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Hao Q, Yang H, Chen S, Zhang C, Chen L, Cao D, Yuan S, Guo W, Yang Z, Huang Y, Qu Y, Qin L, Sheng X, Wang X, Mitra C, Zhong H, Dawson J, Bumann E, Wang W, Jiang Y, Tang G, Carlin R, Chen H, Liu Q, Shan Z, Zhou X. An pair of an atypical NLR encoding genes confer Asian soybean rust resistance in soybean. Nat Commun 2024; 15:3310. [PMID: 38632249 PMCID: PMC11023949 DOI: 10.1038/s41467-024-47611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is a devastating disease that is present in all major soybean-producing regions. The limited availability of resistant germplasm has resulted in a scarcity of commercial soybean cultivars that are resistant to the disease. To date, only the Chinese soybean landrace SX6907 has demonstrated an immune response to ASR. In this study, we present the isolation and characterization of Rpp6907-7 and Rpp6907-4, a gene pair that confer broad-spectrum resistance to ASR. Rpp6907-7 and Rpp6907-4 encode atypic nucleotide-binding leucine-rich repeat (NLR) proteins that are found to be required for NLR-mediated immunity. Genetic analysis shows that only Rpp6907-7 confers resistance, while Rpp6907-4 regulates Rpp6907-7 signaling activity by acting as a repressor in the absence of recognized effectors. Our work highlights the potential value of using Rpp6907 in developing resistant soybean cultivars.
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Affiliation(s)
- Qingnan Hao
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Hongli Yang
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Shuilian Chen
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Chanjuan Zhang
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Limiao Chen
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Dong Cao
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Songli Yuan
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Wei Guo
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Zhonglu Yang
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yi Huang
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yanhui Qu
- The Graduate School of Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Lucy Qin
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Xiaoyan Sheng
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Xueyan Wang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Chandrani Mitra
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Heng Zhong
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - John Dawson
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Eric Bumann
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Wenling Wang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Yaping Jiang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Guozhu Tang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Ryan Carlin
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Haifeng Chen
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China.
| | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA.
| | - Zhihui Shan
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Xinan Zhou
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China.
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Yeo FKS, Wang Y, Vozabova T, Huneau C, Leroy P, Chalhoub B, Qi XQ, Niks RE, Marcel TC. Haplotype divergence and multiple candidate genes at Rphq2, a partial resistance QTL of barley to Puccinia hordei. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:289-304. [PMID: 26542283 PMCID: PMC4733143 DOI: 10.1007/s00122-015-2627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 10/17/2015] [Indexed: 05/04/2023]
Abstract
KEY MESSAGE Rphq2, a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars. ABSTRACT Partial and non-host resistances to rust fungi in barley (Hordeum vulgare) may be based on pathogen-associated molecular pattern (PAMP)-triggered immunity. Understanding partial resistance may help to understand non-host resistance, and vice versa. We constructed two non-gridded BAC libraries from cultivar Vada and line SusPtrit. Vada is immune to non-adapted Puccinia rust fungi, and partially resistant to P. hordei. SusPtrit is susceptible to several non-adapted rust fungi, and has been used for mapping QTLs for non-host and partial resistance. The BAC libraries help to identify genes determining the natural variation for partial and non-host resistances of barley to rust fungi. A major-effect QTL, Rphq2, for partial resistance to P. hordei was mapped in a complete Vada and an incomplete SusPtrit contig. The physical distance between the markers flanking Rphq2 was 195 Kbp in Vada and at least 226 Kbp in SusPtrit. This marker interval was predicted to contain 12 genes in either accession, of which only five genes were in common. The haplotypes represented by Vada and SusPtrit were found in 57 and 43%, respectively, of a 194 barley accessions panel. The lack of homology between the two haplotypes probably explains the suppression of recombination in the Rphq2 area and limit further genetic resolution in fine mapping. The possible candidate genes for Rphq2 encode peroxidases, kinases and a member of seven-in-absentia protein family. This result suggests that Rphq2 does not belong to the NB-LRR gene family and does not resemble any of the partial resistance genes cloned previously.
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Affiliation(s)
- F K S Yeo
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- Department of Plant Science and Environmental Ecology, Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Y Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - T Vozabova
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- The Institute of Botany of the Academy of Science of the Czech Republic, Zámek 1, 252 43, Průhonice, Czech Republic
| | - C Huneau
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - P Leroy
- INRA, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
- Université Blaise Pascal, UMR1095, Genetics Diversity and Ecophysiology of Cereals, 63039, Clermont-Ferrand, France
| | - B Chalhoub
- INRA, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
- Université d'Evry Val d'Essonne, UMR1165, Unité de Recherche en Génomique Végétale, 91057, Evry, France
| | - X Q Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - R E Niks
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands.
| | - T C Marcel
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708PB, 6700 AJ, Wageningen, The Netherlands
- INRA, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
- AgroParisTech, UMR1290, BIOGER, 78850, Thiverval-Grignon, France
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