflavone content. Compared with the wild type, the T3 generation homozygous triple mutants had approximately twice the leaf isoflavone content, and the soya bean mosaic virus (SMV) coat protein content was significantly reduced by one-third after infection with strain SC7, suggesting that increased isoflavone content enhanced the leaf resistance to SMV. The isoflavone content in the seeds of T2 triple mutants was also significantly increased. This study provides not only materials for the improvement of soya bean isoflavone content and resistance to SMV but also a simple system to generate multiplex mutations in soya bean, which may be beneficial for further breeding and metabolic engineering.
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Affiliation(s)
- Peipei Zhang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hongyang Du
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural ScienceHefeiChina
| | - Jiao Wang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Yixiang Pu
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Changyun Yang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Rujuan Yan
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hui Yang
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Hao Cheng
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Deyue Yu
- National Center for Soybean ImprovementNational Key Laboratory of Crop Genetics and Germplasm EnhancementJiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
- School of Life SciencesGuangzhou UniversityGuangzhouChina
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