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Aoyagi LN, Ferreira EGC, da Silva DCG, Dos Santos AB, Avelino BB, Lopes-Caitar VS, de Oliveira MF, Abdelnoor RV, de Souto ER, Arias CA, Belzile F, Marcelino-Guimarães FC. Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association. BMC PLANT BIOLOGY 2024; 24:743. [PMID: 39095733 PMCID: PMC11297723 DOI: 10.1186/s12870-024-05454-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Soybean is a crucial crop for the Brazilian economy, but it faces challenges from the biotrophic fungus Phakopsora pachyrhizi, which causes Asian Soybean Rust (ASR). In this study, we aimed to identify SNPs associated with resistance within the Rpp1 locus, which is effective against Brazilian ASR populations. We employed GWAS and re-sequencing analyzes to pinpoint SNP markers capable of differentiating between soybean accessions harboring the Rpp1, Rpp1-b and other alternative alleles in the Rpp1 locus and from susceptible soybean cultivars. Seven SNP markers were found to be associated with ASR resistance through GWAS, with three of them defining haplotypes that efficiently distinguished the accessions based on their ASR resistance and source of the Rpp gene. These haplotypes were subsequently validated using a bi-parental population and a diverse set of Rpp sources, demonstrating that the GWAS markers co-segregate with ASR resistance. We then examined the presence of these haplotypes in a diverse set of soybean genomes worldwide, finding a few new potential sources of Rpp1/Rpp1-b. Further genomic sequence analysis revealed nucleotide differences within the genes present in the Rpp1 locus, including the ULP1-NBS-LRR genes, which are potential R gene candidates. These results provide valuable insights into ASR resistance in soybean, thus helping the development of resistant soybean varieties through genetic breeding programs.
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Affiliation(s)
- Luciano Nobuhiro Aoyagi
- National Agriculture and Food Research Organization (NARO), 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan
- Maringá State University (UEM), Colombo Avenue, No. 5790, Maringá, PR, Brazil
| | | | - Danielle C Gregorio da Silva
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - Adriana Brombini Dos Santos
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - Bruna Barbosa Avelino
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | | | - Marcelo Fernandes de Oliveira
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - Ricardo V Abdelnoor
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | | | - Carlos Arrabal Arias
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil
| | - François Belzile
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Francismar C Marcelino-Guimarães
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, Londrina, PR, Brazil.
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Clevinger EM, Biyashev R, Schmidt C, Song Q, Batnini A, Bolaños-Carriel C, Robertson AE, Dorrance AE, Saghai Maroof MA. Comparison of Rps loci toward isolates, singly and combined inocula, of Phytophthora sojae in soybean PI 407985, PI 408029, PI 408097, and PI424477. FRONTIERS IN PLANT SCIENCE 2024; 15:1394676. [PMID: 39011302 PMCID: PMC11246922 DOI: 10.3389/fpls.2024.1394676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/05/2024] [Indexed: 07/17/2024]
Abstract
For soybean, novel single dominant Resistance to Phytophthora sojae (Rps) genes are sought to manage Phytophthora root and stem rot. In this study, resistance to P. sojae was mapped individually in four recombinant inbred line (RIL) populations derived from crosses of the susceptible cultivar Williams with PI 407985, PI 408029, PI 408097, and PI424477 previously identified as putative novel sources of disease resistance. Each population was screened for resistance with five to seven isolates of P. sojae separately over multiple F7-F10 generations. Additionally, three of the populations were screened with inoculum from the combination of three P. sojae isolates (PPR), which comprised virulence to 14 Rps genes. Over 2,300 single-nucleotide polymorphism markers were used to construct genetic maps in each population to identify chromosomal regions associated with resistance to P. sojae. Resistance segregated as one or two genes to the individual isolates and one gene toward PPR in each population and mapped to chromosomes 3, 13, or 18 in one or more of the four RIL populations. Resistance to five isolates mapped to the same chromosome 3 region are as follows: OH7 (PI 424477 and PI408029), OH12168, OH7/8, PPR (PI 407985), and 1.S.1.1 (PI408029). The resistance regions on chromosome 13 also overlapped for OH1, OH25, OH-MIA (PI424477), PPR (PI 424477, PI 407985, and PI 408097), PPR and OH0217 (PI 408097), and OH4 (PI 408029), but were distinct for each population suggesting multiple genes confer resistance. Two regions were identified on chromosome 18 but all appear to map to known loci; notably, resistance to the combined inoculum (PPR) did not map at this locus. However, there are putative new alleles in three of four populations, three on chromosome 3 and two on chromosome 13 based on mapping location but also known virulence in the isolate used. This characterization of all the Rps genes segregating in these populations to these isolates will be informative for breeding, but the combined inoculum was able to map a novel loci. Furthermore, within each of these P. sojae isolates, there was virulence to more than the described Rps genes, and the effectiveness of the novel genes requires testing in larger populations.
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Affiliation(s)
- Elizabeth M Clevinger
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Ruslan Biyashev
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Clarice Schmidt
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, Department of Agriculture, Beltsville, MD, United States
| | - Amine Batnini
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | | | - Alison E Robertson
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA, United States
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - M A Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Liu J, Wang L, Jiang S, Wang Z, Li H, Wang H. Mining of Minor Disease Resistance Genes in V. vinifera Grapes Based on Transcriptome. Int J Mol Sci 2023; 24:15311. [PMID: 37894991 PMCID: PMC10607095 DOI: 10.3390/ijms242015311] [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: 09/13/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Intraspecific recurrent selection in V. vinifera is an effective method for grape breeding with high quality and disease resistance. The core theory of this method is the substitution accumulation of multi-genes with low disease resistance. The discovery of multi-genes for disease resistance in V. vinifera may provide a molecular basis for breeding for disease resistance in V. vinifera. In this study, resistance to downy mildew was identified, and genetic analysis was carried out in the intraspecific crossing population of V. vinifera (Ecolly × Dunkelfelder) to screen immune, highly resistant and disease-resistant plant samples; transcriptome sequencing and differential expression analysis were performed using high-throughput sequencing. The results showed that there were 546 differential genes (194 up-regulated and 352 down-regulated) in the immune group compared to the highly resistant group, and 199 differential genes (50 up-regulated and 149 down-regulated) in the highly resistant group compared to the resistant group, there were 103 differential genes (54 up-regulated and 49 down-regulated) in the immune group compared to the resistant group. KEGG analysis of differentially expressed genes in the immune versus high-resistance group. The pathway is mainly concentrated in phenylpropanoid biosynthesis, starch and sucrose metabolism, MAPK signaling pathway-plant, carotenoid biosyn-thesis and isoquinoline alkaloid biosynthesis. The differential gene functions of immune and resistant, high-resistant and resistant combinations were mainly enriched in plant-pathogen interaction pathway. Through the analysis of disease resistance-related genes in each pathway, the potential minor resistance genes in V. vinifera were mined, and the accumulation of minor resistance genes was analyzed from the molecular level.
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Affiliation(s)
- Junli Liu
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Liang Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Shan Jiang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Zhilei Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
| | - Hua Li
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
| | - Hua Wang
- College of Enology, Northwest A&F University, Xianyang 712100, China; (J.L.); (L.W.); (S.J.); (Z.W.)
- China Wine Industry Technology Institute, Yinchuan 750021, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang 712100, China
- Engineering Research Center for Viti-Viniculture, National Forestry and Grassland Administration, Xianyang 712100, China
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Wang S, Zhang X, Zhang Z, Chen Y, Tian Q, Zeng D, Xu M, Wang Y, Dong S, Ma Z, Wang Y, Zheng X, Ye W. Fusarium-produced vitamin B 6 promotes the evasion of soybean resistance by Phytophthora sojae. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2204-2217. [PMID: 37171031 DOI: 10.1111/jipb.13505] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Plants can be infected by multiple pathogens concurrently in natural systems. However, pathogen-pathogen interactions have rarely been studied. In addition to the oomycete Phytophthora sojae, fungi such as Fusarium spp. also cause soybean root rot. In a 3-year field investigation, we discovered that P. sojae and Fusarium spp. frequently coexisted in diseased soybean roots. Out of 336 P. sojae-soybean-Fusarium combinations, more than 80% aggravated disease. Different Fusarium species all enhanced P. sojae infection when co-inoculated on soybean. Treatment with Fusarium secreted non-proteinaceous metabolites had an effect equal to the direct pathogen co-inoculation. By screening a Fusarium graminearum mutant library, we identified Fusarium promoting factor of Phytophthora sojae infection 1 (Fpp1), encoding a zinc alcohol dehydrogenase. Fpp1 is functionally conserved in Fusarium and contributes to metabolite-mediated infection promotion, in which vitamin B6 (VB6) produced by Fusarium is key. Transcriptional and functional analyses revealed that Fpp1 regulates two VB6 metabolism genes, and VB6 suppresses expression of soybean disease resistance-related genes. These results reveal that co-infection with Fusarium promotes loss of P. sojae resistance in soybean, information that will inform the sustainable use of disease-resistant crop varieties and provide new strategies to control soybean root rot.
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Affiliation(s)
- Shuchen Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyi Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Yun Chen
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qing Tian
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Dandan Zeng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Miao Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhonghua Ma
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
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Hale B, Ratnayake S, Flory A, Wijeratne R, Schmidt C, Robertson AE, Wijeratne AJ. Gene regulatory network inference in soybean upon infection by Phytophthora sojae. PLoS One 2023; 18:e0287590. [PMID: 37418376 PMCID: PMC10328377 DOI: 10.1371/journal.pone.0287590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/07/2023] [Indexed: 07/09/2023] Open
Abstract
Phytophthora sojae is a soil-borne oomycete and the causal agent of Phytophthora root and stem rot (PRR) in soybean (Glycine max [L.] Merrill). Yield losses attributed to P. sojae are devastating in disease-conducive environments, with global estimates surpassing 1.1 million tonnes annually. Historically, management of PRR has entailed host genetic resistance (both vertical and horizontal) complemented by disease-suppressive cultural practices (e.g., oomicide application). However, the vast expansion of complex and/or diverse P. sojae pathotypes necessitates developing novel technologies to attenuate PRR in field environments. Therefore, the objective of the present study was to couple high-throughput sequencing data and deep learning to elucidate molecular features in soybean following infection by P. sojae. In doing so, we generated transcriptomes to identify differentially expressed genes (DEGs) during compatible and incompatible interactions with P. sojae and a mock inoculation. The expression data were then used to select two defense-related transcription factors (TFs) belonging to WRKY and RAV families. DNA Affinity Purification and sequencing (DAP-seq) data were obtained for each TF, providing putative DNA binding sites in the soybean genome. These bound sites were used to train Deep Neural Networks with convolutional and recurrent layers to predict new target sites of WRKY and RAV family members in the DEG set. Moreover, we leveraged publicly available Arabidopsis (Arabidopsis thaliana) DAP-seq data for five TF families enriched in our transcriptome analysis to train similar models. These Arabidopsis data-based models were used for cross-species TF binding site prediction on soybean. Finally, we created a gene regulatory network depicting TF-target gene interactions that orchestrate an immune response against P. sojae. Information herein provides novel insight into molecular plant-pathogen interaction and may prove useful in developing soybean cultivars with more durable resistance to P. sojae.
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Affiliation(s)
- Brett Hale
- Molecular Biosciences Graduate Program, Arkansas State University, State University, AR, United States of America
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
| | - Sandaruwan Ratnayake
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
| | - Ashley Flory
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
| | | | - Clarice Schmidt
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States of America
| | - Alison E. Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States of America
| | - Asela J. Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, United States of America
- College of Science and Mathematics, Arkansas State University, State University, AR, United States of America
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Chandra S, Choudhary M, Bagaria PK, Nataraj V, Kumawat G, Choudhary JR, Sonah H, Gupta S, Wani SH, Ratnaparkhe MB. Progress and prospectus in genetics and genomics of Phytophthora root and stem rot resistance in soybean ( Glycine max L.). Front Genet 2022; 13:939182. [PMID: 36452161 PMCID: PMC9702362 DOI: 10.3389/fgene.2022.939182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/21/2022] [Indexed: 09/16/2023] Open
Abstract
Soybean is one of the largest sources of protein and oil in the world and is also considered a "super crop" due to several industrial advantages. However, enhanced acreage and adoption of monoculture practices rendered the crop vulnerable to several diseases. Phytophthora root and stem rot (PRSR) caused by Phytophthora sojae is one of the most prevalent diseases adversely affecting soybean production globally. Deployment of genetic resistance is the most sustainable approach for avoiding yield losses due to this disease. PRSR resistance is complex in nature and difficult to address by conventional breeding alone. Genetic mapping through a cost-effective sequencing platform facilitates identification of candidate genes and associated molecular markers for genetic improvement against PRSR. Furthermore, with the help of novel genomic approaches, identification and functional characterization of Rps (resistance to Phytophthora sojae) have also progressed in the recent past, and more than 30 Rps genes imparting complete resistance to different PRSR pathotypes have been reported. In addition, many genomic regions imparting partial resistance have also been identified. Furthermore, the adoption of emerging approaches like genome editing, genomic-assisted breeding, and genomic selection can assist in the functional characterization of novel genes and their rapid introgression for PRSR resistance. Hence, in the near future, soybean growers will likely witness an increase in production by adopting PRSR-resistant cultivars. This review highlights the progress made in deciphering the genetic architecture of PRSR resistance, genomic advances, and future perspectives for the deployment of PRSR resistance in soybean for the sustainable management of PRSR disease.
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Affiliation(s)
| | | | - Pravin K. Bagaria
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | | | | | | | - Humira Sonah
- National Agri-Food Biotechnology Institute, Mohali, India
| | - Sanjay Gupta
- ICAR-Indian Institute of Soybean Research, Indore, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
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Lin F, Chhapekar SS, Vieira CC, Da Silva MP, Rojas A, Lee D, Liu N, Pardo EM, Lee YC, Dong Z, Pinheiro JB, Ploper LD, Rupe J, Chen P, Wang D, Nguyen HT. Breeding for disease resistance in soybean: a global perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3773-3872. [PMID: 35790543 PMCID: PMC9729162 DOI: 10.1007/s00122-022-04101-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/11/2022] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Sushil Satish Chhapekar
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Caio Canella Vieira
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Marcos Paulo Da Silva
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Dongho Lee
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Nianxi Liu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Esteban Mariano Pardo
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - Yi-Chen Lee
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Zhimin Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Jose Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ/USP), PO Box 9, Piracicaba, SP 13418-900 Brazil
| | - Leonardo Daniel Ploper
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - John Rupe
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Pengyin Chen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
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Lin X, Olave-Achury A, Heal R, Pais M, Witek K, Ahn HK, Zhao H, Bhanvadia S, Karki HS, Song T, Wu CH, Adachi H, Kamoun S, Vleeshouwers VGAA, Jones JDG. A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector. MOLECULAR PLANT 2022; 15:1457-1469. [PMID: 35915586 DOI: 10.1016/j.molp.2022.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Species of the genus Phytophthora, the plant killer, cause disease and reduce yields in many crop plants. Although many Resistance to Phytophthora infestans (Rpi) genes effective against potato late blight have been cloned, few have been cloned against other Phytophthora species. Most Rpi genes encode nucleotide-binding domain, leucine-rich repeat-containing (NLR) immune receptor proteins that recognize RXLR (Arg-X-Leu-Arg) effectors. However, whether NLR proteins can recognize RXLR effectors from multiple Phytophthora species has rarely been investigated. Here, we identified a new RXLR-WY effector AVRamr3 from P. infestans that is recognized by Rpi-amr3 from a wild Solanaceae species Solanum americanum. Rpi-amr3 associates with AVRamr3 in planta. AVRamr3 is broadly conserved in many different Phytophthora species, and the recognition of AVRamr3 homologs by Rpi-amr3 activates resistance against multiple Phytophthora pathogens, including the tobacco black shank disease and cacao black pod disease pathogens P. parasitica and P. palmivora. Rpi-amr3 is thus the first characterized resistance gene that acts against P. parasitica or P. palmivora. These findings suggest a novel path to redeploy known R genes against different important plant pathogens.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Marina Pais
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - He Zhao
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Shivani Bhanvadia
- Wageningen UR Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Vivianne G A A Vleeshouwers
- Wageningen UR Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK.
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9
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Li W, Liu M, Lai YC, Liu JX, Fan C, Yang G, Wang L, Liang WW, Di SF, Yu DY, Bi YD. Genome-Wide Association Study of Partial Resistance to P. sojae in Wild Soybeans from Heilongjiang Province, China. Curr Issues Mol Biol 2022; 44:3194-3207. [PMID: 35877445 PMCID: PMC9319971 DOI: 10.3390/cimb44070221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/02/2023] Open
Abstract
Phytophthora root rot (PRR) is a destructive disease of soybeans (Glycine max (L.) Merr) caused by Phytophthora sojae (P. sojae). The most effective way to prevent the disease is growing resistant or tolerant varieties. Partial resistance provides a more durable resistance against the pathogen compared to complete resistance. Wild soybean (Glycine soja Sieb. & Zucc.) seems to be an extraordinarily important gene pool for soybean improvement due to its high level of genetic variation. In this study, 242 wild soybean germplasms originating from different regions of Heilongjiang province were used to identify resistance genes to P. sojae race 1 using a genome-wide association study (GWAS). A total of nine significant SNPs were detected, repeatedly associated with P. sojae resistance and located on chromosomes 1, 10, 12, 15, 17, 19 and 20. Among them, seven favorable allelic variations associated with P. sojae resistance were evaluated by a t-test. Eight candidate genes were predicted to explore the mechanistic hypotheses of partial resistance, including Glysoja.19G051583, which encodes an LRR receptor-like serine/threonine protein kinase protein, Glysoja.19G051581, which encodes a receptor-like cytosolic serine/threonine protein kinase protein. These findings will provide additional insights into the genetic architecture of P. sojae resistance in a large sample of wild soybeans and P. sojae-resistant breeding through marker-assisted selection.
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Affiliation(s)
- Wei Li
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Miao Liu
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - Yong-Cai Lai
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - Jian-Xin Liu
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - Chao Fan
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - Guang Yang
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - Ling Wang
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - Wen-Wei Liang
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - Shu-Feng Di
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
| | - De-Yue Yu
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China;
| | - Ying-Dong Bi
- Crop Tillage and Cultivation Institute of Heilongjiang Academy of Agricultural Sciences (HAAS), Harbin 150086, China; (W.L.); (M.L.); (Y.-C.L.); (J.-X.L.); (C.F.); (G.Y.); (L.W.); (W.-W.L.); (S.-F.D.)
- Correspondence:
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10
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Karhoff S, Vargas-Garcia C, Lee S, Mian MAR, Graham MA, Dorrance AE, McHale LK. Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance to Phytophthora sojae. FRONTIERS IN PLANT SCIENCE 2022; 13:893652. [PMID: 35774827 PMCID: PMC9237613 DOI: 10.3389/fpls.2022.893652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Phytophthora root and stem rot is a yield-limiting soybean disease caused by the soil-borne oomycete Phytophthora sojae. Although multiple quantitative disease resistance loci (QDRL) have been identified, most explain <10% of the phenotypic variation (PV). The major QDRL explaining up to 45% of the PV were previously identified on chromosome 18 and represent a valuable source of resistance for soybean breeding programs. Resistance alleles from plant introductions 427105B and 427106 significantly increase yield in disease-prone fields and result in no significant yield difference in fields with less to no disease pressure. In this study, high-resolution mapping reduced the QDRL interval to 3.1 cm, and RNA-seq analysis of near-isogenic lines (NILs) varying at QDRL-18 pinpointed a single gene of interest which was downregulated in inoculated NILs carrying the resistant allele compared to inoculated NILs with the susceptible allele. This gene of interest putatively encodes a serine-threonine kinase (STK) related to the AtCR4 family and may be acting as a susceptibility factor, based on the specific increase of jasmonic acid concentration in inoculated NILs. This work facilitates further functional analyses and marker-assisted breeding efforts by prioritizing candidate genes and narrowing the targeted region for introgression.
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Affiliation(s)
- Stephanie Karhoff
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
| | - Christian Vargas-Garcia
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - Sungwoo Lee
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - M. A. Rouf Mian
- United States Department of Agriculture-Agricultural Research Service, Soybean Research Unit, Raleigh, NC, United States
| | - Michelle A. Graham
- Department of Agronomy, Iowa State University, Ames, IA, United States
- United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Resources Unit, Ames, IA, United States
| | - Anne E. Dorrance
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
| | - Leah K. McHale
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Center for Soybean Research, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
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11
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de Ronne M, Santhanam P, Cinget B, Labbé C, Lebreton A, Ye H, Vuong TD, Hu H, Valliyodan B, Edwards D, Nguyen HT, Belzile F, Bélanger R. Mapping of partial resistance to Phytophthora sojae in soybean PIs using whole-genome sequencing reveals a major QTL. THE PLANT GENOME 2022; 15:e20184. [PMID: 34964282 DOI: 10.1002/tpg2.20184] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
In the last decade, more than 70 quantitative trait loci (QTL) related to soybean [Glycine max (L.) Merr.] partial resistance (PR) against Phytophthora sojae have been identified by genome-wide association studies (GWAS). However, most of them have either a minor effect on the resistance level or are specific to a single phenotypic variable or one isolate, thereby limiting their use in breeding programs. In this study, we have used an analytical approach combining (a) the phenotypic characterization of a diverse panel of 357 soybean accessions for resistance to P. sojae captured through a single variable, corrected dry weight; (b) a new hydroponic assay allowing the inoculation of a combination of P. sojae isolates covering the spectrum of commercially relevant Rps genes; and (c) exhaustive genotyping through whole-genome resequencing (WGS). This led to the identification of a novel P. sojae resistance QTL with a relatively major effect compared with the previously reported QTL. The QTL interval, spanning ∼500 kb on chromosome (Chr) 15, does not colocalize with previously reported QTL for P. sojae resistance. Plants carrying the favorable allele at this QTL were 60% more resistant. Eight genes were found to reside in the linkage disequilibrium (LD) block containing the peak single-nucleotide polymorphism (SNP) including Glyma.15G217100, which encodes a major latex protein (MLP)-like protein, with a functional annotation related to pathogen resistance. Expression analysis of Glyma.15G217100 indicated that it was nearly eight times more highly expressed in a group of plant introductions (PIs) carrying the resistant (R) allele compared with those carrying the susceptible (S) allele within a short period after inoculation. These results offer new and valuable options to develop improved soybean cultivars with broad resistance to P. sojae through marker-assisted selection.
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Affiliation(s)
| | | | | | | | | | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Tri D Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
- Dep. of Agriculture and Environmental Sciences, Lincoln Univ., Jefferson City, MO, 65101, USA
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, Univ. of Western Australia, Perth, Western Australia, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, 65211, USA
| | - François Belzile
- Dép. de phytologie, Univ. Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Univ. Laval, Québec, Canada
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12
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Hu Y, He Z, Kang Y, Cui L. Mutations in the Promoter and Coding Regions of Avr3a Cause Gain of Virulence of Phytophthora sojae to Rps3a in Soybean. Front Microbiol 2021; 12:759196. [PMID: 34858371 PMCID: PMC8632523 DOI: 10.3389/fmicb.2021.759196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Phytophthora sojae threatens soybean production worldwide, and the cultivation of soybean cultivars carrying Rps genes is the most effective way to control this pathogen. However, DNA mutations in the Avr genes of P. sojae can escape recognization of the corresponding Rps genes, leading to the loss of soybean resistance. In this study, we investigated sequence polymorphism and transcript level of the Avr3a gene in Chinese isolates of P. sojae. Twenty-four mutations resulting in five unique Avr3a alleles were discovered in the Avr3a coding region from 32 P. sojae isolates. The Avr3a transcripts were detectable in the isolates containing Avr3a(I), Avr3a(II), Avr3a(III), and Avr3a(IV) but not in the isolates containing Avr3a(V). Promoter and 5'-UTR sequence analysis revealed eight unique mutations in the promoter region of Avr3a(V), suggesting that the mutations could result in the loss of Avr3a(V) transcription. Virulence tests indicated the isolates containing Avr3a(II) and Avr3a(IV) were virulent, suggesting that the mutations in the coding regions of Avr3a(II) and Avr3a(IV) caused the gain of virulence to Rps3a. Based on DNA mutations of Avr3a in virulent alleles, two SNP markers and one PCR-based marker were developed successfully for detecting the virulence of P. sojae isolates to Rps3a. These findings provide new insights into escape mechanisms of Avr3a and effective support for accurate pathotype identification of P. sojae using molecular methods.
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Affiliation(s)
- Yanhong Hu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Zhihua He
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Yebin Kang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Linkai Cui
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
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13
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Chen L, Wang W, Ping J, Fitzgerald JC, Cai G, Clark CB, Aggarwal R, Ma J. Identification and molecular mapping of Rps14, a gene conferring broad-spectrum resistance to Phytophthora sojae in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3863-3872. [PMID: 34370048 DOI: 10.1007/s00122-021-03933-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE A soybean landrace carries broad-spectrum resistance to Phytophthora sojae, which is conferred by a single gene, designated Rps14, on the short arm of chromosome 3. Phytophthora sojae is the causative agent for Phytophthora root and stem rot in soybean [Glycine max (L.) Merr.] and can be managed by deployment of resistance to P. sojae (Rps) genes. PI 340,029 is a soybean landrace carrying broad-spectrum resistance to the pathogen. Analysis of an F2 population derived from a cross between PI 340,029 and a susceptible cultivar 'Williams' reveals that the resistance to P. sojae race 1 is conferred by a single gene, designated Rps14, which was initially mapped to a 4.5-cM region on the short arm of chromosome 3 by bulked segregant analysis (BSA), and subsequently narrowed to a 1.48 cM region corresponding to 229-kb in the Williams 82 reference genome (Wm82 v2.a1), using F3:4 families derived from the F2 population. Further analysis indicates that the broad-spectrum resistance carried by PI 340,029 is fully attributable to Rps14. The genomic sequences corresponding to the defined Rps14 region from a set of diverse soybean varieties exhibit drastic NBS-LRR gene copy number variation, ranging from 3 to 17 copies. Ultimate isolation of Rps14 would be critical for precise selection and deployment of the gene for soybean protection.
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Affiliation(s)
- Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Jieqing Ping
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- Seed Technologies and Analytics, BASF Corporation, Morrisville, NC, 27560, USA
| | - Joshua C Fitzgerald
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- Virginia Agricultural Research and Extension Centers, Virginia Polytechnic Institute and State University, Warsaw, VA, 22572, USA
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, USDA, ARS, West Lafayette, IN, 47907, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Rajat Aggarwal
- Research and Development, Corteva AgriscienceTM, Johnston, IA, 50131, USA.
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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14
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Sahoo DK, Das A, Huang X, Cianzio S, Bhattacharyya MK. Tightly linked Rps12 and Rps13 genes provide broad-spectrum Phytophthora resistance in soybean. Sci Rep 2021; 11:16907. [PMID: 34413429 PMCID: PMC8377050 DOI: 10.1038/s41598-021-96425-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
The Phytophtora root and stem rot is a serious disease in soybean. It is caused by the oomycete pathogen Phytophthora sojae. Growing Phytophthora resistant cultivars is the major method of controlling this disease. Resistance is race- or gene-specific; a single gene confers immunity against only a subset of the P. sojae isolates. Unfortunately, rapid evolution of new Phytophthora sojae virulent pathotypes limits the effectiveness of an Rps ("resistance to Phytophthora sojae") gene to 8-15 years. The current study was designed to investigate the effectiveness of Rps12 against a set of P. sojae isolates using recombinant inbred lines (RILs) that contain recombination break points in the Rps12 region. Our study revealed a unique Rps gene linked to the Rps12 locus. We named this novel gene as Rps13 that confers resistance against P. sojae isolate V13, which is virulent to recombinants that contains Rps12 but lack Rps13. The genetic distance between the two Rps genes is 4 cM. Our study revealed that two tightly linked functional Rps genes with distinct race-specificity provide broad-spectrum resistance in soybean. We report here the molecular markers for incorporating the broad-spectrum Phytophthora resistance conferred by the two Rps genes in commercial soybean cultivars.
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Affiliation(s)
- Dipak K Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Anindya Das
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA
| | - Xiaoqiu Huang
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA
| | - Silvia Cianzio
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
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15
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Ding J, Liu C, Zheng Q, Cai W. A new method of co-author credit allocation based on contributor roles taxonomy: proof of concept and evaluation using papers published in PLOS ONE. Scientometrics 2021. [DOI: 10.1007/s11192-021-04075-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Van K, Rolling W, Biyashev RM, Matthiesen RL, Abeysekara NS, Robertson AE, Veney DJ, Dorrance AE, McHale LK, Saghai Maroof MA. Mining germplasm panels and phenotypic datasets to identify loci for resistance to Phytophthora sojae in soybean. THE PLANT GENOME 2021; 14:e20063. [PMID: 33200586 DOI: 10.1002/tpg2.20063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Phytophthora sojae causes Phytophthora root and stem rot of soybean and has been primarily managed through deployment of qualitative Resistance to P. sojae genes (Rps genes). The effectiveness of each individual or combination of Rps gene(s) depends on the diversity and pathotypes of the P. sojae populations present. Due to the complex nature of P. sojae populations, identification of more novel Rps genes is needed. In this study, phenotypic data from previous studies of 16 panels of plant introductions (PIs) were analyzed. Panels 1 and 2 consisted of 448 Glycine max and 520 G. soja, which had been evaluated for Rps gene response with a combination of P. sojae isolates. Panels 3 and 4 consisted of 429 and 460 G. max PIs, respectively, which had been evaluated using individual P. sojae isolates with complex virulence pathotypes. Finally, Panels 5-16 (376 G. max PIs) consisted of data deposited in the USDA Soybean Germplasm Collection from evaluations with 12 races of P. sojae. Using these panels, genome-wide association (GWA) analyses were carried out by combining phenotypic and SoySNP50K genotypic data. GWA models identified two, two, six, and seven novel Rps loci with Panels 1, 2, 3, and 4, respectively. A total of 58 novel Rps loci were identified using Panels 5-16. Genetic and phenotypic dissection of these loci may lead to the characterization of novel Rps genes that can be effectively deployed in new soybean cultivars against diverse P. sojae populations.
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Affiliation(s)
- Kyujung Van
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - William Rolling
- Center for Applied Plant Sciences, Ohio State University, Columbus, OH, 43210, USA
| | - Ruslan M Biyashev
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rashelle L Matthiesen
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Nilwala S Abeysekara
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Alison E Robertson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Deloris J Veney
- Department of Plant Pathology, Ohio State University, Wooster, OH, 44691, USA
| | - Anne E Dorrance
- Center for Applied Plant Sciences, Ohio State University, Columbus, OH, 43210, USA
- Department of Plant Pathology, Ohio State University, Wooster, OH, 44691, USA
- Center for Soybean Research, Ohio State University, Wooster, OH, 44691, USA
| | - Leah K McHale
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
- Center for Applied Plant Sciences, Ohio State University, Columbus, OH, 43210, USA
- Center for Soybean Research, Ohio State University, Wooster, OH, 44691, USA
| | - M A Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
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17
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Jang IH, Kang IJ, Kim JM, Kang ST, Jang YE, Lee S. Genetic Mapping of a Resistance Locus to Phytophthora sojae in the Korean Soybean Cultivar Daewon. THE PLANT PATHOLOGY JOURNAL 2020; 36:591-599. [PMID: 33312094 PMCID: PMC7721532 DOI: 10.5423/ppj.oa.09.2020.0173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 05/19/2023]
Abstract
Phytophthora root and stem rot reduce soybean yields worldwide. The use of R-gene type resistance is currently crucial for protecting soybean production. The present study aimed to identify the genomic location of a gene conferring resistance to Phytophthora sojae isolate 2457 in the recombinant inbred line population developed by a cross of Daepung × Daewon. Single-marker analysis identified 20 single nucleotide polymorphisms associated with resistance to the P. sojae isolate 2457, which explained ~67% of phenotypic variance. Daewon contributed a resistance allele for the locus. This region is a well-known location for Rps1 and Rps7. The present study is the first, however, to identify an Rps gene locus from a major soybean variety cultivated in South Korea. Linkage analysis also identified a 573 kb region on chromosome 3 with high significance (logarithm of odds = 13.7). This genomic region was not further narrowed down due to lack of recombinants within the interval. Based on the latest soybean genome, ten leucine-rich repeat coding genes and four serine/threonine protein kinase-coding genes are annotated in this region, which all are well-known types of genes for conferring disease resistance in crops. These genes would be candidates for molecular characterization of the resistance in further studies. The identified R-gene locus would be useful in developing P. sojae resistant varieties in the future. The results of the present study provide foundational knowledge for researchers who are interested in soybean-P. sojae interaction.
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Affiliation(s)
- Ik-Hyun Jang
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 3434, Korea
| | - In Jeong Kang
- Department of Central Area Crop Science, National Institute of Crop Science, Suwon 16613, Korea
| | - Ji-Min Kim
- Department of Crop Science and Biotechnology, College of Bioresource Science, Dankook University, Cheonan 1116, Korea
| | - Sung-Taeg Kang
- Department of Crop Science and Biotechnology, College of Bioresource Science, Dankook University, Cheonan 1116, Korea
| | - Young Eun Jang
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 3434, Korea
| | - Sungwoo Lee
- Department of Crop Science, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 3434, Korea
- Corresponding author. Phone) +82-42-821-5727 , FAX) +82-42-822-2631, E-mail) , ORCID, Sungwoo Lee, https://orcid.org/0000-0003-3564-236
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18
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Zhong C, Sun S, Zhang X, Duan C, Zhu Z. Fine Mapping, Candidate Gene Identification and Co-segregating Marker Development for the Phytophthora Root Rot Resistance Gene RpsYD25. Front Genet 2020; 11:799. [PMID: 32849803 PMCID: PMC7399351 DOI: 10.3389/fgene.2020.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/03/2020] [Indexed: 12/18/2022] Open
Abstract
Phytophthora root rot (PRR) caused by Phytophthora sojae is a serious disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Rps genes. Soybean cultivar Yudou25 can effectively resist pathotypes of P. sojae in China. Previous studies have mapped the Rps gene in Yudou25, RpsYD25, on chromosome 3. In this study, at first RpsYD25 was located between SSR markers Satt1k3 (2.2 cM) and BARCSOYSSR_03_0253 (4.5 cM) by using an F2:3 population containing 165 families derived from Zaoshu18 and Yudou25. Then the recombination sites were identified in 1127 F3:4 families derived from Zaoshu18 and Yudou25 using the developed PCR-based SNP, InDel and SSR markers, and RpsYD25 was finely mapped in the a 101.3 kb genomic region. In this region, a zinc ion binding and nucleic acid binding gene Glyma.03g034700 and two NBS-LRR genes Glyma.03g034800 and Glyma.03g034900 were predicted as candidate genes of RpsYD25, and five co-segregated SSR markers with RpsYD25 were identified and validated to be diagnostic markers. Combined with the resistance reaction to multiple P. sojae isolates, seven of 178 soybean genotypes were detected to contain RpsYD25 using the five co-segregated SSR markers. The soybean genotypes carrying RpsYD25 and the developed co-segregated markers can be effectively applied in the breeding for P. sojae resistance in China.
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Affiliation(s)
- Chao Zhong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Suli Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuecui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhendong Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Ramalingam J, Alagarasan G, Savitha P, Lydia K, Pothiraj G, Vijayakumar E, Sudhagar R, Singh A, Vedna K, Vanniarajan C. Improved host-plant resistance to Phytophthora rot and powdery mildew in soybean (Glycine max (L.) Merr.). Sci Rep 2020; 10:13928. [PMID: 32811867 PMCID: PMC7434881 DOI: 10.1038/s41598-020-70702-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/10/2020] [Indexed: 11/08/2022] Open
Abstract
Soybean is an important oilseed cum vegetable crop, susceptible to various biotic stresses which is attributed to recent decline in crop productivity. The emergence of virulent biotypes/strains of different plant pathogens necessitates the development of new crop varieties with enhanced host resistance mechanisms. Pyramiding of multiple disease-resistant genes is one of the strategies employed to develop durable disease-resistant cultivars to the prevailing and emerging biotypes of pathogens. The present study, reports the successful introgression of two major R-genes, including Rps2 (Phytophthora rot resistance), Rmd-c (complete-powdery mildew resistance) and effective nodulating gene (rj2) through functional Marker-Assisted Backcross Breeding (MABB) in the genetic background of well-adapted and high yielding soybean varieties, CO 3 and JS 335. We have identified several promising introgressed lines with enhanced resistance to Phytophthora rot and powdery mildew. The improved soybean lines have exhibited medium to high level of resistance against powdery mildew and Phytophthora rot as well as displayed effective nodulation capacity. Our study has proven the generation of resistant genotypes to realize the potential of MABB for achieving host plant resistance in soybean. The improved lines developed can greatly assist the soybean breeding programs in India and other soybean growing countries for evolving disease-resistant varieties.
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Affiliation(s)
- Jegadeesan Ramalingam
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.
- Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India.
| | - Ganesh Alagarasan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Palanisamy Savitha
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Kelsey Lydia
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Govindan Pothiraj
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Eswaramoorthy Vijayakumar
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Rajaprakasam Sudhagar
- Centre for Plant Breeding and Genetics, Department of Pulses, Tamil Nadu Agricultural University, Coimbatore, India
| | - Amar Singh
- Department of Plant Pathology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Kumari Vedna
- Department of Plant Breeding and Genetics, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
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20
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Yang J, Zheng S, Wang X, Ye W, Zheng X, Wang Y. Identification of Resistance Genes to Phytophthora sojae in Domestic Soybean Cultivars from China Using Particle Bombardment. PLANT DISEASE 2020; 104:1888-1893. [PMID: 32396460 DOI: 10.1094/pdis-10-19-2201-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phytophthora root and stem rot caused by Phytophthora sojae is a destructive disease that afflicts soybean plants throughout the world. The use of resistant soybean cultivars is the primary means of managing this disease, as well as the most effective and economical approach. There are abundant soybean germplasm resources in China that could be deployed for breeding programs; however, the resistance genes (Rps genes) in most cultivars are unknown, leading to uncertainty concerning which are resistant cultivars for use. The resistance genes Rps1a, Rps1c, and Rps1k prevent root and stem rot caused by most P. sojae isolates within a Chinese field population. This study identified three Rps genes in Chinese domestic soybean cultivars using three related avirulence genes by particle bombardment. The complex genetic diversity of soybean cultivars and P. sojae strains has made it difficult to define single Rps genes without molecular involvement. Gene cobombardment is a method for identifying Rps genes quickly and specifically. We showed that cultivars Dongnong 60 and Henong 72 contained Rps1a, while Hedou 19, Henong 76, 75-3, Wandou 21020, Zheng 196, Wandou 28, Heinong 71, and Wandou 29 all contained Rps1c. The cultivars Jidou 12, Henong 72, Heinong 71, and Wandou 29 contained Rps1k. The cultivar Henong 72 contained both Rps1a and Rps1k, while Wandou 29 and Heinong 71 contained both Rps1c and Rps1k. We then evaluated the phenotype of 11 domestic soybean cultivars reacting to P. sojae using the isolates P6497 and Ps1. The 11 domestic cultivars were all resistant to P6497 and Ps1. This research provides source materials and parent plant strains containing Rps1a, Rps1c, and Rps1k for soybean breeding programs.
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Affiliation(s)
- Jin Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Sujiao Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Xiaomen Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
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21
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Jiang B, Cheng Y, Cai Z, Li M, Jiang Z, Ma R, Yuan Y, Xia Q, Nian H. Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing. BMC Genomics 2020; 21:280. [PMID: 32245402 PMCID: PMC7126358 DOI: 10.1186/s12864-020-6668-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Phytophthora root rot (PRR) caused by Phytophthora sojae (P. sojae) is one of the most serious limitations to soybean production worldwide. The identification of resistance gene(s) and their incorporation into elite varieties is an effective approach for breeding to prevent soybean from being harmed by this disease. A valuable mapping population of 228 F8:11 recombinant inbred lines (RILs) derived from a cross of the resistant cultivar Guizao1 and the susceptible cultivar BRSMG68 and a high-density genetic linkage map with an average distance of 0.81 centimorgans (cM) between adjacent bin markers in this population were used to map and explore candidate gene(s). RESULTS PRR resistance in Guizao1 was found to be controlled by a single Mendelian locus and was finely mapped to a 367.371-kb genomic region on chromosome 3 harbouring 19 genes, including 7 disease resistance (R)-like genes, in the reference Willliams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed that Glyma.03 g05300 was likely involved in PRR resistance. CONCLUSIONS These findings from the fine mapping of a novel Rps locus will serve as a basis for the cloning and transfer of resistance genes in soybean and the breeding of P. sojae-resistant soybean cultivars through marker-assisted selection.
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Affiliation(s)
- Bingzhi Jiang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Mu Li
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Ze Jiang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Ruirui Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Yeshan Yuan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI) Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 People’s Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
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22
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Rolling W, Lake R, Dorrance AE, McHale LK. Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions. PLoS One 2020; 15:e0227710. [PMID: 32196522 PMCID: PMC7083333 DOI: 10.1371/journal.pone.0227710] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/25/2019] [Indexed: 12/17/2022] Open
Abstract
Phytophthora sojae is one of the costliest soybean pathogens in the US. Quantitative disease resistance (QDR) is a vital part of Phytophthora disease management. In this study, QDR was measured in 478 and 495 plant introductions (PIs) towards P. sojae isolates OH.121 and C2.S1, respectively, in genome-wide association (GWA) analyses to identify genetic markers linked to QDR loci (QDRL). Populations were generated by sampling PIs from the US, the Republic of Korea, and the full collection of PIs maintained by the USDA. Additionally, a meta-analysis of QDRL reported from bi-parental studies was done to compare past and present findings. Twenty-four significant marker-trait associations were identified from the 478 PIs phenotyped with OH.121, and an additional 24 marker-trait associations were identified from the 495 PIs phenotyped with C2.S1. In total, 48 significant markers were distributed across 16 chromosomes and based on linkage analysis, represent a total of 44 QDRL. The majority of QDRL were identified with only one of the two isolates, and only a region on chromosome 13 was consistently identified. Regions on chromosomes 3, 13, and 17 were identified in previous GWA-analyses and were re-identified in this study. Five QDRL co-localized with P. sojae meta-QDRL identified from QDRL reported in previous biparental mapping studies. The remaining regions represent novel QDRL, in the soybean-P. sojae pathosystem and were primarily identified in germplasm from the Republic of Korea. Overall, the number of loci identified in this study highlights the complexity of QDR to P. sojae.
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Affiliation(s)
- William Rolling
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, Ohio, United States of America
| | - Rhiannon Lake
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
| | - Anne E. Dorrance
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Plant Pathology, The Ohio State University, Wooster, Ohio, United States of America
| | - Leah K. McHale
- Center for Applied Plant Science and Center for Soybean Research, The Ohio State University, Columbus, Ohio, United States of America
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, United States of America
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23
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Yang J, Ye W, Wang X, Ren L, Yao Y, Wang X, Wang Y, Dong S, Zheng X, Wang Y. An Improved Method for the Identification of Soybean Resistance to Phytophthora sojae Applied to Germplasm Resources from the Huanghuaihai and Dongbei Regions of China. PLANT DISEASE 2020; 104:408-413. [PMID: 31790644 DOI: 10.1094/pdis-01-19-0168-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora root and stem rot (PRR) caused by Phytophthora sojae is a destructive disease afflicting soybean. The use of resistant cultivars is the most effective method to combat PRR. PRR resistance was assessed in 223 soybean cultivars from Huanghuaihai and Dongbei, major soybean-producing regions in east central and northeastern China. To evaluate levels of soybean resistance to P. sojae, we used eight representative P. sojae isolates and a modified etiolated hypocotyl-slit inoculation method. The cultivars Wandou21020, Xu9302-A, Kedou10, and Lidi055 showed resistance to all eight isolates; 14 cultivars showed intermediate resistance to all eight P. sojae isolates, and 53 cultivars were resistant to seven isolates. Thirty-three cultivars (15%) were susceptible only to the highly virulent PsJS2 isolate, which is consistent with the reactions of the Chapman differential line that carries Rps3a. The diverse reaction patterns seen in germplasm from different regions (provinces/cities) in this study reflect the variety of PRR-resistant soybean sources in China. Our research indicates that sources of P. sojae resistance are present in the major soybean production areas of China. This study provides useful information for soybean breeding programs.
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Affiliation(s)
- Jin Yang
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Xiaomen Wang
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Linrong Ren
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Yan Yao
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Xiaoli Wang
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China
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24
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Cui X, Yan Q, Gan S, Xue D, Wang H, Xing H, Zhao J, Guo N. GmWRKY40, a member of the WRKY transcription factor genes identified from Glycine max L., enhanced the resistance to Phytophthora sojae. BMC PLANT BIOLOGY 2019; 19:598. [PMID: 31888478 PMCID: PMC6937711 DOI: 10.1186/s12870-019-2132-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 11/12/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND The WRKY proteins are a superfamily of transcription factors and members play essential roles in the modulation of diverse physiological processes, such as growth, development, senescence and response to biotic and abiotic stresses. However, the biological roles of the majority of the WRKY family members remains poorly understood in soybean relative to the research progress in model plants. RESULTS In this study, we identified and characterized GmWRKY40, which is a group IIc WRKY gene. Transient expression analysis revealed that the GmWRKY40 protein is located in the nucleus of plant cells. Expression of GmWRKY40 was strongly induced in soybean following infection with Phytophthora sojae, or treatment with methyl jasmonate, ethylene, salicylic acid, and abscisic acid. Furthermore, soybean hairy roots silencing GmWRKY40 enhanced susceptibility to P. sojae infection compared with empty vector transgenic roots. Moreover, suppression of GmWRKY40 decreased the accumulation of reactive oxygen species (ROS) and modified the expression of several oxidation-related genes. Yeast two-hybrid experiment combined with RNA-seq analysis showed that GmWRKY40 interacted with 8 JAZ proteins with or without the WRKY domain or zinc-finger domain of GmWRKY40, suggesting there were different interaction patterns among these interacted proteins. CONCLUSIONS Collectively, these results suggests that GmWRKY40 functions as a positive regulator in soybean plants response to P. sojae through modulating hydrogen peroxide accumulation and JA signaling pathway.
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Affiliation(s)
- Xiaoxia Cui
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qiang Yan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shuping Gan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dong Xue
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Haitang Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Han Xing
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jinming Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Na Guo
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
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25
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Kang IJ, Kang S, Jang IH, Jang YW, Shim HK, Heu S, Lee S. Identification of New Isolates of Phytophthora sojae and the Reactions of Korean Soybean Cultivars Following Hypocotyl Inoculation. THE PLANT PATHOLOGY JOURNAL 2019; 35:698-704. [PMID: 31832050 PMCID: PMC6901254 DOI: 10.5423/ppj.nt.09.2019.0249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 05/29/2023]
Abstract
Phytophthora root and stem rot (PRSR) caused by Phytophthora sojae is one of the most destructive diseases of soybean. PRSR recently became an issue as soybean cultivation in paddy fields increased in South Korea. The management of PRSR mainly involves R-gene-mediated resistance, however, little is known about the resistance in Korean cultivars. Major Korean soybean cultivars were investigated for the presence or absence of R-gene-mediated resistance to four P. sojae isolates, two of which were new isolates. Isolate-specific reactions were observed following P. sojae inoculation. Of 21 cultivars, 15-20 cultivars (71.4-95.2%) showed susceptible reaction for each isolate. Ten cultivars were susceptible to all the isolates, and six cultivars were identified to have R-gene-mediated resistance to one or two isolates. The results of this study would provide a framework for the discovery of resistant cultivars, development of new cultivars resistant to P. sojae, and investigation of pathogenic diversity of P. sojae population in South Korea.
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Affiliation(s)
- In Jeong Kang
- Division of Crop Cultivation and Environment Research, Department of Central Area Crop Science, National Institute of Crop Science, Suwon 16613,
Korea
| | - Sunjoo Kang
- Department of Crop Science, Chungnam National University, Daejeon 34134,
Korea
| | - Ik Hyun Jang
- Department of Crop Science, Chungnam National University, Daejeon 34134,
Korea
| | - Yun Woo Jang
- Department of Southern Area Crop Science, National Institute of Crop Science, Miryang 50424,
Korea
| | - Hyung Kwon Shim
- Division of Crop Cultivation and Environment Research, Department of Central Area Crop Science, National Institute of Crop Science, Suwon 16613,
Korea
| | - Sunggi Heu
- Division of Crop Cultivation and Environment Research, Department of Central Area Crop Science, National Institute of Crop Science, Suwon 16613,
Korea
| | - Sungwoo Lee
- Department of Crop Science, Chungnam National University, Daejeon 34134,
Korea
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26
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Zhebentyayeva TN, Sisco PH, Georgi LL, Jeffers SN, Perkins MT, James JB, Hebard FV, Saski C, Nelson CD, Abbott AG. Dissecting Resistance to Phytophthora cinnamomi in Interspecific Hybrid Chestnut Crosses Using Sequence-Based Genotyping and QTL Mapping. PHYTOPATHOLOGY 2019; 109:1594-1604. [PMID: 31287366 DOI: 10.1094/phyto-11-18-0425-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The soilborne oomycete Phytophthora cinnamomi-which causes root rot, trunk cankers, and stem lesions on an estimated 5,000 plant species worldwide-is a lethal pathogen of American chestnut (Castanea dentata) as well as many other woody plant species. P. cinnamomi is particularly damaging to chestnut and chinquapin trees (Castanea spp.) in the southern portion of its native range in the United States due to relatively mild climatic conditions that are conductive to disease development. Introduction of resistant genotypes is the most practical solution for disease management in forests because treatment with fungicides and eradication of the pathogen are neither practical nor economically feasible in natural ecosystems. Using backcross families derived from crosses of American chestnuts with two resistant Chinese chestnut cultivars Mahogany and Nanking, we constructed linkage maps and identified quantitative trait loci (QTLs) for resistance to P. cinnamomi that had been introgressed from these Chinese chestnut cultivars. In total, 957 plants representing five cohorts of three hybrid crosses were genotyped by sequencing and phenotyped by standardized inoculation and visual examination over a 6-year period from 2011 to 2016. Eight parental linkage maps comprising 7,715 markers were constructed, and 17 QTLs were identified on four linkage groups (LGs): LG_A, LG_C, LG_E, and LG_K. The most consistent QTLs were detected on LG_E in seedlings from crosses with both 'Mahogany' and 'Nanking' and LG_K in seedlings from 'Mahogany' crosses. Two consistent large and medium effect QTLs located ∼10 cM apart were present in the middle and at the lower end of LG_E; other QTLs were considered to have small effects. These results imply that the genetic architecture of resistance to P. cinnamomi in Chinese chestnut × American chestnut hybrid progeny may resemble the P. sojae-soybean pathosystem, with a few dominant QTLs along with quantitatively inherited partial resistance conferred by multiple small-effect QTLs.
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Affiliation(s)
- Tetyana N Zhebentyayeva
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802
- Clemson University Genomics and Computational Biology Laboratory, Clemson, SC 29634
| | - Paul H Sisco
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Laura L Georgi
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Steven N Jeffers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - M Taylor Perkins
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403
| | | | - Frederick V Hebard
- Meadowview Research Farms, The American Chestnut Foundation, Meadowview, VA 24361
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - C Dana Nelson
- Southern Institute of Forest Genetics, Southern Research Station, U.S. Department of Agriculture Forest Service, Saucier, MS 39574
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
| | - Albert G Abbott
- Forest Health Research and Education Center, University of Kentucky, Lexington, KY 40546
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27
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Zhong C, Li Y, Sun S, Duan C, Zhu Z. Genetic Mapping and Molecular Characterization of a Broad-spectrum Phytophthora sojae Resistance Gene in Chinese Soybean. Int J Mol Sci 2019; 20:E1809. [PMID: 31013701 PMCID: PMC6515170 DOI: 10.3390/ijms20081809] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 01/26/2023] Open
Abstract
Phytophthora root rot (PRR) causes serious annual soybean yield losses worldwide. The most effective method to prevent PRR involves growing cultivars that possess genes conferring resistance to Phytophthora sojae (Rps). In this study, QTL-sequencing combined with genetic mapping was used to identify RpsX in soybean cultivar Xiu94-11 resistance to all P. sojae isolates tested, exhibiting broad-spectrum PRR resistance. Subsequent analysis revealed RpsX was located in the 242-kb genomic region spanning the RpsQ locus. However, a phylogenetic investigation indicated Xiu94-11 carrying RpsX is distantly related to the cultivars containing RpsQ, implying RpsX and RpsQ have different origins. An examination of candidate genes revealed RpsX and RpsQ share common nonsynonymous SNP and a 144-bp insertion in the Glyma.03g027200 sequence encoding a leucine-rich repeat (LRR) region. Glyma.03g027200 was considered to be the likely candidate gene of RpsQ and RpsX. Sequence analyses confirmed that the 144-bp insertion caused by an unequal exchange resulted in two additional LRR-encoding fragments in the candidate gene. A marker developed based on the 144-bp insertion was used to analyze the genetic population and germplasm, and proved to be useful for identifying the RpsX and RpsQ alleles. This study implies that the number of LRR units in the LRR domain may be important for PRR resistance in soybean.
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Affiliation(s)
- Chao Zhong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yinping Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China.
| | - Suli Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Canxing Duan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhendong Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Pedley KF, Pandey AK, Ruck A, Lincoln LM, Whitham SA, Graham MA. Rpp1 Encodes a ULP1-NBS-LRR Protein That Controls Immunity to Phakopsora pachyrhizi in Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:120-133. [PMID: 30303765 DOI: 10.1094/mpmi-07-18-0198-fi] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phakopsora pachyrhizi is the causal agent of Asian soybean rust. Susceptible soybean plants infected by virulent isolates of P. pachyrhizi are characterized by tan-colored lesions and erumpent uredinia on the leaf surface. Germplasm screening and genetic analyses have led to the identification of seven loci, Rpp1 to Rpp7, that provide varying degrees of resistance to P. pachyrhizi (Rpp). Two genes, Rpp1 and Rpp1b, map to the same region on soybean chromosome 18. Rpp1 is unique among the Rpp genes in that it confers an immune response (IR) to avirulent P. pachyrhizi isolates. The IR is characterized by a lack of visible symptoms, whereas resistance provided by Rpp1b to Rpp7 results in red-brown foliar lesions. Rpp1 maps to a region spanning approximately 150 kb on chromosome 18 between markers Sct_187 and Sat_064 in L85-2378 (Rpp1), an isoline developed from Williams 82 and PI 200492 (Rpp1). To identify Rpp1, we constructed a bacterial artificial chromosome library from soybean accession PI 200492. Sequencing of the Rpp1 locus identified three homologous nucleotide binding site-leucine rich repeat (NBS-LRR) candidate resistance genes between Sct_187 and Sat_064. Each candidate gene is also predicted to encode an N-terminal ubiquitin-like protease 1 (ULP1) domain. Cosilencing of the Rpp1 candidates abrogated the immune response in the Rpp1 resistant soybean accession PI 200492, indicating that Rpp1 is a ULP1-NBS-LRR protein and plays a key role in the IR.
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Affiliation(s)
- Kerry F Pedley
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Ajay K Pandey
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
- 3 Iowa State University, Department of Plant Pathology and Microbiology, Ames, IA 50011, U.S.A
| | - Amy Ruck
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Lori M Lincoln
- 2 USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, U.S.A.; and
| | - Steven A Whitham
- 3 Iowa State University, Department of Plant Pathology and Microbiology, Ames, IA 50011, U.S.A
| | - Michelle A Graham
- 2 USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, U.S.A.; and
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Sukumaran A, McDowell T, Chen L, Renaud J, Dhaubhadel S. Isoflavonoid-specific prenyltransferase gene family in soybean: GmPT01, a pterocarpan 2-dimethylallyltransferase involved in glyceollin biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:966-981. [PMID: 30195273 DOI: 10.1111/tpj.14083] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 05/27/2023]
Abstract
Phytoalexin glyceollins are soybean-specific antimicrobial compounds that are derived from the isoflavonoid pathway. They are synthesized by soybean in response to extrinsic stress such as pathogen attack or injury, thereby conferring partial resistance if synthesized rapidly at the site of infection and at the required concentration. Soybean produces multiple forms of glyceollins that result from the differential prenylation reaction catalyzed by prenyltransferases (PTs) on either the C-2 or C-4 carbon of a pterocarpan glycinol. The soybean genome contains 77 PT-encoding genes (GmPTs) where at least 11 are (iso)flavonoid-specific. Transcript accumulation of five candidates GmPTs was increased in response to Phytophthora sojae infection, suggesting their role in phytoalexin synthesis. The induced GmPTs localize to plastids and display tissue-specific expression. We have in this study identified two additional GmPTs: an isoflavone dimethylallyltransferase 3 (IDT3); and a glycinol 2-dimethylallyl transferase GmPT01. GmPT01 prenylates (-)-glycinol at the C-2 position, localizes in the plastid, and exhibits root-specific gene expression. Furthermore, its expression is induced rapidly in response to stress, and is associated with a quantitative trait loci linked with resistance to P. sojae. Based on these results, we conclude that GmPT01 are possibly one of the loci involved in conferring partial resistance against stem and root rot disease in soybean.
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Affiliation(s)
- Arjun Sukumaran
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
| | - Ling Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
| | - Justin Renaud
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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30
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Zhu L, Zhou Y, Li X, Zhao J, Guo N, Xing H. Metabolomics Analysis of Soybean Hypocotyls in Response to Phytophthora sojae Infection. FRONTIERS IN PLANT SCIENCE 2018; 9:1530. [PMID: 30405667 PMCID: PMC6206292 DOI: 10.3389/fpls.2018.01530] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/28/2018] [Indexed: 05/03/2023]
Abstract
Soybean is one of the most important economic and oil crops across the world. Phytophthora root rot (PRR), caused by Phytophthora sojae (P. sojae), is a major disease in most soybean-growing regions worldwide. Here, we investigated metabolic changes in hypocotyls of two soybean lines, Nannong 10-1 (resistant line, R) and 06-070583 (susceptible line, S), at two time points (12 and 36 hpi) after P. sojae infection and metabolic differences between the R line and the S line. In total, 90 differentially accumulated metabolites (DAMs) were identified after P. sojae infection; the levels of 50 metabolites differed between the R line and the S line. There are 28 DAMs that not only differentially accumulated between the R line and the S line but also differentially accumulated after P. sojae infection. Based on the changes of these DAMs in response to P. sojae infection in different lines and at different timepoints, and the differences in the contents of these DAMs between the R line and the S line, we speculated that DAMs, including sugars (monosaccharides and oligosaccharides), organic acids (oxalic acid, cumic acid), amino acid derivatives, and other secondary metabolites (mannitol, octanal, hypoxanthine, and daidzein etc.) may participate in the metabolic-level defense response of soybean to P. sojae. In this study, an integrated pathway-level analysis of transcriptomics (obtained by RNA-Seq) and metabolomics data illustrated the poor connections and interdependencies between the metabolic and transcriptional responses of soybean to P. sojae infection. This work emphasizes the value of metabolomic studies of plant-pathogen interactions and paves the way for future research of critical metabolic determinants of the soybean-P. sojae interaction.
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Affiliation(s)
| | | | | | | | - Na Guo
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Han Xing
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
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31
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Arsenault-Labrecque G, Sonah H, Lebreton A, Labbé C, Marchand G, Xue A, Belzile F, Knaus BJ, Grünwald NJ, Bélanger RR. Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates. BMC Biol 2018; 16:80. [PMID: 30049268 PMCID: PMC6060493 DOI: 10.1186/s12915-018-0549-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/19/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid diversification of P. sojae Avr genes in soybean fields and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines. RESULTS We sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions. CONCLUSIONS This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.
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Affiliation(s)
| | - Humira Sonah
- Département de Phytologie, Université Laval, Québec, QC Canada
| | | | - Caroline Labbé
- Département de Phytologie, Université Laval, Québec, QC Canada
| | | | - Allen Xue
- Agriculture and Agri-Food Canada, Ontario, ON Canada
| | | | - Brian J. Knaus
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR USA
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR USA
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32
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Zhong C, Sun S, Li Y, Duan C, Zhu Z. Next-generation sequencing to identify candidate genes and develop diagnostic markers for a novel Phytophthora resistance gene, RpsHC18, in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:525-538. [PMID: 29138903 DOI: 10.1007/s00122-017-3016-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/04/2017] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates. Quantitative trait loci sequencing (QTL-seq), based on the whole-genome resequencing (WGRS) of two extreme resistant and susceptible phenotype bulks from an F2:3 population, was performed, and one 767-kb genomic region with ΔSNP-index ≥ 0.9 on chromosome 3 was identified as the RpsHC18 candidate region in Huachun 18. The candidate region was reduced to a 146-kb region by fine mapping. Nonsynonymous SNP and haplotype analyses were carried out in the 146-kb region among ten soybean genotypes using WGRS. Four specific nonsynonymous SNPs were identified in two nucleotide-binding sites-leucine-rich repeat (NBS-LRR) genes, RpsHC18-NBL1 and RpsHC18-NBL2, which were considered to be the candidate genes. Finally, one specific SNP marker in each candidate gene was successfully developed using a tetra-primer ARMS-PCR assay, and the two markers were verified to be specific for RpsHC18 and to effectively distinguish other known Rps genes. In this study, we applied an integrated genomic-based strategy combining WGRS with traditional genetic mapping to identify RpsHC18 candidate genes and develop diagnostic markers. These results suggest that next-generation sequencing is a precise, rapid and cost-effective way to identify candidate genes and develop diagnostic markers, and it can accelerate Rps gene cloning and marker-assisted selection for breeding of P. sojae-resistant soybean cultivars.
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Affiliation(s)
- Chao Zhong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Suli Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yinping Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Canxing Duan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhendong Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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33
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Zhong C, Sun S, Yao L, Ding J, Duan C, Zhu Z. Fine Mapping and Identification of a Novel Phytophthora Root Rot Resistance Locus RpsZS18 on Chromosome 2 in Soybean. FRONTIERS IN PLANT SCIENCE 2018; 9:44. [PMID: 29441079 PMCID: PMC5797622 DOI: 10.3389/fpls.2018.00044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/09/2018] [Indexed: 05/19/2023]
Abstract
Phytophthora root rot (PRR) caused by Phytophthora sojae is a major soybean disease that causes severe economic losses worldwide. Using soybean cultivars carrying a Rps resistance gene is the most effective strategy for controlling this disease. We previously detected a novel Phytophthora resistance gene, RpsZS18, on chromosome 2 of the soybean cultivar Zaoshu18. The aim of the present study was to identify and finely map RpsZS18. We used 232 F2:3 families generated from a cross between Zaoshu18 (resistant) and Williams (susceptible) as the mapping population. Simple sequence repeat (SSR) markers distributed on chromosome 2 were used to map RpsZS18. First, 12 SSR markers linked with RpsZS18 were identified by linkage analyses, including two newly developed SSR markers, ZCSSR33 and ZCSSR46, that flanked the gene at distances of 0.9 and 0.5 cM, respectively. Second, PCR-based InDel markers were developed based on sequence differences between the two parents and used to further narrow down the mapping region of RpsZS18 to 71.3 kb. Third, haplotype analyses were carried out in the RpsZS18 region using 14 soybean genotypes with whole-genome resequencing. We detected six genes with unique haplotype sequences in Zaoshu18. Finally, quantitative real-time PCR assays of the six genes revealed an EF-hand calcium-binding domain containing protein encoding gene (Glyma.02g245700), a pfkB carbohydrate kinase encoding gene (Glyma.02g245800), and a gene with no functional annotation (Glyma.02g246300), are putative candidate PRR resistance genes. This study provides useful information for breeding P. sojae-resistant soybean cultivars.
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Affiliation(s)
- Chao Zhong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suli Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Canxing Duan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhendong Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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34
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Lebreton A, Labbé C, De Ronne M, Xue AG, Marchand G, Bélanger RR. Development of a Simple Hydroponic Assay to Study Vertical and Horizontal Resistance of Soybean and Pathotypes of Phytophthora sojae. PLANT DISEASE 2018; 102:114-123. [PMID: 30673456 DOI: 10.1094/pdis-04-17-0586-re] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Phytophthora root rot, caused by Phytophthora sojae, is one of the most damaging diseases of soybean and the introgression of Rps (Resistance to P. sojae) genes into elite soybean lines is arguably the best way to manage this disease. Current bioassays to phenotype the gene-for-gene relationship are hampered with respect to reproducibility and long-term stability of isolates, and do not accurately predict horizontal resistance individually. The aim of our study was to investigate a new way of phenotyping P. sojae isolates and vertical and horizontal resistance in soybean that relies on zoospores inoculated directly into a hydroponic system. Inoculation of P. sojae isolates against a set of eight differentials accurately and reproducibly identified pathotypes over a period of two years. When applied to test vertical resistance of soybean lines with known and unknown Rps genes, the bioassay relied on plant dry weight to correctly identify all genes. In addition, simultaneous inoculations of three P. sojae isolates, collectively carrying eight major virulence factors against 64 soybean lines with known and unknown levels of horizontal resistance, separated the plants into five distinct groups of root rot, allowing the discrimination of lines with various degrees of partial resistance. Based on those results, this bioassay offers several advantages in facilitating efforts in breeding soybean for P. sojae resistance and in identifying virulence factors in P. sojae.
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Affiliation(s)
- A Lebreton
- Département de Phytologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - C Labbé
- Département de Phytologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - M De Ronne
- Département de Phytologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - A G Xue
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - G Marchand
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, Ontario N0R 1G0, Canada
| | - R R Bélanger
- Département de Phytologie, Université Laval, Québec, Québec, G1V 0A6, Canada
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35
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Sepiol CJ, Yu J, Dhaubhadel S. Genome-Wide Identification of Chalcone Reductase Gene Family in Soybean: Insight into Root-Specific GmCHRs and Phytophthora sojae Resistance. FRONTIERS IN PLANT SCIENCE 2017; 8:2073. [PMID: 29270182 PMCID: PMC5725808 DOI: 10.3389/fpls.2017.02073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/20/2017] [Indexed: 05/02/2023]
Abstract
Soybean (Glycine max [L.] Merr) is one of the main grain legumes worldwide. Soybean farmers lose billions of dollars' worth of yield annually due to root and stem rot disease caused by the oomycete Phytophthora sojae. Many strategies have been developed to combat the disease, however, these methods have proven ineffective in the long term. A more cost effective and durable approach is to select a trait naturally found in soybean that can increase resistance. One such trait is the increased production of phytoalexin glyceollins in soybean. Glyceollins are isoflavonoids, synthesized via the legume-specific branch of general phenylpropanoid pathway. The first key enzyme exclusively involved in glyceollin synthesis is chalcone reductase (CHR) which coacts with chalcone synthase for the production of isoliquiritigenin, the precursor for glyceollin biosynthesis. Here we report the identification of 14 putative CHR genes in soybean where 11 of them are predicted to be functional. Our results show that GmCHRs display tissue-specific gene expression, and that only root-specific GmCHRs are induced upon P. sojae infection. Among 4 root-specific GmCHRs, GmCHR2A is located near a QTL that is linked to P. sojae resistance suggesting GmCHR2A as a novel locus for partial resistance that can be utilized for resistance breeding.
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Affiliation(s)
- Caroline J. Sepiol
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Jaeju Yu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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