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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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Al-Bader N, Meier A, Geniza M, Gongora YS, Oard J, Jaiswal P. Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 ( WAK91) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance. Genes (Basel) 2023; 14:1673. [PMID: 37761813 PMCID: PMC10530950 DOI: 10.3390/genes14091673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10-30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease.
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Affiliation(s)
- Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR 97331, USA
| | - Austin Meier
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR 97331, USA
| | - Yamid Sanabria Gongora
- Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (Y.S.G.); (J.O.)
| | - James Oard
- Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (Y.S.G.); (J.O.)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (N.A.-B.); (A.M.); (M.G.)
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Ma X, Zhu M, Liu W, Li J, Liao Y, Liu D, Jin M, Fu C, Wang F. Bulk segregant analysis coupled with transcriptomics and metabolomics revealed key regulators of bacterial leaf blight resistance in rice. BMC PLANT BIOLOGY 2023; 23:332. [PMID: 37349684 DOI: 10.1186/s12870-023-04347-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 06/14/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Bacterial leaf blight (BLB) is a highly destructive disease, causing significant yield losses in rice (Oryza sativa). Genetic variation is contemplated as the most effective measure for inducing resistance in plants. The mutant line T1247 derived from R3550 (BLB susceptible) was highly resistant to BLB. Therefore, by utilizing this valuable source, we employed bulk segregant analysis (BSA) and transcriptome profiling to identify the genetic basis of BLB resistance in T1247. RESULTS The differential subtraction method in BSA identified a quantitative trait locus (QTL) on chromosome 11 spanning a 27-27.45 Mb region with 33 genes and 4 differentially expressed genes (DEGs). Four DEGs (P < 0.01) with three putative candidate genes, OsR498G1120557200, OsR498G1120555700, and OsR498G1120563600,0.01 in the QTL region were identified with specific regulation as a response to BLB inoculation. Moreover, transcriptome profiling identified 37 resistance analogs genes displaying differential regulation. CONCLUSIONS Our study provides a substantial addition to the available information regarding QTLs associated with BLB, and further functional verification of identified candidate genes can broaden the scope of understanding the BLB resistance mechanism in rice.
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Affiliation(s)
- Xiaozhi Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Manshan Zhu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wuge Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jinhua Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Yilong Liao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Mengya Jin
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Chongyun Fu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China.
- Guangdong Rice Engineering Laboratory, Guangzhou, China.
| | - Feng Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China.
- Guangdong Rice Engineering Laboratory, Guangzhou, China.
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Li J, Shi X, Wang C, Li Q, Lu J, Zeng D, Xie J, Shi Y, Zhai W, Zhou Y. Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm. Int J Mol Sci 2023; 24:ijms24108810. [PMID: 37240156 DOI: 10.3390/ijms24108810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate Japonica accessions inoculated with two Chinese Xoo strains (KS6-6 and GV) and one Philippine Xoo strain (PXO99A). Based on the 55K SNPs Array dataset of the 359 Japonica accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six R genes were localized in the qBBV-11.1, qBBV-11.2, and qBBV-11.3 loci on chromosome 11 in this Japonica collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, LOC_Os11g47290 in qBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of LOC_Os11g47290 exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.
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Affiliation(s)
- Jianmin Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xiaorong Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chunchao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quanlin Li
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Jialing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dan Zeng
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junping Xie
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yongli Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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My PDT, Vinh TQ, Ngoc TH, Anh PNQ, Duyen LTM, Thien NM, Tien LTT, Phuc VT, Oanh HN, Nga LP, Hoang HA. Complete genome sequence of a novel lytic phage of Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen in rice. Arch Virol 2023; 168:157. [PMID: 37160612 DOI: 10.1007/s00705-023-05788-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
Bacteriophage L522, which infects Xanthomonas oryzae pv. oryzae, was isolated from a paddy leaf sample collected in Long An province, Vietnam. The phage shows myovirus morphology based on transmission electron microscopy. It displays a latent period and burst size of approximately 3 h and 63 new virions per infected cell (PFU/infected cell), respectively. The genome of L522 is 44,497 bp in length, with 52% GC content. Of the 63 genes identified, functions were predicted for 26. No virulence or antibiotic-resistance genes were detected. The results of a BLASTn search showed similarity to a previously reported Xanthomonas phage, with 85% average nucleotide sequence identity and 87.15% query coverage. Thus, this L522 is a representative of a new species in the genus Xipdecavirus.
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Affiliation(s)
- Pham D T My
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Tu Q Vinh
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - To H Ngoc
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Pham N Q Anh
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Le T M Duyen
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Nguyen M Thien
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Le T T Tien
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Vo T Phuc
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Huynh N Oanh
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Le P Nga
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Hoang A Hoang
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet, District 10, Ho Chi Minh City, Vietnam.
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam.
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Ma L, Yu Y, Li C, Wang P, Liu K, Ma W, Wang W, Fan Y, Xiong Z, Jiang T, Zhang J, Wang Z, Wang J, Zhang H, Bao Y. Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene Pb3 Encoding NLR Protein. Int J Mol Sci 2022; 23:ijms232214032. [PMID: 36430507 PMCID: PMC9698523 DOI: 10.3390/ijms232214032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Rice blast is a worldwide fungal disease that seriously affects the yield and quality of rice. Identification of resistance genes against rice blast disease is one of the effective ways to control this disease. However, panicle blast resistance genes, which are useful in the fields, have rarely been studied due to the difficulty in phenotypic identification and the environmental influences. Here, panicle blast resistance-3 (Pb3) was identified by a genome-wide association study (GWAS) based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel I (RDP-I) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A total of 16 panicle blast resistance loci (PBRLs) within three years including one repeated locus PBRL3 located in chromosome 11 were identified. In addition, 7 genes in PBRL3 were identified as candidate genes by haplotype analysis, which showed significant differences between resistant and susceptible varieties. Among them, one nucleotide-binding domain and Leucine-rich Repeat (NLR) gene Pb3 was highly conserved in multiple resistant rice cultivars, and its expression was significantly induced after rice blast inoculation. Evolutionary analysis showed that Pb3 was a typical disease resistance gene containing coiled-coil, NB-ARC, and LRR domains. T-DNA insertion mutants and CRISPR lines of Pb3 showed significantly reduced panicle blast resistance. These results indicate that Pb3 is a panicle blast resistance gene and GWAS is a rapid method for identifying panicle blast resistance in rice.
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Affiliation(s)
- Lu Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yao Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Changqing Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Panting Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kunquan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunxin Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziwei Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingran Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhixue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Park JR, Lee CM, Ji H, Baek MK, Seo J, Jeong OY, Park HS. Characterization and QTL Mapping of a Major Field Resistance Locus for Bacterial Blight in Rice. PLANTS 2022; 11:plants11111404. [PMID: 35684177 PMCID: PMC9182613 DOI: 10.3390/plants11111404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022]
Abstract
Bacterial blight (BB) disease, caused by Xanthomonas oryzae pv. oryzae (Xoo), is among the major factors that can cause rice yields to decrease. To address BB disease, researchers have been looking for ways to change pesticides and cultivation methods, but developing resistant cultivars is the most effective method. However, the resistance and genetic factors of cultivars may be destroyed due to the emergence of new Xoo species caused by recent and rapid climate changes. Therefore, breeders need to identify resistance genes that can be sustained during unpredictable climate changes and utilized for breeding. Here, qBBR11, a quantitative trait locus (QTL) for resistance to BB disease, was detected in KJ (Korea Japonica varieties) 11_067 to KJ11_068 on chromosome 11 in a population derived by crossing JJ (Jeonju) 623 and HR(High resistant)27,195, which possess similar genetic backgrounds but different degrees of resistance to BB disease. qBBR11 was reduced from 18.49–18.69 Mbp of chromosome 11 to 200 kbp segment franked. In this region, 16 candidate genes were detected, and we identified 24 moderate-impact variations and four high-impact variations. In particular, high-impact variations were detected in Os11g0517800 which encode the domain region of GCN2 which is the eIF-2-alpha kinase associated with the resistance of abiotic/biotic stress in rice. In JJ623, which is moderately resistant to BB disease, a stop codon was created due to single nucleotide polymorphism (SNP). Therefore, compared with HR27195, JJ623 has weaker resistance to BB disease, though the two have similar genetic backgrounds. The results suggest that variation in the qBBR11 region regulates an important role in improving resistance to BB diseases, and qBBR11 is useful in providing an important resource for marker-assisted selection to improve mechanisms of resistance to BB disease.
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Affiliation(s)
- Jae-Ryoung Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea;
| | - Man-Kee Baek
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Jeonghwan Seo
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - O-Young Jeong
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
| | - Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (J.-R.P.); (C.-M.L.); (M.-K.B.); (J.S.); (O.-Y.J.)
- Correspondence: ; Tel.: +82-63-238-5214
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Mao F, Wu D, Lu F, Yi X, Gu Y, Liu B, Liu F, Tang T, Shi J, Zhao X, Liu L, Ji L. QTL mapping and candidate gene analysis of low temperature germination in rice ( Oryza sativa L.) using a genome wide association study. PeerJ 2022; 10:e13407. [PMID: 35578671 PMCID: PMC9107303 DOI: 10.7717/peerj.13407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/18/2022] [Indexed: 01/14/2023] Open
Abstract
Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.
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Affiliation(s)
- Feng Mao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China,Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Depeng Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fangfang Lu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Xin Yi
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Bin Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Jianxin Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lilian Ji
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China
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9
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Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xanthomonas oryzae pv. oryzae in the F 6 Generation. PLANTS 2021; 10:plants10102048. [PMID: 34685858 PMCID: PMC8540907 DOI: 10.3390/plants10102048] [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: 08/24/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022]
Abstract
Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is one of the most important diseases in rice. It results in significantly reduced productivity throughout all rice-growing regions of the world. Four BB resistance genes have been reported; however, introgression of a single gene into rice has not been able to sufficiently protect rice against BB infection. Pyramiding of effective BB resistance genes (i.e., Xa genes) into background varieties is a potential approach to controlling BB infection. In this study, combinations of four BB resistance genes, Xa4, xa5, xa13, and Xa21, were pyramided into populations. The populations were derived from crossing Ciherang (a widespread Indonesian rice variety) with IRBB60 (resistance to BB). Promising recombinants from the F6 generation were identified by scoring the phenotype against three virulent bacterial strains, C5, P6, and V, which cause widespread BB infection in most rice-growing countries. Pyramiding of genes for BB resistance in 265 recombinant introgressed lines (RILs) were confirmed through marker-assisted selection (MAS) of the F5 and F6 generations using gene-specific primers. Of these 265 RILs, 11, 34 and 45 lines had four, three, or two BB resistance genes, respectively. The RILs had pyramiding of two or three resistance genes, with the Xa4 resistance gene showing broad spectrum resistance against Xoo races with higher agronomic performance compared to their donor and recipients parents. The developed BB-resistant RILs have high yield potential to be further developed for cultivation or as sources of BB resistance donor material for varietal improvement in other rice lines.
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10
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Jacobs JM, Wang GL. Next Generation Rice Disease Research. RICE (NEW YORK, N.Y.) 2021; 14:84. [PMID: 34570288 PMCID: PMC8476694 DOI: 10.1186/s12284-021-00523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210 USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210 USA
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210 USA
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