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Shu G, Wang A, Wang X, Ding J, Chen R, Gao F, Wang A, Li T, Wang Y. Identification of southern corn rust resistance QTNs in Chinese summer maize germplasm via multi-locus GWAS and post-GWAS analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1221395. [PMID: 37810381 PMCID: PMC10552154 DOI: 10.3389/fpls.2023.1221395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 10/10/2023]
Abstract
Southern corn rust (SCR) caused by Puccinia polysora Underw is a major disease leading to severe yield losses in China Summer Corn Belt. Using six multi-locus GWAS methods, we identified a set of SCR resistance QTNs from a diversity panel of 140 inbred lines collected from China Summer Corn Belt. Thirteen QTNs on chromosomes 1, 2, 4, 5, 6, and 8 were grouped into three types of allele effects and their associations with SCR phenotypes were verified by post-GWAS case-control sampling, allele/haplotype effect analysis. Relative resistance (RRR) and relative susceptibility (RRs) catering to its inbred carrier were estimated from single QTN and QTN-QTN combos and epistatitic effects were estimated for QTN-QTN combos. By transcriptomic annotation, a set of candidate genes were predicted to be involved in transcriptional regulation (S5_145, Zm00001d01613, transcription factor GTE4), phosphorylation (S8_123, Zm00001d010672, Pgk2- phosphoglycerate kinase 2), and temperature stress response (S6_164a/S6_164b, Zm00001d038806, hsp101, and S5_211, Zm00001d017978, cellulase25). The breeding implications of the above findings were discussed.
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Affiliation(s)
- Guoping Shu
- Center of Biotechnology, Beijing Lantron Seed, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Aifang Wang
- Center of Biotechnology, Beijing Lantron Seed, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Xingchuan Wang
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruijie Chen
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Fei Gao
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Aifen Wang
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Ting Li
- Center of Biotechnology, Beijing Lantron Seed, LongPing High-tech Corp., Zhengzhou, Henan, China
| | - Yibo Wang
- Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, LongPing High-tech Corp., Zhengzhou, Henan, China
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2
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Li J, Cheng D, Guo S, Chen C, Wang Y, Zhong Y, Qi X, Liu Z, Wang D, Wang Y, Liu W, Liu C, Chen S. Genome-wide association and genomic prediction for resistance to southern corn rust in DH and testcross populations. FRONTIERS IN PLANT SCIENCE 2023; 14:1109116. [PMID: 36778694 PMCID: PMC9908600 DOI: 10.3389/fpls.2023.1109116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Southern corn rust (SCR), caused by Puccinia polysora Underw, is a destructive disease that can severely reduce grain yield in maize (Zea mays L.). Owing to P. polysora being multi-racial, it is very important to explore more resistance genes and develop more efficient selection approaches in maize breeding programs. Here, four Doubled Haploid (DH) populations with 384 accessions originated from selected parents and their 903 testcross hybrids were used to perform genome-wide association (GWAS). Three GWAS processes included the additive model in the DH panel, additive and dominant models in the hybrid panel. As a result, five loci were detected on chromosomes 1, 7, 8, 8, and 10, with P-values ranging from 4.83×10-7 to 2.46×10-41. In all association analyses, a highly significant locus on chromosome 10 was detected, which was tight chained with the known SCR resistance gene RPPC and RPPK. Genomic prediction (GP), has been proven to be effective in plant breeding. In our study, several models were performed to explore predictive ability in hybrid populations for SCR resistance, including extended GBLUP with different genetic matrices, maker based prediction models, and mixed models with QTL as fixed factors. For GBLUP models, the prediction accuracies ranged from 0.56-0.60. Compared with traditional prediction only with additive effect, prediction ability was significantly improved by adding additive-by-additive effect (P-value< 0.05). For maker based models, the accuracy of BayesA and BayesB was 0.65, 8% higher than other models (i.e., RRBLUP, BRR, BL, BayesC). Finally, by adding QTL into the mixed linear prediction model, the accuracy can be further improved to 0.67, especially for the G_A model, the prediction performance can be increased by 11.67%. The prediction accuracy of the BayesB model can be further improved significantly by adding QTL information (P-value< 0.05). This study will provide important valuable information for understanding the genetic architecture and the application of GP for SCR in maize breeding.
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Affiliation(s)
- Jinlong Li
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Dehe Cheng
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Shuwei Guo
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Chen Chen
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
- Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuwen Wang
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Yu Zhong
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Xiaolong Qi
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Zongkai Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Dong Wang
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Yuandong Wang
- Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wenxin Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Chenxu Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
| | - Shaojiang Chen
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization Ministry of Education (MOE), China Agricultural University, Beijing, China
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3
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Sun Q, Liu J, Huang C, Liu X, Gao J, Li L, Luo Y, Ma Z. Clonal Expansion and Dispersal Pathways of Puccinia polysora in China. PHYTOPATHOLOGY 2023; 113:21-30. [PMID: 35918852 DOI: 10.1094/phyto-06-21-0256-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Southern corn rust (SCR) caused by Puccinia polysora is one of the most devastating diseases in the world. In recent years, SCR has been upgraded from a minor to a major disease around the world, including in China. However, little is known about its population genetics and structure in China. In this study, we analyzed 288 isolates collected from various localities during 2017 in seven Chinese provinces: Guangxi, Guangdong, Anhui, Hunan, Shandong, Henan, and Shaanxi. The isolates were analyzed using nine microsatellite markers. The population structure, genetic diversity, and reproduction mode of P. polysora were investigated based on genotype data. Strong genotypic diversity was detected and clonal reproduction was dominant. The populations collected from the pathogen's winter-reproductive regions harbored more genotypes than those collected from the pathogen's epidemic regions. The spatial differences in genotypic richness, and evenness among the populations were significant, and showed a decreasing trend from south to north. Most isolates were clustered into two clonal groups. Two high-frequency multilocus genotypes (MLGs), MLG1 and MLG2, were widely distributed in all populations. Our analyses confirmed that P. polysora employed clone dispersal from the pathogen's winter-reproductive regions to the pathogen's epidemic regions, and in addition to the sources from the pathogen's winter-reproductive regions, the pathogen in Anhui and Hunan might also have other sources from areas such as Taiwan, China, or/and Southeast Asia, and the pathogen went through a genetic bottleneck during its dispersal. These findings provide initial insights into the reproduction mode and dispersal pathways of P. polysora in China.
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Affiliation(s)
- Qiuyu Sun
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- National Agro-tech Extension and Service Center, Beijing 100125, China
| | - Chong Huang
- National Agro-tech Extension and Service Center, Beijing 100125, China
| | - Xiufeng Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crops Sciences, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Jianmeng Gao
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Leifu Li
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Yong Luo
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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Guo L, You C, Zhang H, Wang Y, Zhang R. Genome-wide analysis of NBS-LRR genes in Rosaceae species reveals distinct evolutionary patterns. Front Genet 2022; 13:1052191. [PMID: 36437946 PMCID: PMC9685399 DOI: 10.3389/fgene.2022.1052191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
The nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes, one of the largest gene families in plants, are evolving rapidly and playing a critical role in plant resistance to pathogens. In this study, a genome-wide search in 12 Rosaceae genomes screened out 2188 NBS-LRR genes, with the gene number varied distinctively across different species. The reconciled phylogeny revealed 102 ancestral genes (7 RNLs, 26 TNLs, and 69 CNLs), which underwent independent gene duplication and loss events during the divergence of the Rosaceae. The NBS-LRR genes exhibited dynamic and distinct evolutionary patterns in the 12 Rosaceae species due to independent gene duplication/loss events, which resulted the discrepancy of NBS-LRR gene number among Rosaceae species. Specifically, Rubus occidentalis, Potentilla micrantha, Fragaria iinumae and Gillenia trifoliata, displayed a “first expansion and then contraction” evolutionary pattern; Rosa chinensis exhibited a “continuous expansion” pattern; F. vesca had a “expansion followed by contraction, then a further expansion” pattern, three Prunus species and three Maleae species shared a “early sharp expanding to abrupt shrinking” pattern. Overall, this study elucidated the dynamic and complex evolutionary patterns of NBS-LRR genes in the 12 Rosaceae species, and could assist further investigation of mechanisms driving these evolutionary patterns.
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Affiliation(s)
- Liping Guo
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Chen You
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Hanghang Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Yukun Wang
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, China
- *Correspondence: Yukun Wang, ; Rui Zhang,
| | - Rui Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
- *Correspondence: Yukun Wang, ; Rui Zhang,
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Zhang N, Qi X, Li X, Li G, Li G, Hu J. Introgression of the RppQ gene from field corn improves southern rust resistance in sweet corn. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:53. [PMID: 37309374 PMCID: PMC10248694 DOI: 10.1007/s11032-022-01315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/28/2022] [Indexed: 06/14/2023]
Abstract
Southern rust, one of the most destructive foliar diseases of sweet corn (Zea mays convar. saccharata var. rugosa), is caused by Puccinia polysora Underw. and leads to enormous yield losses and reduced quality of sweet corn in China. Utilization of resistance genes is an effective and environmentally friendly strategy for improving southern rust resistance of sweet corn. However, improvement is hampered by a lack of resistance genes in Chinese sweet corn germplasm. In this study, we introgress the southern rust resistance gene RppQ from Qi319, an inbred line of southern rust-resistant field corn, into four elite sweet corn inbred lines (1401, 1413, 1434, and 1445) using marker-assisted backcross breeding. These are parental inbred lines of four popular sweet corn varieties: Yuetian 28, Yuetian 13, Yuetian 26, and Yuetian 27. We developed five RppQ-based markers (M0607, M0801, M0903, M3301, and M3402) and employed these markers for foreground selection; 92.3 to 97.9% of the recurrent parent genomes were recovered following three or four rounds of backcrossing. The four newly developed sweet corn lines all showed significant improvement of southern rust resistance compared with their respective parent lines. Meanwhile, there was no significant difference in phenotypic data for agronomic traits. In addition, reconstituted hybrids derived from the converted lines retained resistance to southern rust, while other agronomic traits and sugar content remained unchanged. Our study provides an example of successful development of southern rust-resistant sweet corn using a resistance gene from field corn. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01315-7.
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Affiliation(s)
- Nan Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510640 China
| | - Xitao Qi
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510640 China
| | - Xiaofeng Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510640 China
| | - Guangyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510640 China
| | - Gaoke Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510640 China
| | - Jianguang Hu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Crops Genetics and Improvement, Guangzhou, 510640 China
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6
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Chen G, Zhang B, Ding J, Wang H, Deng C, Wang J, Yang Q, Pi Q, Zhang R, Zhai H, Dong J, Huang J, Hou J, Wu J, Que J, Zhang F, Li W, Min H, Tabor G, Li B, Liu X, Zhao J, Yan J, Lai Z. Cloning southern corn rust resistant gene RppK and its cognate gene AvrRppK from Puccinia polysora. Nat Commun 2022; 13:4392. [PMID: 35906218 PMCID: PMC9338322 DOI: 10.1038/s41467-022-32026-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Broad-spectrum resistance has great values for crop breeding. However, its mechanisms are largely unknown. Here, we report the cloning of a maize NLR gene, RppK, for resistance against southern corn rust (SCR) and its cognate Avr gene, AvrRppK, from Puccinia polysora (the causal pathogen of SCR). The AvrRppK gene has no sequence variation in all examined isolates. It has high expression level during infection and can suppress pattern-triggered immunity (PTI). Further, the introgression of RppK into maize inbred lines and hybrids enhances resistance against multiple isolates of P. polysora, thereby increasing yield in the presence of SCR. Together, we show that RppK is involved in resistance against multiple P. polysora isolates and it can recognize AvrRppK, which is broadly distributed and conserved in P. polysora isolates. Southern corn rust (SCR) caused by Puccinia polysora is a major maize disease that can result in major yield loss. Here, the authors report the expression of a CC-NB-LRR type of R gene RppK results in SCR resistance in susceptible maize lines and it can recognize the effector AvrRppK produced by P. polysora.
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Affiliation(s)
- Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, Henan, China.,The Shennong Laboratory, 450002, Zhengzhou, Henan, China
| | - Hongze Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Ce Deng
- College of Agronomy, Henan Agricultural University, 450002, Zhengzhou, Henan, China
| | - Jiali Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Qianhui Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Qianyu Pi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Ruyang Zhang
- Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
| | - Haoyu Zhai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junfei Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junshi Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jiabao Hou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Junhua Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jiamin Que
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Fan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Haoxuan Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Girma Tabor
- Corteva Agriscience, Johnston, IA, 50131, USA
| | - Bailin Li
- Corteva Agriscience, Johnston, IA, 50131, USA
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, 130033, Changchun, Jilin, China
| | - Jiuran Zhao
- Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China. .,Hubei Hongshan Laboratory, 430070, Wuhan, Hubei, China.
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7
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Deng C, Leonard A, Cahill J, Lv M, Li Y, Thatcher S, Li X, Zhao X, Du W, Li Z, Li H, Llaca V, Fengler K, Marshall L, Harris C, Tabor G, Li Z, Tian Z, Yang Q, Chen Y, Tang J, Wang X, Hao J, Yan J, Lai Z, Fei X, Song W, Lai J, Zhang X, Shu G, Wang Y, Chang Y, Zhu W, Xiong W, Sun J, Li B, Ding J. The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize. MOLECULAR PLANT 2022; 15:904-912. [PMID: 35032688 DOI: 10.1016/j.molp.2022.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 05/26/2023]
Abstract
Southern corn rust (SCR), caused by the fungal pathogen Puccinia polysora, is a major threat to maize production worldwide. Efficient breeding and deployment of resistant hybrids are key to achieving durable control of SCR. Here, we report the molecular cloning and characterization of RppC, which encodes an NLR-type immune receptor and is responsible for a major SCR resistance quantitative trait locus. Furthermore, we identified the corresponding avirulence effector, AvrRppC, which is secreted by P. polysora and triggers RppC-mediated resistance. Allelic variation of AvrRppC directly determines the effectiveness of RppC-mediated resistance, indicating that monitoring of AvrRppC variants in the field can guide the rational deployment of RppC-containing hybrids in maize production. Currently, RppC is the most frequently deployed SCR resistance gene in China, and a better understanding of its mode of action is critical for extending its durability.
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Affiliation(s)
- Ce Deng
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | | | | | - Meng Lv
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Yurong Li
- Corteva Agriscience, Johnston, IA 50131, USA
| | | | - Xueying Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaodi Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Wenjie Du
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Zheng Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Huimin Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | | | | | | | | | - Girma Tabor
- Corteva Agriscience, Johnston, IA 50131, USA
| | - Zhimin Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhiqiang Tian
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Qinghua Yang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanhui Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Jihua Tang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China
| | - Xintao Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Junjie Hao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohong Fei
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237 Texcoco, Mexico
| | - Guoping Shu
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou 450001, China
| | - Yibo Wang
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou 450001, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weiling Zhu
- Henan Dingyou Agricultural Science and Technology Co., Ltd, Zhengzhou 450001, China
| | - Wei Xiong
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China; International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237 Texcoco, Mexico
| | - Juan Sun
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China.
| | - Bailin Li
- Corteva Agriscience, Johnston, IA 50131, USA.
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; The State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, China.
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Wang S, Wang X, Zhang R, Liu Q, Sun X, Wang J, Wang Y, Xing J, Liu Y, Zhao Y, Shi Z, Su A, Li C, Xiao S, Jiao Y, Li Z, Wang R, Song W, Zhao J. RppM, Encoding a Typical CC-NBS-LRR Protein, Confers Resistance to Southern Corn Rust in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:951318. [PMID: 35903220 PMCID: PMC9317930 DOI: 10.3389/fpls.2022.951318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 05/12/2023]
Abstract
Southern corn rust (SCR) caused by Puccinia polysora Underw. poses a major threat to maize production worldwide. The utilization of host SCR-resistance genes and the cultivation of resistant cultivars are the most effective, economical strategies for controlling SCR. Here, we identified and cloned a new SCR resistance gene, RppM, from the elite maize inbred line Jing2416K. RppM was found to encode a typical CC-NBS-LRR protein localized in both the nucleus and cytoplasm. This gene was constitutively expressed at all developmental stages and in all tissues examined, with the strongest expression detected in leaves at the mature stage. A transcriptome analysis provided further evidence that multiple defense systems were initiated in Jing2416K, including pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity, reinforcement of cell walls, accumulation of antimicrobial compounds, and activation of phytohormone signaling pathways. Finally, we developed functional Kompetitive allele-specific PCR markers for RppM using two conserved SNP sites and successfully applied these functional markers for the detection of RppM and the cultivation of resistant maize cultivars, demonstrating their great potential utility in maize breeding.
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