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Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice. PLANTS 2021; 10:plants10102039. [PMID: 34685848 PMCID: PMC8541590 DOI: 10.3390/plants10102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Bacterial leaf streak (BLS) is a devastating rice disease caused by the bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), which can result in severe damage to rice production worldwide. Based on a total of 510 rice accessions, trialed in two seasons and using six different multi-locus GWAS methods (mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA and pKWmEB), 79 quantitative trait nucleotides (QTNs) reflecting 69 QTLs for BLS resistance were identified (LOD > 3). The QTNs were distributed on all chromosomes, with the most distributed on chromosome 11, followed by chromosomes 1 and 5. Each QTN had an additive effect of 0.20 (cm) and explained, on average, 2.44% of the phenotypic variance, varying from 0.00–0.92 (cm) and from 0.00–9.86%, respectively. Twenty-five QTNs were detected by at least two methods. Among them, qnBLS11.17 was detected by as many as five methods. Most of the QTNs showed a significant interaction with their environment, but no QTNs were detected in both seasons. By defining the QTL range for each QTN according to the LD half-decay distance, a total of 848 candidate genes were found for nine top QTNs. Among them, more than 10% were annotated to be related to biotic stress resistance, and five showed a significant response to Xoc infection. Our results could facilitate the in-depth study and marker-assisted improvement of rice resistance to BLS.
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Xie X, Chen Z, Zhang B, Guan H, Zheng Y, Lan T, Zhang J, Qin M, Wu W. Transcriptome analysis of xa5-mediated resistance to bacterial leaf streak in rice (Oryza sativa L.). Sci Rep 2020; 10:19439. [PMID: 33173096 PMCID: PMC7656458 DOI: 10.1038/s41598-020-74515-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/30/2020] [Indexed: 11/25/2022] Open
Abstract
Bacterial leaf steak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a devastating disease in rice production. The resistance to BLS in rice is a quantitatively inherited trait, of which the molecular mechanism is still unclear. It has been proved that xa5, a recessive bacterial blast resistance gene, is the most possible candidate gene of the QTL qBlsr5a for BLS resistance. To study the molecular mechanism of xa5 function in BLS resistance, we created transgenic lines with RNAi of Xa5 (LOC_Os05g01710) and used RNA-seq to analyze the transcriptomes of a Xa5-RNAi line and the wild-type line at 9 h after inoculation with Xoc, with the mock inoculation as control. We found that Xa5-RNAi could (1) increase the resistance to BLS as expected from xa5; (2) alter (mainly up-regulate) the expression of hundreds of genes, most of which were related to disease resistance; and (3) greatly enhance the response of thousands of genes to Xoc infection, especially of the genes involved in cell death pathways. The results suggest that xa5 is the cause of BLS-resistance of QTL qBlsr5a and it displays BLS resistance effect probably mainly because of the enhanced response of the cell death-related genes to Xoc infection.
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Affiliation(s)
- Xiaofang Xie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiwei Chen
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binghui Zhang
- Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou, China
| | - Huazhong Guan
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Zheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tao Lan
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Zhang
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyue Qin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiren Wu
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China. .,Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
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Xie X, Chen Z, Cao J, Guan H, Lin D, Li C, Lan T, Duan Y, Mao D, Wu W. Toward the positional cloning of qBlsr5a, a QTL underlying resistance to bacterial leaf streak, using overlapping sub-CSSLs in rice. PLoS One 2014; 9:e95751. [PMID: 24752581 PMCID: PMC3994123 DOI: 10.1371/journal.pone.0095751] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/30/2014] [Indexed: 11/19/2022] Open
Abstract
Bacterial leaf steak (BLS) is one of the most destructive diseases in rice. Studies have shown that BLS resistance in rice is quantitatively inherited, controlled by multiple quantitative trait loci (QTLs). A QTL with relatively large effect, qBlsr5a, was previously mapped in a region of ∼380 kb on chromosome 5. To fine map qBlsr5a further, a set of overlapping sub-chromosome segment substitution lines (sub-CSSLs) were developed from a large secondary F2 population (containing more than 7000 plants), in which only the chromosomal region harboring qBlsr5a was segregated. By genotyping the sub-CSSLs with molecular markers covering the target region and phenotyping the sub-CSSLs with artificial inoculation, qBlsr5a was delimited to a 30.0-kb interval, in which only three genes were predicted. qRT-PCR analysis indicated that the three putative genes did not show significant response to the infection of BLS pathogen in both resistant and susceptible parental lines. However, two nucleotide substitutions were found in the coding sequence of gene LOC_Os05g01710, which encodes the gamma chain of transcription initiation factor IIA (TFIIAγ). The nucleotide substitutions resulted in a change of the 39th amino acid from valine (in the susceptible parent) to glutamic acid (in the resistant parent). Interestingly, the resistant parent allele of LOC_Os05g01710 is identical to xa5, a major gene resistant to bacterial leaf blight (another bacterial disease of rice). These results suggest that LOC_Os05g01710 is very possibly the candidate gene of qBlsr5a.
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Affiliation(s)
- Xiaofang Xie
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhiwei Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail: (WW); (ZC)
| | - Jinliang Cao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huazhong Guan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Degong Lin
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chunlan Li
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Tao Lan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuanlin Duan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Damei Mao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Weiren Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail: (WW); (ZC)
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Quenouille J, Montarry J, Palloix A, Moury B. Farther, slower, stronger: how the plant genetic background protects a major resistance gene from breakdown. MOLECULAR PLANT PATHOLOGY 2013; 14:109-18. [PMID: 23046402 PMCID: PMC6638760 DOI: 10.1111/j.1364-3703.2012.00834.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genetic resistance provides efficient control of crop diseases, but is limited by pathogen evolution capacities which often result in resistance breakdown. It has been demonstrated recently, in three different pathosystems, that polygenic resistances combining a major-effect gene and quantitative resistance controlled by the genetic background are more durable than monogenic resistances (with the same major gene in a susceptible genetic background), but the underlying mechanisms are unknown. Using the pepper-Potato virus Y system, we examined three mechanisms that could account for the greater durability of the polygenic resistances: (i) the additional quantitative resistance conferred by the genetic background; (ii) the increase in the number of mutations required for resistance breakdown; and (iii) the slower selection of adapted resistance-breaking mutants within the viral population. The three mechanisms were experimentally validated. The first explained a large part of the variation in resistance breakdown frequency and is therefore expected to be a major determinant of resistance durability. Quantitative resistance factors also had an influence on the second mechanism by modifying the virus mutational pathways towards resistance breakdown and could also have an influence on the third mechanism by increasing genetic drift effects on the viral population. The relevance of these results for other plant-pathogen systems and their importance in plant breeding are discussed.
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Belcher AR, Zwonitzer JC, Santa Cruz J, Krakowsky MD, Chung CL, Nelson R, Arellano C, Balint-Kurti PJ. Analysis of quantitative disease resistance to southern leaf blight and of multiple disease resistance in maize, using near-isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:433-445. [PMID: 21997760 DOI: 10.1007/s00122-011-1718-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 09/27/2011] [Indexed: 05/31/2023]
Abstract
Maize inbred lines NC292 and NC330 were derived by repeated backcrossing of an elite source of southern leaf blight (SLB) resistance (NC250P) to the SLB-susceptible line B73, with selection for SLB resistance among and within backcross families at each generation. Consequently, while B73 is very SLB susceptible, its sister lines NC292 and NC330 are both SLB resistant. Previously, we identified the 12 introgressions from NC250P that differentiate NC292 and NC330 from B73. The goals of this study were to determine the effects of each introgression on resistance to SLB and to two other foliar fungal diseases of maize, northern leaf blight and gray leaf spot. This was achieved by generating and testing a set of near isogenic lines carry single or combinations of just two or three introgressions in a B73 background. Introgressions 3B, 6A, and 9B (bins 3.03-3.04, 6.01, and 9.02-9.03) all conferred significant levels of SLB resistance in the field. Introgression 6A was the only introgression that had a significant effect on juvenile plant resistance to SLB. Introgressions 6A and 9B conferred resistance to multiple diseases.
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Affiliation(s)
- Araby R Belcher
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695-7616, USA
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Identification of genes contributing to quantitative disease resistance in rice. SCIENCE CHINA-LIFE SCIENCES 2010; 53:1263-73. [PMID: 21046317 DOI: 10.1007/s11427-010-4081-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 08/25/2010] [Indexed: 10/18/2022]
Abstract
Despite the importance of quantitative disease resistance during a plant's life, little is known about the molecular basis of this type of host-pathogen interaction, because most of the genes underlying resistance quantitative trait loci (QTLs) are unknown. To identify genes contributing to resistance QTLs in rice, we analyzed the colocalization of a set of characterized rice defense-responsive genes and resistance QTLs against different pathogens. We also examined the expression patterns of these genes in response to pathogen infection in the parents of the mapping populations, based on the strategy of validation and functional analysis of the QTLs. The results suggest that defense-responsive genes are important resources of resistance QTLs in rice. OsWRKY45-1 is the gene contributing to a major resistance QTL. NRR, OsGH3-1, and OsGLP members on chromosome 8 contribute alone or collectively to different minor resistance QTLs. These genes function in a basal resistance pathway or in major disease resistance gene-mediated race-specific pathways.
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