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Devanna BN, Sucharita S, Sunitha NC, Anilkumar C, Singh PK, Pramesh D, Samantaray S, Behera L, Katara JL, Parameswaran C, Rout P, Sabarinathan S, Rajashekara H, Sharma TR. Refinement of rice blast disease resistance QTLs and gene networks through meta-QTL analysis. Sci Rep 2024; 14:16458. [PMID: 39013915 PMCID: PMC11252161 DOI: 10.1038/s41598-024-64142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 06/05/2024] [Indexed: 07/18/2024] Open
Abstract
Rice blast disease is the most devastating disease constraining crop productivity. Vertical resistance to blast disease is widely studied despite its instability. Clusters of genes or QTLs conferring blast resistance that offer durable horizontal resistance are important in resistance breeding. In this study, we aimed to refine the reported QTLs and identify stable meta-QTLs (MQTLs) associated with rice blast resistance. A total of 435 QTLs were used to project 71 MQTLs across all the rice chromosomes. As many as 199 putative rice blast resistance genes were identified within 53 MQTL regions. The genes included 48 characterized resistance gene analogs and related proteins, such as NBS-LRR type, LRR receptor-like kinase, NB-ARC domain, pathogenesis-related TF/ERF domain, elicitor-induced defense and proteins involved in defense signaling. MQTL regions with clusters of RGA were also identified. Fifteen highly significant MQTLs included 29 candidate genes and genes characterized for blast resistance, such as Piz, Nbs-Pi9, pi55-1, pi55-2, Pi3/Pi5-1, Pi3/Pi5-2, Pikh, Pi54, Pik/Pikm/Pikp, Pb1 and Pb2. Furthermore, the candidate genes (42) were associated with differential expression (in silico) in compatible and incompatible reactions upon disease infection. Moreover, nearly half of the genes within the MQTL regions were orthologous to those in O. sativa indica, Z. mays and A. thaliana, which confirmed their significance. The peak markers within three significant MQTLs differentiated blast-resistant and susceptible lines and serve as potential surrogates for the selection of blast-resistant lines. These MQTLs are potential candidates for durable and broad-spectrum rice blast resistance and could be utilized in blast resistance breeding.
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Affiliation(s)
| | - Sumali Sucharita
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - N C Sunitha
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - C Anilkumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Pankaj K Singh
- Department of Biotechnology, University Centre for Research and Development, Chandigarh University, Mohali, Punjab, 140413, India
| | - D Pramesh
- University of Agricultural Sciences, Raichur, Karnataka, India
| | | | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | | | - C Parameswaran
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Prachitara Rout
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | | | | | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India.
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Sahu PK, Sao R, Choudhary DK, Thada A, Kumar V, Mondal S, Das BK, Jankuloski L, Sharma D. Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease. PLANTS 2022; 11:plants11182386. [PMID: 36145787 PMCID: PMC9504543 DOI: 10.3390/plants11182386] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 01/02/2023]
Abstract
Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | | | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Ljupcho Jankuloski
- Plant Breeding and Genetics Section, Joint FAO/IAEA Centre, International Atomic Energy Agency, 1400 Vienna, Austria
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
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Jia Y, Jia MH, Yan Z. Mapping Blast Resistance Genes in Rice Varieties 'Minghui 63' and 'M-202'. PLANT DISEASE 2022; 106:1175-1182. [PMID: 34739330 DOI: 10.1094/pdis-09-21-2095-re] [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: 06/13/2023]
Abstract
Rice blast caused by the fungus Magnaporthe oryzae (syn. Magnaporthe grisea) is one of the most lethal diseases for sustainable rice production worldwide. Blast resistance mediated by major resistance genes is often broken down after a short period of deployment, while minor blast resistance genes, each providing a small effect on disease reactions, are more durable. In the present study, we first evaluated disease reactions of two rice breeding parents 'Minghui 63' and 'M-202' with 11 blast races, IA45, IB1, IB45, IB49, IB54, IC1, IC17, ID1, IE1, IG1, and IH1, commonly present in the United States, under greenhouse conditions using a category disease rating resembling infection types under field conditions. 'Minghui 63' exhibited differential resistance responses in comparison with those of 'M-202' to the tested blast races. A recombinant inbred line (RIL) population of 275 lines from a cross between 'Minghui 63' and 'M-202' was also evaluated with the above-mentioned blast races. The population was genotyped with 156 simple sequence repeat (SSR) and insertion and deletion (Indel) markers. A linkage map with a genetic distance of 1,022.84 cM was constructed using inclusive composite interval mapping (ICIM) software. A total of 10 resistance QTLs, eight from 'Minghui 63' and two from 'M-202', were identified. One major QTL, qBLAST2 on chromosome 2, was identified by seven races/isolates. The remaining nine minor resistance QTLs were mapped on chromosomes 1, 3, 6, 9, 10, 11, and 12. These findings provide useful genetic markers and resources to tag minor blast resistance genes for marker-assisted selection in rice breeding program and for further studies of underlying genes.
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Affiliation(s)
- Yulin Jia
- U.S. Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160
| | - Melissa H Jia
- U.S. Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160
| | - Zhongbu Yan
- University of Arkansas Rice Research and Extension Center, Stuttgart, AR 72160
- Texas A&M AgriLife Research Center, Beaumont, TX 77713
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A Meta-Analysis of Quantitative Trait Loci Associated with Multiple Disease Resistance in Rice ( Oryza sativa L.). PLANTS 2020; 9:plants9111491. [PMID: 33167299 PMCID: PMC7694349 DOI: 10.3390/plants9111491] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Rice blast, sheath blight and bacterial leaf blight are major rice diseases found worldwide. The development of resistant cultivars is generally perceived as the most effective way to combat these diseases. Plant disease resistance is a polygenic trait where a combinatorial effect of major and minor genes affects this trait. To locate the source of this trait, various quantitative trait loci (QTL) mapping studies have been performed in the past two decades. However, investigating the congruency between the reported QTL is a daunting task due to the heterogeneity amongst the QTLs studied. Hence, the aim of our study is to integrate the reported QTLs for resistance against rice blast, sheath blight and bacterial leaf blight and objectively analyze and consolidate the location of QTL clusters in the chromosomes, reducing the QTL intervals and thus identifying candidate genes within the selected meta-QTL. A total of twenty-seven studies for resistance QTLs to rice blast (8), sheath blight (15) and bacterial leaf blight (4) was compiled for QTL projection and analyses. Cumulatively, 333 QTLs associated with rice blast (114), sheath blight (151) and bacterial leaf blight (68) resistance were compiled, where 303 QTLs could be projected onto a consensus map saturated with 7633 loci. Meta-QTL analysis on 294 QTLs yielded 48 meta-QTLs, where QTLs with membership probability lower than 60% were excluded, reducing the number of QTLs within the meta-QTL to 274. Further, three meta-QTL regions (MQTL2.5, MQTL8.1 and MQTL9.1) were selected for functional analysis on the basis that MQTL2.5 harbors the highest number of QTLs; meanwhile, MQTL8.1 and MQTL9.1 have QTLs associated with all three diseases mentioned above. The functional analysis allows for determination of enriched gene ontology and resistance gene analogs (RGAs) and other defense-related genes. To summarize, MQTL2.5, MQTL8.1 and MQTL9.1 have a considerable number of R-genes that account for 10.21%, 4.08% and 6.42% of the total genes found in these meta-QTLs, respectively. Defense genes constitute around 3.70%, 8.16% and 6.42% of the total number of genes in MQTL2.5, MQTL8.1 and MQTL9.1, respectively. This frequency is higher than the total frequency of defense genes in the rice genome, which is 0.0096% (167 defense genes/17,272 total genes). The integration of the QTLs facilitates the identification of QTL hotspots for rice blast, sheath blight and bacterial blight resistance with reduced intervals, which helps to reduce linkage drag in breeding. The candidate genes within the promising regions could be utilized for improvement through genetical engineering.
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Goad DM, Jia Y, Gibbons A, Liu Y, Gealy D, Caicedo AL, Olsen KM. Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations. RICE (NEW YORK, N.Y.) 2020; 13:21. [PMID: 32206941 PMCID: PMC7090113 DOI: 10.1186/s12284-020-00381-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rice sheath blight (ShB) disease, caused by the pathogenic fungus Rhizoctonia solani, causes significant yield losses globally. US weedy rice populations, which are de-domesticated forms of indica and aus cultivated rice, appear to be more resistant to ShB than local japonica cultivated rice. We mapped quantitative trait loci (QTL) associated with ShB resistance using two F8 recombinant inbred line populations generated from crosses of an indica crop variety, Dee-Geo-Woo-Gen (DGWG), with individuals representing the two major US weed biotypes, straw hull (SH) and black hull awned (BHA). RESULTS We identified nine ShB resistance QTL across both mapping populations. Five were attributable to alleles that affect plant height (PH) and heading date (HD), two growth traits that are known to be highly correlated with ShB resistance. By utilizing an approach that treated growth traits as covariates in the mapping model, we were able to infer that the remaining four QTL are involved in ShB resistance. Two of these, qShB1-2 and qShB4, are different from previously identified ShB QTL and represent new candidates for further study. CONCLUSION Our findings suggest that ShB resistance can be improved through favorable plant growth traits and the combined effects of small to moderate-effect resistance QTL. Additionally, we show that including PH and HD as covariates in QTL mapping models is a powerful way to identify new ShB resistance QTL.
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Affiliation(s)
- David M Goad
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1137, St. Louis, MO, 63110, USA
| | - Yulin Jia
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, 2890 HWY 130 E, Stuttgart, AR, 72160, USA.
| | - Andrew Gibbons
- University of Arkansas Rice Research and Extension Center, 2900 AR-130, Stuttgart, AR, 72160, USA
- Present address: Arkansas Department of Health, Little Rock, AR, 72205, USA
| | - Yan Liu
- Present address: Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - David Gealy
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, 2890 HWY 130 E, Stuttgart, AR, 72160, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1137, St. Louis, MO, 63110, USA
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Vo KTX, Lee SK, Halane MK, Song MY, Hoang TV, Kim CY, Park SY, Jeon J, Kim ST, Sohn KH, Jeon JS. Pi5 and Pii Paired NLRs Are Functionally Exchangeable and Confer Similar Disease Resistance Specificity. Mol Cells 2019; 42:637-645. [PMID: 31564075 PMCID: PMC6776156 DOI: 10.14348/molcells.2019.0070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 01/06/2023] Open
Abstract
Effector-triggered immunity (ETI) is an effective layer of plant defense initiated upon recognition of avirulence (Avr) effectors from pathogens by cognate plant disease resistance (R) proteins. In rice, a large number of R genes have been characterized from various cultivars and have greatly contributed to breeding programs to improve resistance against the rice blast pathogen Magnaporthe oryzae. The extreme diversity of R gene repertoires is thought to be a result of co-evolutionary history between rice and its pathogens including M. oryzae. Here we show that Pii is an allele of Pi5 by DNA sequence characterization and complementation analysis. Pii-1 and Pii-2 cDNAs were cloned by reverse transcription polymerase chain reaction from the Pii -carrying cultivar Fujisaka5 . The complementation test in susceptible rice cultivar Dongjin demonstrated that the rice blast resistance mediated by Pii , similar to Pi5 , requires the presence of two nucleotide-binding leucine-rich repeat genes, Pii-1 and Pii-2 . Consistent with our hypothesis that Pi5 and Pii are functionally indistinguishable, the replacement of Pii-1 by Pi5-1 and Pii-2 by Pi5-2 , respectively, does not change the level of disease resistance to M. oryzae carrying AVR-Pii. Surprisingly, Exo70F3, required for Pii-mediated resistance, is dispensable for Pi5-mediated resistance. Based on our results, despite similarities observed between Pi5 and Pii, we hypothesize that Pi5 and Pii pairs require partially distinct mechanisms to function.
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Affiliation(s)
- Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Sang-Kyu Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Morgan K. Halane
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Min-Young Song
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Trung Viet Hoang
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Chi-Yeol Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Sook-Young Park
- Department of Plant Medicine, Sunchon National University, Suncheon 57922,
Korea
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541,
Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 46241,
Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
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Chen X, Jia Y, Jia MH, Pinson SRM, Wang X, Wu BM. Functional Interactions Between Major Rice Blast Resistance Genes, Pi-ta and Pi-b, and Minor Blast Resistance Quantitative Trait Loci. PHYTOPATHOLOGY 2018; 108:1095-1103. [PMID: 29658844 DOI: 10.1094/phyto-02-18-0032-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Major blast resistance (R) genes confer resistance in a gene-for-gene manner. However, little information is available on interactions between R genes. In this study, interactions between two rice blast R genes, Pi-ta and Pi-b, and other minor blast resistance quantitative trait loci (QTLs) were investigated in a recombinant inbred line (RIL) population comprising 243 RILs from a Cybonnet (CYBT) × Saber (SB) cross. CYBT has the R gene Pi-ta and SB has Pi-b. Ten differential isolates of four Magnaporthe oryzae races (IB-1, IB-17, IB-49, and IE-1K) were used to evaluate disease reactions of the 243 RILs under greenhouse conditions. Five resistance QTLs were mapped on chromosomes 2, 3, 8, 9, and 12 with a linkage map of 179 single nucleotide polymorphism markers. Among them, qBR12 (Q1), was mapped at the Pi-ta locus and accounted for 45.41% of phenotypic variation while qBR2 (Q2) was located at the Pi-b locus and accounted for 24.81% of disease reactions. The additive-by-additive epistatic interaction between Q1 (Pi-ta) and Q2 (Pi-b) was detected; they can enhance the disease resistance by an additive 0.93 using the 0 to 9 standard phenotyping method. These results suggest that Pi-ta interacts synergistically with Pi-b.
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Affiliation(s)
- Xinglong Chen
- First and sixth authors: Department of Plant Pathology, China Agricultural University, Beijing, China 100193; and first, second, third, fourth, and fifth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center (DB NRRC), Stuttgart, AR 72160
| | - Yulin Jia
- First and sixth authors: Department of Plant Pathology, China Agricultural University, Beijing, China 100193; and first, second, third, fourth, and fifth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center (DB NRRC), Stuttgart, AR 72160
| | - Melissa H Jia
- First and sixth authors: Department of Plant Pathology, China Agricultural University, Beijing, China 100193; and first, second, third, fourth, and fifth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center (DB NRRC), Stuttgart, AR 72160
| | - Shannon R M Pinson
- First and sixth authors: Department of Plant Pathology, China Agricultural University, Beijing, China 100193; and first, second, third, fourth, and fifth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center (DB NRRC), Stuttgart, AR 72160
| | - Xueyan Wang
- First and sixth authors: Department of Plant Pathology, China Agricultural University, Beijing, China 100193; and first, second, third, fourth, and fifth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center (DB NRRC), Stuttgart, AR 72160
| | - B M Wu
- First and sixth authors: Department of Plant Pathology, China Agricultural University, Beijing, China 100193; and first, second, third, fourth, and fifth authors: U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Dale Bumpers National Rice Research Center (DB NRRC), Stuttgart, AR 72160
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Sheng X, Qiu Y, Zhou Y, Zhu W. Joint parameter estimation in the QTL mapping of ordinal traits. J Theor Biol 2017; 432:100-108. [PMID: 28807804 DOI: 10.1016/j.jtbi.2017.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 07/09/2017] [Accepted: 08/05/2017] [Indexed: 11/19/2022]
Abstract
With the rapid development of statistical genetics, the deep researches of ordinal traits have been gradually emphasized. The data of these traits bear relatively less information than those of continuous phenotypes, therefore it is more complex to map the quantitative trait loci (QTL) of ordinal traits. In this paper, the multiple-interval mapping method is considered in the genetic mapping of ordinal traits. By combining threshold model and statistical model, we build a cumulative logistic regression model to express the relationship between the ordinal data and the QTL genotypes. In order to make the interval mapping more straightforward, we treat the recombination rates as unknown parameters, and then simultaneously obtain the estimates of QTL positions, QTL effects and threshold parameters via the EM algorithm. We perform simulation experiments to investigate and compare the proposed method. We also present a real example to test the reasonableness of the considered model and estimate both model parameters and QTL parameters. Both results of simulations and example show that the method we proposed is reasonable and effective.
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Affiliation(s)
- Xiaona Sheng
- School of Information Engineering, Harbin University, Harbin 150086, China
| | - Yihong Qiu
- School of Mathematical Sciences, Heilongjiang University, Harbin 150080, China
| | - Ying Zhou
- School of Mathematical Sciences, Heilongjiang University, Harbin 150080, China.
| | - Wensheng Zhu
- School of Mathematics and Statistics,Northeast Normal University, Changchun 130024, China.
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9
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Kang H, Wang Y, Peng S, Zhang Y, Xiao Y, Wang D, Qu S, Li Z, Yan S, Wang Z, Liu W, Ning Y, Korniliev P, Leung H, Mezey J, McCouch SR, Wang GL. Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2016; 17:959-72. [PMID: 26574735 PMCID: PMC6638458 DOI: 10.1111/mpp.12340] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 05/12/2023]
Abstract
Resistance in rice cultivars to the rice blast fungus Magnaporthe oryzae is complex and is controlled by both major genes and quantitative trait loci (QTLs). We undertook a genome-wide association study (GWAS) using the rice diversity panel 1 (RDP1) that was genotyped using a high-density (700 000 single nucleotide polymorphisms) array and inoculated with five diverse M. oryzae isolates. We identified 97 loci associated with blast resistance (LABRs). Among them, 82 were new regions and 15 co-localized with known blast resistance loci. The top 72 LABRs explained up to 98% of the phenotypic variation. The candidate genes in the LABRs encode nucleotide-binding site leucine-rich repeat (NBS-LRR) resistance proteins, receptor-like protein kinases, transcription factors and defence-related proteins. Among them, LABR_64 was strongly associated with resistance to all five isolates. We analysed the function of candidate genes underlying LABR_64 using RNA interference (RNAi) technology and identified two new resistance alleles at the Pi5 locus. We demonstrate an efficient strategy for rapid allele discovery using the power of GWAS, coupled with RNAi technology, for the dissection of complex blast resistance in rice.
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Affiliation(s)
- Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yue Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Shasha Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanli Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yinghui Xiao
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Dan Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Shaohong Qu
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shuangyong Yan
- Tianjin Crop Research Institute, Tianjin Academy of Agriculture Sciences, Tianjin, 300112, China
| | - Zhilong Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Pavel Korniliev
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Hei Leung
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila 1301, Philippines
| | - Jason Mezey
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Susan R McCouch
- Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA
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Jia Y, Zhou E, Lee S, Bianco T. Coevolutionary Dynamics of Rice Blast Resistance Gene Pi-ta and Magnaporthe oryzae Avirulence Gene AVR-Pita 1. PHYTOPATHOLOGY 2016; 106:676-83. [PMID: 27070427 DOI: 10.1094/phyto-02-16-0057-rvw] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The Pi-ta gene in rice is effective in preventing infections by Magnaporthe oryzae strains that contain the corresponding avirulence gene, AVR-Pita1. Diverse haplotypes of AVR-Pita1 have been identified from isolates of M. oryzae from rice production areas in the United States and worldwide. DNA sequencing and mapping studies have revealed that AVR-Pita1 is highly unstable, while expression analysis and quantitative resistance loci mapping of the Pi-ta locus revealed complex evolutionary mechanisms of Pi-ta-mediated resistance. Among these studies, several Pi-ta transcripts were identified, most of which are probably derived from alternative splicing and exon skipping, which could produce functional resistance proteins that support a new concept of coevolution of Pi-ta and AVR-Pita1. User-friendly DNA markers for Pi-ta have been developed to support marker-assisted selection, and development of new rice varieties with the Pi-ta markers. Genome-wide association studies revealed a link between Pi-ta-mediated resistance and yield components suggesting that rice has evolved a complicated defense mechanism against the blast fungus. In this review, we detail the current understanding of Pi-ta allelic variation, its linkage with rice productivity, AVR-Pita allelic variation, and the coevolution of Pi-ta and AVR-Pita in Oryza species and M. oryzae populations, respectively. We also review the genetic and molecular basis of Pi-ta and AVR-Pita interaction, and its value in marker-assisted selection and engineering resistance.
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Affiliation(s)
- Yulin Jia
- First and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160; second author: Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China; and third author: Department of Horticultural Science, Gulf Coast Research & Education Center, Institute of Food & Agricultural Science, University of Florida, Wimauma 33598
| | - Erxun Zhou
- First and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160; second author: Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China; and third author: Department of Horticultural Science, Gulf Coast Research & Education Center, Institute of Food & Agricultural Science, University of Florida, Wimauma 33598
| | - Seonghee Lee
- First and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160; second author: Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China; and third author: Department of Horticultural Science, Gulf Coast Research & Education Center, Institute of Food & Agricultural Science, University of Florida, Wimauma 33598
| | - Tracy Bianco
- First and fourth authors: U.S. Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR 72160; second author: Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China; and third author: Department of Horticultural Science, Gulf Coast Research & Education Center, Institute of Food & Agricultural Science, University of Florida, Wimauma 33598
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Liu Y, Qi X, Gealy DR, Olsen KM, Caicedo AL, Jia Y. QTL Analysis for Resistance to Blast Disease in U.S. Weedy Rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:834-44. [PMID: 25761210 DOI: 10.1094/mpmi-12-14-0386-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Understanding the genetic architecture of adaptation is of great importance in evolutionary biology. U.S. weedy rice is well adapted to the local conditions in U.S. rice fields. Rice blast disease is one of the most destructive diseases of cultivated rice worldwide. However, information about resistance to blast in weedy rice is limited. Here, we evaluated the disease reactions of 60 U.S. weedy rice accessions with 14 blast races, and investigated the quantitative trait loci (QTL) associated with blast resistance in two major ecotypes of U.S. weedy rice. Our results revealed that U.S. weedy rice exhibited a broad resistance spectrum. Using genotyping by sequencing, we identified 28 resistance QTL in two U.S. weedy rice ecotypes. The resistance QTL with relatively large and small effects suggest that U.S. weedy rice groups have adapted to blast disease using two methods, both major resistance (R) genes and QTL. Three genomic loci shared by some of the resistance QTL indicated that these loci may contribute to no-race-specific resistance in weedy rice. Comparing with known blast disease R genes, we found that the R genes at these resistance QTL are novel, suggesting that U.S. weedy rice is a potential source of novel blast R genes for resistant breeding.
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Affiliation(s)
- Yan Liu
- 1 Rice Research and Extension Center, University of Arkansas, Stuttgart 72160, U.S.A
- 2 United States Department of Agriculture-Agricultural Research Service Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, U.S.A
| | - Xinshuai Qi
- 3 Department of Biology, Washington University in St. Louis, St. Louis 63130-4899, U.S.A.; and
| | - Dave R Gealy
- 2 United States Department of Agriculture-Agricultural Research Service Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, U.S.A
| | - Kenneth M Olsen
- 3 Department of Biology, Washington University in St. Louis, St. Louis 63130-4899, U.S.A.; and
| | - Ana L Caicedo
- 4 Biology Department, University of Massachusetts Amherst, 01003, U.S.A
| | - Yulin Jia
- 2 United States Department of Agriculture-Agricultural Research Service Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, U.S.A
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Wu Y, Xiao N, Yu L, Pan C, Li Y, Zhang X, Liu G, Dai Z, Pan X, Li A. Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L.). PLoS One 2015; 10:e0126130. [PMID: 26030358 PMCID: PMC4452627 DOI: 10.1371/journal.pone.0126130] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/29/2015] [Indexed: 11/18/2022] Open
Abstract
Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as 'Pi9+Pi54', 'Pid3+Pigm', 'Pi5+Pid3+Pigm', 'Pi5+Pi54+Pid3+Pigm', 'Pi5+Pid3' and 'Pi5+Pit+Pid3' in indica-type accessions and 'Pik+Pib', 'Pik+Pita', 'Pik+Pb1', 'Pizt+Pia' and 'Pizt+Pita' in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance.
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Affiliation(s)
- Yunyu Wu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou, 225009, P.R. China
| | - Ning Xiao
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
| | - Ling Yu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
| | - Cunhong Pan
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
| | - Yuhong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
| | - Xiaoxiang Zhang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
| | - Guangqing Liu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
| | - Zhengyuan Dai
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
| | - Xuebiao Pan
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou, 225009, P.R. China
- * E-mail: (XBP); (AHL)
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou, 225007, P.R. China
- * E-mail: (XBP); (AHL)
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Fukuoka S, Mizobuchi R, Saka N, Suprun I, Matsumoto T, Okuno K, Yano M. A multiple gene complex on rice chromosome 4 is involved in durable resistance to rice blast. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:551-9. [PMID: 22446930 PMCID: PMC3397134 DOI: 10.1007/s00122-012-1852-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/10/2012] [Indexed: 05/03/2023]
Abstract
Quantitative trait loci (QTLs) for resistance to rice blast offer a potential source of durable disease resistance in rice. However, few QTLs have been validated in progeny testing, on account of their small phenotypic effects. To understand the genetic basis for QTL-mediated resistance to blast, we dissected a resistance QTL, qBR4-2, using advanced backcross progeny derived from a chromosome segment substitution line in which a 30- to 34-Mb region of chromosome 4 from the resistant cultivar Owarihatamochi was substituted into the genetic background of the highly susceptible Aichiasahi. The analysis resolved qBR4-2 into three loci, designated qBR4-2a, qBR4-2b, and qBR4-2c. The sequences of qBR4-2a and qBR4-2b, which lie 181 kb apart from each other and measure, 113 and 32 kb, respectively, appear to encode proteins with a putative nucleotide-binding site (NBS) and leucine-rich repeats (LRRs). Sequence analysis of the donor allele of qBR4-2a, the region with the largest effect among the three, revealed sequence variations in the NBS-LRR region. The effect of qBR4-2c was smallest among the three, but its combination with the donor alleles of qBR4-2a and qBR4-2b significantly enhanced blast resistance. qBR4-2 comprises three tightly linked QTLs that control blast resistance in a complex manner, and thus gene pyramiding or haplotype selection is the recommended strategy for improving QTL-mediated resistance to blast disease through the use of this chromosomal region.
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Affiliation(s)
- S Fukuoka
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
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Wang Y, Wang D, Deng X, Liu J, Sun P, Liu Y, Huang H, Jiang N, Kang H, Ning Y, Wang Z, Xiao Y, Liu X, Liu E, Dai L, Wang GL. Molecular mapping of the blast resistance genes Pi2-1 and Pi51(t) in the durably resistant rice 'Tianjingyeshengdao'. PHYTOPATHOLOGY 2012; 102:779-86. [PMID: 22779744 DOI: 10.1094/phyto-03-12-0042-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Tianjingyeshengdao' (TY) is a rice cultivar with durable resistance to populations of Magnaporthe oryzae (the causal agent of blast) in China. To understand the genetic basis of its resistance to blast, we developed a population of recombinant inbred lines from a cross between TY and the highly susceptible 'CO39' for gene mapping analysis. In total, 22 quantitative trait loci (QTLs) controlling rice blast resistance were identified on chromosomes 1, 3, 4, 5, 6, 9, 11, and 12 from the evaluation of four disease parameters in both greenhouse and blast nursery conditions. Among these QTLs, 19 were contributed by TY and three by CO39. Two QTL clusters on chromosome 6 and 12 were named Pi2-1 and Pi51(t), respectively. Pi2-1 was detected under both growth chamber and natural blast nursery conditions, and explained 31.24 to 59.73% of the phenotypic variation. Pi51(t) was only detected in the natural blast nursery and explained 3.67 to 10.37% of the phenotypic variation. Our results demonstrate that the durable resistance in TY is controlled by two major and seven minor genes. Identification of the markers linked to both Pi2-1 and Pi51(t) in this study should be useful for marker-aided selection in rice breeding programs as well as for molecular cloning of the identified resistance genes.
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Affiliation(s)
- Yue Wang
- Hunan Key Laboratory of Crop Germplasm Innovation and Utilization and College of Agronomy, Hunan Agriculture University, Cahngsha, China
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