1
|
Vasquez-Teuber P, Rouxel T, Mason AS, Soyer JL. Breeding and management of major resistance genes to stem canker/blackleg in Brassica crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:192. [PMID: 39052130 PMCID: PMC11272824 DOI: 10.1007/s00122-024-04641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/29/2024] [Indexed: 07/27/2024]
Abstract
Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.
Collapse
Affiliation(s)
- Paula Vasquez-Teuber
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
- Department of Plant Production, Faculty of Agronomy, University of Concepción, Av. Vicente Méndez 595, Chillán, Chile
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany.
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Wang C, Liu WJ, Liao XW, Xu X, Yang S, Zhang XB, Zhou H, Zhuang C, Gong J, Wu JL. The Identification and Gene Mapping of Spotted Leaf Mutant spl43 in Rice. Int J Mol Sci 2024; 25:6637. [PMID: 38928342 PMCID: PMC11203680 DOI: 10.3390/ijms25126637] [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: 04/29/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Our study investigates the genetic mechanisms underlying the spotted leaf phenotype in rice, focusing on the spl43 mutant. This mutant is characterized by persistent reddish-brown leaf spots from the seedling stage to maturity, leading to extensive leaf necrosis. Using map-based cloning, we localized the responsible locus to a 330 Kb region on chromosome 2. We identified LOC_Os02g56000, named OsRPT5A, as the causative gene. A point mutation in OsRPT5A, substituting valine for glutamic acid, was identified as the critical factor for the phenotype. Functional complementation and the generation of CRISPR/Cas9-mediated knockout lines in the IR64 background confirmed the central role of OsRPT5A in controlling this trait. The qPCR results from different parts of the rice plant revealed that OsRPT5A is constitutively expressed across various tissues, with its subcellular localization unaffected by the mutation. Notably, we observed an abnormal accumulation of reactive oxygen species (ROS) in spl43 mutants by examining the physiological indexes of leaves, suggesting a disruption in the ROS system. Complementation studies indicated OsRPT5A's involvement in ROS homeostasis and catalase activity regulation. Moreover, the spl43 mutant exhibited enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo), highlighting OsRPT5A's role in rice pathogen resistance mechanisms. Overall, our results suggest that OsRPT5A plays a critical role in regulating ROS homeostasis and enhancing pathogen resistance in rice.
Collapse
Affiliation(s)
- Chen Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (C.Z.)
| | - Wen-Jun Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
| | - Xin-Wei Liao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
| | - Xia Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
| | - Xiao-Bo Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (C.Z.)
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (H.Z.); (C.Z.)
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
| | - Jian-Li Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; (C.W.); (W.-J.L.); (X.-W.L.); (X.X.); (S.Y.); (X.-B.Z.)
| |
Collapse
|
4
|
Aloryi KD, Okpala NE, Guo H, Karikari B, Amo A, Bello SF, Saini DK, Akaba S, Tian X. Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice. BMC Genomics 2024; 25:338. [PMID: 38575927 PMCID: PMC10993490 DOI: 10.1186/s12864-024-10219-z] [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: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.
Collapse
Grants
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- Key R&D Project in Hubei Province, China
Collapse
Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Hong Guo
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Benjamin Karikari
- Département de phytologie, Université Laval, Québec, QC, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Aduragbemi Amo
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, USA
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China.
| |
Collapse
|
5
|
Švara A, De Storme N, Carpentier S, Keulemans W, De Coninck B. Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab ( Venturia inaequalis) in apple cultivars ( Malus × domestica). HORTICULTURE RESEARCH 2024; 11:uhae002. [PMID: 38371632 PMCID: PMC10873587 DOI: 10.1093/hr/uhae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/27/2023] [Indexed: 02/20/2024]
Abstract
Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent "-omics" approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different "-omics" approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.
Collapse
Affiliation(s)
- Anže Švara
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Nico De Storme
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Genetic resources, Bioversity International, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Wannes Keulemans
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
- KU Leuven Plant Institute, KU Leuven 3001 Leuven, Belgium
| | - Barbara De Coninck
- Laboratory of Plant Health and Protection, Division of Crop Biotechnics, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Laboratory for Plant Genetics and Crop Improvement, Division of Crop Biotechnics, KU Leuven Plant Institute, Willem de Croylaan 42, 3001 Leuven, Belgium
| |
Collapse
|
6
|
Scheuermann KK, Pereira A. Development of a molecular marker for the Pi1 gene based on the association of the SNAP protocol with the touch-up gradient amplification method. J Microbiol Methods 2023; 214:106845. [PMID: 37858898 DOI: 10.1016/j.mimet.2023.106845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Genetic resistance is the most effective and eco-friendly approach to combat rice blast. The application of resistance genes may be facilitated by the availability of molecular markers that allow marker-assisted selection during the breeding process. The Pi1 gene, considered to be a broad-spectrum resistance gene, might contribute to enhancing resistance to rice blast, but it lacks a suitable marker that can be used. In this study, we investigated nucleotide polymorphism in the Pik locus and combined the SNAP protocol with the touch-up gradient amplification method to develop a SNAP marker. The Pi1 SNAP marker could distinguish Pi1 from Pik alleles, and when used for screening a germplasm bank and an F2 population, it consistently identified germplasms carrying the Pi1 gene. The P1 SNAP marker offers as advantages to involve only the presence/absence analysis of PCR amplicons resolved on an agarose gel.
Collapse
Affiliation(s)
- Klaus Konrad Scheuermann
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Estação Experimental de Itajaí - Epagri-EEI. C.P. 277, Itajaí, SC CEP 88318-112, Brazil.
| | - Adriana Pereira
- Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Estação Experimental de Itajaí - Epagri-EEI. C.P. 277, Itajaí, SC CEP 88318-112, Brazil
| |
Collapse
|
7
|
Nagata K, Nonoue Y, Matsubara K, Mizobuchi R, Ono N, Shibaya T, Ebana K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Sun J, Kuya N, Kitomi Y, Iijima K, Nagasaki H, Shomura A, Mizubayashi T, Kitazawa N, Hori K, Ando T, Yamamoto T, Fukuoka S, Yano M. Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice. BREEDING SCIENCE 2023; 73:332-342. [PMID: 37840983 PMCID: PMC10570878 DOI: 10.1270/jsbbs.23006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 10/17/2023]
Abstract
Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.
Collapse
Affiliation(s)
- Kazufumi Nagata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuki Matsubara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ritsuko Mizobuchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Taeko Shibaya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kaworu Ebana
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eri Ogiso-Tanaka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takanari Tanabata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuhiko Sugimoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fumio Taguchi-Shiobara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Atsunori Fukuda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tadamasa Ueda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shin-ichi Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Utako Yamanouchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshiyuki Takai
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takashi Ikka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Katsuhiko Kondo
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoki Hoshino
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eiji Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shunsuke Adachi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jian Sun
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kuya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yuka Kitomi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ken Iijima
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hideki Nagasaki
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ayahiko Shomura
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tatsumi Mizubayashi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kitazawa
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kiyosumi Hori
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tsuyu Ando
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshio Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| |
Collapse
|
8
|
Thi Le L, Adreit H, Thi Ha L, Milazzo J, Lebrun M, Tharreau D, Hoi Pham X, Thanh Nguyen H, Fournier E, Thi Hoang G. Population structure of Pyricularia oryzae on rice in Vietnam reveals diversified populations with four pandemic and two endemic clusters. Fungal Genet Biol 2023; 166:103794. [PMID: 37003467 DOI: 10.1016/j.fgb.2023.103794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
We characterized the genetic structure of 609 strains of Pyricularia oryzae, the fungal pathogen causing rice blast disease, in three main regions in Vietnam using microsatellites (SSR) markers. From the 447 distinct multilocus genotypes identified, six genetic clusters were defined, all of them showing elevated genetic and genotypic diversities. Four of these clusters were related to rice-attacking lineages already described at the worldwide scale, whereas the two remaining clusters were endemic to Vietnam. Strains were unevenly distributed into the six clusters depending on their groups of rice variety (indica / japonica) or type of varieties (traditional / modern) of origin, but none of the clusters was specifically related to these two factors. The highest diversity of blast population was found in Northern mountainous area, and the lowest in Red River Delta in both term of genetic diversity and gene diversity. Hierarchical AMOVAs confirmed that all three factors considered (rice variety group, type of variety origin and geography) significantly contributed to the population structure of P. oryzae in Vietnam, with highest contribution from rice variety group. Mating types were unevenly distributed among clusters. Combined with results of female fertility and linkage disequilibirum, we hypothesized that clonal reproduction probably occurred in all clusters, but that sexual reproduction likely took place at least in some restricted areas in the Northern mountainous area for strains belonging to the cluster related to the previously described recombinant lineage (worldwide lineage 1). Our study pictures the genetic diversity, population structure and reproductive mode of the blast fungus in central and north Vietnam, and shows that the observed population structure is explained by several factors, the most important one being the variability of rice variety. All these new information might help for elaborating appropriate strategies to controlling the blast disease.
Collapse
Affiliation(s)
- Lieu Thi Le
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam; University of Science and Technology of Hanoi, Hanoi, Vietnam
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Loan Thi Ha
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam
| | - Joelle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Michel Lebrun
- University of Science and Technology of Hanoi, Hanoi, Vietnam
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Xuan Hoi Pham
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam
| | - Hai Thanh Nguyen
- Vietnam National University of Agriculture, Faculty of Biotechnology, Faculty of Agronomy, Hanoi, Vietnam
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France.
| | - Giang Thi Hoang
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam; Vietnam National University of Agriculture, Faculty of Biotechnology, Faculty of Agronomy, Hanoi, Vietnam.
| |
Collapse
|
9
|
Ma J, Liu Y, Zhang P, Chen T, Tian T, Wang P, Che Z, Shahinnia F, Yang D. Identification of quantitative trait loci (QTL) and meta-QTL analysis for kernel size-related traits in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:607. [PMID: 36550393 PMCID: PMC9784057 DOI: 10.1186/s12870-022-03989-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Kernel size-related traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR) and kernel thickness (KT), are critical determinants for wheat kernel weight and yield and highly governed by a type of quantitative genetic basis. Genome-wide identification of major and stable quantitative trait loci (QTLs) and functional genes are urgently required for genetic improvement in wheat kernel yield. A hexaploid wheat population consisting of 120 recombinant inbred lines was developed to identify QTLs for kernel size-related traits under different water environments. The meta-analysis and transcriptome evaluation were further integrated to identify major genomic regions and putative candidate genes. RESULTS The analysis of variance (ANOVA) revealed more significant genotypic effects for kernel size-related traits, indicating the moderate to high heritability of 0.61-0.89. Thirty-two QTLs for kernel size-related traits were identified, explaining 3.06%-14.2% of the phenotypic variation. Eleven stable QTLs were detected in more than three water environments. The 1103 original QTLs from the 34 previous studies and the present study were employed for the MQTL analysis and refined into 58 MQTLs. The average confidence interval of the MQTLs was 3.26-fold less than that of the original QTLs. The 1864 putative candidate genes were mined within the regions of 12 core MQTLs, where 70 candidate genes were highly expressed in spikes and kernels by comprehensive analysis of wheat transcriptome data. They were involved in various metabolic pathways, such as carbon fixation in photosynthetic organisms, carbon metabolism, mRNA surveillance pathway, RNA transport and biosynthesis of secondary metabolites. CONCLUSIONS Major genomic regions and putative candidate genes for kernel size-related traits in wheat have been revealed by an integrative strategy with QTL linkage mapping, meta-analysis and transcriptomic assessment. The findings provide a novel insight into understanding the genetic determinants of kernel size-related traits and will be useful for the marker-assisted selection of high yield in wheat breeding.
Collapse
Grants
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- GHSJ 2020-Z4 Research Program Sponsored by State Key Laboratory of Aridland Crop Science, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 21YF5NA089 Key Research and Development Program of Gansu Province, China
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 2022CYZC-44 Industrial Support Plan of Colleges and Universities in Gansu Province
- 31760385 National Natural Science Foundation of China
- 31760385 National Natural Science Foundation of China
- 31760385 National Natural Science Foundation of China
- 31760385 National Natural Science Foundation of China
- 31760385 National Natural Science Foundation of China
- 31760385 National Natural Science Foundation of China
- 31760385 National Natural Science Foundation of China
- 31760385 National Natural Science Foundation of China
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- 22ZD6NA010 Key Sci & Tech Special Project of Gansu Province
- Key Sci & Tech Special Project of Gansu Province
Collapse
Affiliation(s)
- Jingfu Ma
- State Key Lab of Aridland Crop Science, Lanzhou, Gansu, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Peipei Zhang
- State Key Lab of Aridland Crop Science, Lanzhou, Gansu, China
| | - Tao Chen
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Tian Tian
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Peng Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Lanzhou, Gansu, China
| | - Fahimeh Shahinnia
- Institute for Crop Science and Plant Breeding, Bavarian State Research Centre for Agriculture, Freising, Germany
| | - Delong Yang
- State Key Lab of Aridland Crop Science, Lanzhou, Gansu, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China.
| |
Collapse
|
10
|
Aloryi KD, Okpala NE, Amo A, Bello SF, Akaba S, Tian X. A meta-quantitative trait loci analysis identified consensus genomic regions and candidate genes associated with grain yield in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1035851. [PMID: 36466247 PMCID: PMC9709451 DOI: 10.3389/fpls.2022.1035851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Improving grain yield potential in rice is an important step toward addressing global food security challenges. The meta-QTL analysis offers stable and robust QTLs irrespective of the genetic background of mapping populations and phenotype environment and effectively narrows confidence intervals (CI) for candidate gene (CG) mining and marker-assisted selection improvement. To achieve these aims, a comprehensive bibliographic search for grain yield traits (spikelet fertility, number of grains per panicle, panicles number per plant, and 1000-grain weight) QTLs was conducted, and 462 QTLs were retrieved from 47 independent QTL research published between 2002 and 2022. QTL projection was performed using a reference map with a cumulative length of 2,945.67 cM, and MQTL analysis was conducted on 313 QTLs. Consequently, a total of 62 MQTLs were identified with reduced mean CI (up to 3.40 fold) compared to the mean CI of original QTLs. However, 10 of these MQTLs harbored at least six of the initial QTLs from diverse genetic backgrounds and environments and were considered the most stable and robust MQTLs. Also, MQTLs were compared with GWAS studies and resulted in the identification of 16 common significant loci modulating the evaluated traits. Gene annotation, gene ontology (GO) enrichment, and RNA-seq analyses of chromosome regions of the stable MQTLs detected 52 potential CGs including those that have been cloned in previous studies. These genes encode proteins known to be involved in regulating grain yield including cytochrome P450, zinc fingers, MADs-box, AP2/ERF domain, F-box, ubiquitin ligase domain protein, homeobox domain, DEAD-box ATP domain, and U-box domain. This study provides the framework for molecular dissection of grain yield in rice. Moreover, the MQTLs and CGs identified could be useful for fine mapping, gene cloning, and marker-assisted selection to improve rice productivity.
Collapse
Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Aduragbemi Amo
- Institute of Plant Breeding, Genetics and Genomics University of Georgia, Athens, GA, United States
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| |
Collapse
|
11
|
Liang D, Yu J, Song T, Zhang R, Du Y, Yu M, Cao H, Pan X, Qiao J, Liu Y, Qi Z, Liu Y. Genome-Wide Prediction and Analysis of Oryza Species NRP Genes in Rice Blast Resistance. Int J Mol Sci 2022; 23:ijms231911967. [PMID: 36233270 PMCID: PMC9569735 DOI: 10.3390/ijms231911967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 11/26/2022] Open
Abstract
Members of the N-rich proteins (NRPs) gene family play important roles in the plant endoplasmic reticulum stress in response, which can be triggered by plant pathogens’ infection. Previous studies of the NRP gene family have been limited to only a few plants, such as soybean and Arabidopsis thaliana. Thus, their evolutionary characteristics in the Oryza species and biological functions in rice defense against the pathogenic fungus Magnaporthe oryzae have remained unexplored. In the present study, we demonstrated that the NRP genes family may have originated in the early stages of plant evolution, and that they have been strongly conserved during the evolution of the Oryza species. Domain organization of NRPs was found to be highly conserved within but not between subgroups. OsNRP1, an NRP gene in the Oryza sativa japonica group, was specifically up-regulated during the early stages of rice-M. oryzae interactions-inhibited M. oryzae infection. Predicted protein-protein interaction networks and transcription-factor binding sites revealed a candidate interactor, bZIP50, which may be involved in OsNRP1-mediated rice resistance against M. oryzae infection. Taken together, our results established a basis for future studies of the NRP gene family and provided molecular insights into rice immune responses to M. oryzae.
Collapse
Affiliation(s)
| | | | | | | | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | | | | | | | | | | | | | | |
Collapse
|
12
|
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.
Collapse
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.)
| |
Collapse
|
13
|
Shin NH, Han JH, Vo KTX, Seo J, Navea IP, Yoo SC, Jeon JS, Chin JH. Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci. RICE (NEW YORK, N.Y.) 2022; 15:22. [PMID: 35397732 PMCID: PMC8994804 DOI: 10.1186/s12284-022-00568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Successful cultivation of rice (Oryza sativa L.) in many Asian countries requires submergence stress tolerance at the germination and early establishment stages. Two quantitative trait loci, Sub1 (conferring submergence tolerance) and AG1 (conferring anaerobic germination), were recently pyramided into a single genetic background, without compromising any desirable agronomic traits, leading to the development of Ciherang-Sub1 + AG1 (CSA). However, little research has been conducted to enhance plant tolerance to abiotic stress (submergence) and biotic stress (rice blast), which occur in a damp climate following flooding. The BC2F5 breeding line was phenotypically characterized using the AvrPi9 isolate. The biotic and abiotic stress tolerance of selected lines was tested under submergence stress and anaerobic germination conditions, and lines tolerant to each stress condition were identified through phenotypic and gene expression analyses. The Ciherang-Sub1 + AG1 + Pi9 (CSA-Pi9) line showed similar agronomic performance to its recurrent parent, CSA, but had significantly reduced chalkiness in field trials conducted in temperate regions. Unexpectedly, the CSA-Pi9 line also showed salinity tolerance. Thus, the breeding line newly developed in this study, CSA-Pi9, functioned under stress conditions, in which Sub1, AG1, and Pi9 play a role and had superior grain quality traits compared to its recurrent parent in temperate regions. We speculate that CSA-Pi9 will enable the establishment of climate-resilient rice cropping systems, particularly in East Asia.
Collapse
Affiliation(s)
- Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea
| | - Jeonghwan Seo
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Korea
| | - Ian Paul Navea
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Banos, Philippines
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Anseong, Gyeonggi-do, 17579, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea.
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Kumar K, Jan I, Saripalli G, Sharma PK, Mir RR, Balyan HS, Gupta PK. An Update on Resistance Genes and Their Use in the Development of Leaf Rust Resistant Cultivars in Wheat. Front Genet 2022; 13:816057. [PMID: 35432483 PMCID: PMC9008719 DOI: 10.3389/fgene.2022.816057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
Wheat is one of the most important cereal crops in the world. The production and productivity of wheat is adversely affected by several diseases including leaf rust, which can cause yield losses, sometimes approaching >50%. In the present mini-review, we provide updated information on (i) all Lr genes including those derived from alien sources and 14 other novel resistance genes; (ii) a list of QTLs identified using interval mapping and MTAs identified using GWAS (particular those reported recently i.e., after 2018) and their association with known Lr genes; (iii) introgression/pyramiding of individual Lr genes in commercial/prominent cultivars from 18 different countries including India. Challenges and future perspectives of breeding for leaf rust resistance are also provided at the end of this mini-review. We believe that the information in this review will prove useful for wheat geneticists/breeders, not only in the development of leaf rust-resistant wheat cultivars, but also in the study of molecular mechanism of leaf rust resistance in wheat.
Collapse
Affiliation(s)
- Kuldeep Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - P. K. Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura, India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- *Correspondence: P. K. Gupta, ,
| |
Collapse
|
16
|
Tian T, Chen L, Ai Y, He H. Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq. Genes (Basel) 2022; 13:224. [PMID: 35205268 PMCID: PMC8871662 DOI: 10.3390/genes13020224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 02/04/2023] Open
Abstract
Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.
Collapse
Affiliation(s)
| | | | - Yufang Ai
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.T.); (L.C.)
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (T.T.); (L.C.)
| |
Collapse
|
17
|
Lo KL, Chen YN, Chiang MY, Chen MC, Panibe JP, Chiu CC, Liu LW, Chen LJ, Chen CW, Li WH, Wang CS. Two genomic regions of a sodium azide induced rice mutant confer broad-spectrum and durable resistance to blast disease. RICE (NEW YORK, N.Y.) 2022; 15:2. [PMID: 35006368 PMCID: PMC8748607 DOI: 10.1186/s12284-021-00547-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Rice blast, one of the most destructive epidemic diseases, annually causes severe losses in grain yield worldwide. To manage blast disease, breeding resistant varieties is considered a more economic and environment-friendly strategy than chemical control. For breeding new resistant varieties, natural germplasms with broad-spectrum resistance are valuable resistant donors, but the number is limited. Therefore, artificially induced mutants are an important resource for identifying new broad-spectrum resistant (R) genes/loci. To pursue this approach, we focused on a broad-spectrum blast resistant rice mutant line SA0169, which was previously selected from a sodium azide induced mutation pool of TNG67, an elite japonica variety. We found that SA0169 was completely resistant against the 187 recently collected blast isolates and displayed durable resistance for almost 20 years. Linkage mapping and QTL-seq analysis indicated that a 1.16-Mb region on chromosome 6 (Pi169-6(t)) and a 2.37-Mb region on chromosome 11 (Pi169-11(t)) conferred the blast resistance in SA0169. Sequence analysis and genomic editing study revealed 2 and 7 candidate R genes in Pi169-6(t) and Pi169-11(t), respectively. With the assistance of mapping results, six blast and bacterial blight double resistant lines, which carried Pi169-6(t) and/or Pi169-11(t), were established. The complementation of Pi169-6(t) and Pi169-11(t), like SA0169, showed complete resistance to all tested isolates, suggesting that the combined effects of these two genomic regions largely confer the broad-spectrum resistance of SA0169. The sodium azide induced mutant SA0169 showed broad-spectrum and durable blast resistance. The broad resistance spectrum of SA0169 is contributed by the combined effects of two R regions, Pi169-6(t) and Pi169-11(t). Our study increases the understanding of the genetic basis of the broad-spectrum blast resistance induced by sodium azide mutagenesis, and lays a foundation for breeding new rice varieties with durable resistance against the blast pathogen.
Collapse
Affiliation(s)
- Kuan-Lin Lo
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Nian Chen
- Division of Plant Pathology, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Min-Yu Chiang
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chun Chen
- Division of Plant Pathology, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Jerome P Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chung-Chun Chiu
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Lu-Wei Liu
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chun-Wei Chen
- Division of Plant Pathology, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan.
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
| |
Collapse
|
18
|
Daryani P, Darzi Ramandi H, Dezhsetan S, Mirdar Mansuri R, Hosseini Salekdeh G, Shobbar ZS. Pinpointing genomic regions associated with root system architecture in rice through an integrative meta-analysis approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:81-106. [PMID: 34623472 DOI: 10.1007/s00122-021-03953-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Applying an integrated meta-analysis approach led to identification of meta-QTLs/ candidate genes associated with rice root system architecture, which can be used in MQTL-assisted breeding/ genetic engineering of root traits. Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA-related MQTLs were detected and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance-associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA), and lignification (e.g. C4H, PAL, PRX and CAD). The genes located within both the SNP peak positions and the QTL-overview peaks for RSA are suggested as novel candidate genes for further functional analysis. The promising candidate genes and MQTLs can be used as basis for genetic engineering and MQTL-assisted breeding of root phenotypes to improve yield potential, stability and performance in a water-stressed environment.
Collapse
Affiliation(s)
- Parisa Daryani
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Sara Dezhsetan
- Department of Agronomy & Plant Breeding, University of Mohaghegh Ardabili, Ardabil, Iran.
| | - Raheleh Mirdar Mansuri
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), 31535-1897, Karaj, Iran.
| |
Collapse
|
19
|
Frontini M, Boisnard A, Frouin J, Ouikene M, Morel JB, Ballini E. Genome-wide association of rice response to blast fungus identifies loci for robust resistance under high nitrogen. BMC PLANT BIOLOGY 2021; 21:99. [PMID: 33602120 PMCID: PMC7893971 DOI: 10.1186/s12870-021-02864-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/01/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Nitrogen fertilization is known to increase disease susceptibility, a phenomenon called Nitrogen-Induced Susceptibility (NIS). In rice, this phenomenon has been observed in infections with the blast fungus Magnaporthe oryzae. A previous classical genetic study revealed a locus (NIS1) that enhances susceptibility to rice blast under high nitrogen fertilization. In order to further address the underlying genetics of plasticity in susceptibility to rice blast after fertilization, we analyzed NIS under greenhouse-controlled conditions in a panel of 139 temperate japonica rice strains. A genome-wide association analysis was conducted to identify loci potentially involved in NIS by comparing susceptibility loci identified under high and low nitrogen conditions, an approach allowing for the identification of loci validated across different nitrogen environments. We also used a novel NIS Index to identify loci potentially contributing to plasticity in susceptibility under different nitrogen fertilization regimes. RESULTS A global NIS effect was observed in the population, with the density of lesions increasing by 8%, on average, under high nitrogen fertilization. Three new QTL, other than NIS1, were identified. A rare allele of the RRobN1 locus on chromosome 6 provides robust resistance in high and low nitrogen environments. A frequent allele of the NIS2 locus, on chromosome 5, exacerbates blast susceptibility under the high nitrogen condition. Finally, an allele of NIS3, on chromosome 10, buffers the increase of susceptibility arising from nitrogen fertilization but increases global levels of susceptibility. This allele is almost fixed in temperate japonicas, as a probable consequence of genetic hitchhiking with a locus involved in cold stress adaptation. CONCLUSIONS Our results extend to an entire rice subspecies the initial finding that nitrogen increases rice blast susceptibility. We demonstrate the usefulness of estimating plasticity for the identification of novel loci involved in the response of rice to the blast fungus under different nitrogen regimes.
Collapse
Affiliation(s)
- Mathias Frontini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Julien Frouin
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Malika Ouikene
- Groupe de Valorisation des Produits Agricoles (GVAPRO), Alger, Algeria
| | - Jean Benoit Morel
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Elsa Ballini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| |
Collapse
|
20
|
Metabolomics Intervention Towards Better Understanding of Plant Traits. Cells 2021; 10:cells10020346. [PMID: 33562333 PMCID: PMC7915772 DOI: 10.3390/cells10020346] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).
Collapse
|
21
|
Abstract
Rice blast disease is both the most explosive and potentially damaging disease of the world's rice (Oryza sativa) crop and a model system for research on the molecular mechanisms that fungi use to cause plant disease. The blast fungus, Magnaporthe oryzae, is highly evolved to sense when it is on a leaf surface; to develop a pressurized cell, the appressorium, to punch through the leaf cuticle; and then to hijack living rice cells to assist it in causing disease. Host specificity, determining which plants particular fungal strains can infect, is also an important topic for research. The blast fungus is a moving target, quickly overcoming rice resistance genes we deploy to control it, and recently emerging to cause devastating disease on an entirely new cereal crop, wheat. M. oryzae is highly adaptable, with multiple examples of genetic instability at certain gene loci and in certain genomic regions. Understanding the biology of the fungus in the field, and its potential for genetic and genome variability, is key to keep it from adapting to life in the research laboratory and losing relevance to the significant impact it has on global food security.
Collapse
Affiliation(s)
- Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
22
|
Sharma SK, Sharma D, Meena RP, Yadav MK, Hosahatti R, Dubey AK, Sharma P, Kumar S, Pramesh D, Nabi SU, Bhuvaneshwari S, Anand YR, Dubey SK, Singh TS. Recent Insights in Rice Blast Disease Resistance. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60585-8_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
23
|
Zhou Y, Lei F, Wang Q, He W, Yuan B, Yuan W. Identification of Novel Alleles of the Rice Blast-Resistance Gene Pi9 through Sequence-Based Allele Mining. RICE (NEW YORK, N.Y.) 2020; 13:80. [PMID: 33284383 PMCID: PMC7721961 DOI: 10.1186/s12284-020-00442-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND As rice (Oryza sativa) is the staple food of more than half the world's population, rice production contributes greatly to global food security. Rice blast caused by the fungus Magnaporthe oryzae (M. oryzae) is a devastating disease that affects rice yields and grain quality, resulting in substantial economic losses annually. Because the fungus evolves rapidly, the resistance conferred by most the single blast-resistance genes is broken after a few years of intensive agricultural use. Therefore, effective resistance breeding in rice requires continual enrichment of the reservoir of resistance genes, alleles, or QTLs. Seed banks represent a rich source of genetic diversity; however, they have not been extensively used to identify novel genes and alleles. RESULTS We carried out a large-scale screen for novel blast-resistance alleles in 1883 rice varieties from major rice-producing areas across China. Of these, 361 varieties showed at least moderate resistance to natural infection by rice blast at rice blast nurseries in Enshi and Yichang, Hubei Province. We used sequence-based allele mining to amplify and sequence the allelic variants of the major rice blast-resistance genes at the Pi2/Pi9 locus of chromosome 6 from the 361 blast-resistant varieties, and the full-length coding region of this gene could be amplified from 107 varieties. Thirteen novel Pi9 alleles (named Pi9-Type1 to Pi9-Type13) were identified in these 107 varieties based on comparison to the Pi9 referenced sequence. Based on the sequencing results, the Pi2/Pi9 locus of the 107 varieties was divided into 15 genotypes (including three different genotypes of Pi9-Type5). Fifteen varieties, each representing one genotype, were evaluated for resistance to 34 M. oryzae isolates. The alleles from seven varieties with the highest resistance and widest resistance spectra were selected for transformation into the susceptible variety J23B to construct near-isogenic lines (NILs). These NILs showed resistance in a field test in Enshi and Yichang, indicating that the seven novel rice blast-resistance tandem-repeat regions at the Pi2/Pi9 locus of chromosome 6 could potentially serve as a genetic resource for molecular breeding of resistance to rice blast. CONCLUSIONS The thirteen novel Pi9 alleles identified in this study expand the list of available of blast-resistance alleles. Seven tandem-repeat regions of the Pi2/Pi9 locus from different donors were characterized as broad-spectrum rice blast-resistance fragments; these donors enrich the genetic resources available for rice blast-resistance breeding programs.
Collapse
Affiliation(s)
- Ying Zhou
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065 People’s Republic of China
| | - Fang Lei
- Institute of Model Animal of Wuhan University, Basic Medical School of Wuhan University, Wuhan, 430071 People’s Republic of China
| | - Qiong Wang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065 People’s Republic of China
| | - Weicong He
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065 People’s Republic of China
| | - Bin Yuan
- Key Laboratory of Integrated Management of Crops of Central China, Ministry of Agriculture, Wuhan, 430064 People’s Republic of China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan, 430064 People’s Republic of China
| | - Wenya Yuan
- College of Life Sciences, Hubei University, Wuhan, 430062 People’s Republic of China
| |
Collapse
|
24
|
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.
Collapse
|
25
|
Yang L, Lei L, Liu H, Wang J, Zheng H, Zou D. Whole-genome mining of abiotic stress gene loci in rice. PLANTA 2020; 252:85. [PMID: 33052473 DOI: 10.1007/s00425-020-03488-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
We projected meta-QTL (MQTL) for drought, salinity, cold state, and high metal ion tolerance in rice using a meta-analysis based on high-density consensus maps. In addition, a genome-wide association analysis was used to validate the results of the meta-analysis, and four new chromosome intervals for mining abiotic stress candidate genes were obtained. Drought, severe cold, high salinity, and high metallic ion concentrations severely restrict rice production. Consequently, the breeding of abiotic stress-tolerant variety is being paid increasingly more attention. This study aimed to identify meta-quantitative trait loci (MQTL) for abiotic stress tolerance in rice, as well as the molecular markers and potential candidate genes of the MQTL regions. We summarized 2785 rice QTL and conducted a meta-analysis of 159 studies. We found 82 drought tolerance (DT), 70 cold tolerance (CT), 70 salt tolerance (ST), and 51 heavy metal ion tolerance (IT) meta-QTL, as well as 20 DT, 11 CT, 22 ST, and 5 IT candidate genes in the MQTL interval. Thirty-one multiple-tolerance related MQTL regions, which were highly enriched, were also detected, and 13 candidate genes related to multiple-tolerance were obtained. In addition, the correlation between DT, CT, and ST was significant in the rice genome. Four candidate genes and four MM-QTL regions were detected simultaneously by GWAS and meta-analysis. The four candidate genes showed distinct genetic differentiation and substantial genetic distance between indica and japonica rice, and the four MM-QTL are potential intervals for mining abiotic stress-related candidate genes. The candidate genes identified in this study will not only be useful for marker-assisted selection and pyramiding but will also accelerate the fine mapping and cloning of the candidate genes associated with abiotic stress-tolerance mechanisms in rice.
Collapse
Affiliation(s)
- Luomiao Yang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Lei Lei
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - HuaLong Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China.
| |
Collapse
|
26
|
Dong L, Liu S, Kyaing MS, Xu P, Tharreau D, Deng W, Li X, Bi Y, Zeng L, Li J, Zhou J, Tao D, Yang Q. Identification and Fine Mapping of Pi69(t), a New Gene Conferring Broad-Spectrum Resistance Against Magnaporthe oryzae From Oryza glaberrima Steud. FRONTIERS IN PLANT SCIENCE 2020; 11:1190. [PMID: 32849738 PMCID: PMC7426465 DOI: 10.3389/fpls.2020.01190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/22/2020] [Indexed: 05/28/2023]
Abstract
The discovery and deployment of new broad-spectrum resistance (R) genes from cultivated rice and its wild relatives is a strategy to broaden the genetic basis of modern rice cultivars to combat rice blast disease. Oryza glaberrima possessing many valuable traits for tolerance to biotic and abiotic stresses, is an elite gene pool for improvement of Asian cultivated rice. An introgression line IL106 derived from O. glaberrima (Acc. IRGC100137) confers complete resistance to Magnaporthe oryzae in blast nursery. Genetic analysis using 2185 BC6F2 progenies derived from a cross between IL106 and the recurrent parent Dianjingyou 1 showed that IL106 harbors a single dominant resistance gene against M. oryzae strain 09BSH-10-5A. This gene was preliminarily mapped on the long arm of chromosome 6 of rice in a region of ca. 0.9 cM delimited by two SSR markers (RM20650 and RM20701). In order to finely map this gene, 17,100 additional progenies were further analyzed. As a result, this gene was further narrowed down to a region flanked by two molecular markers STS69-15 and STS69-7, and co-segregated with 3 molecular markers, RM20676, STS69-21 and STS69-22 on the long arm of chromosome 6. Based on reference genome sequences, this R gene was mapped in silico in 76.1-Kb and 67.7-Kb physical intervals, and containing 4 and 3 NBS-LRR candidate genes in O. sativa cultivar Nipponbare and O. glaberrima cultivar CG14, respectively. Because no blast resistance gene was finely mapped in this physical interval before, this R gene was considered as not described yet and designated as Pi69(t), which is the first identified and finely mapped blast R gene from O. glaberrima, as far as we know. Evaluation of IL106 with 151 blast strains collected from 6 countries in Asia showed that 148 strains are avirulent on IL106, suggesting that Pi69(t) is a broad-spectrum blast R gene, and a promising resistant resource for improvement of Asian cultivated rice.
Collapse
Affiliation(s)
- Liying Dong
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Shufang Liu
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - May Sandar Kyaing
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Biotechnology Research Department, Ministry of Education, Mandalay, Myanmar
| | - Peng Xu
- Food Crops Research Institute/Yunnan Key Laboratory for Rice Genetic Improvement, Yunnan Academy of Agricultural Sciences, Kunming, China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Kunming, China
| | - Didier Tharreau
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR BGPI, TA A 54 K, Montpellier, France
- BGPI, Univ Montpellier, CIRAD, INRA, Montpellier, SupAgro, Montpellier, France
| | - Wei Deng
- Food Crops Research Institute/Yunnan Key Laboratory for Rice Genetic Improvement, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xundong Li
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yunqing Bi
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Li Zeng
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jing Li
- Food Crops Research Institute/Yunnan Key Laboratory for Rice Genetic Improvement, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jiawu Zhou
- Food Crops Research Institute/Yunnan Key Laboratory for Rice Genetic Improvement, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Dayun Tao
- Food Crops Research Institute/Yunnan Key Laboratory for Rice Genetic Improvement, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qinzhong Yang
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| |
Collapse
|
27
|
Kumar A, Saripalli G, Jan I, Kumar K, Sharma PK, Balyan HS, Gupta PK. Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1713-1725. [PMID: 32801498 PMCID: PMC7415061 DOI: 10.1007/s12298-020-00847-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 05/18/2023]
Abstract
Meta-QTL (MQTL) analysis for drought tolerance was undertaken in bread wheat to identify consensus and robust MQTLs using 340 known QTLs from 11 earlier studies; 13 MQTLs located on 6 chromosomes (1D, 3B, 5A, 6D, 7A and 7D) were identified, with maximum of 4 MQTLs on chromosome 5A. Mean confidence intervals for MQTLs were much narrower (mean, 6.01 cM; range 2.07-19.46 cM), relative to those in original QTLs (mean, 13.6 cM; range, 1.0-119.1 cM). Two MQTLs, namely MQTL4 and MQTL12, were major MQTLs with potential for use in marker-assisting breeding. As many as 228 candidate genes (CGs) were also identified using 6 of the 13 MQTLs. In-silico expression analysis of these 228 CGs allowed identification of 14 important CGs, with + 3 to - 8 fold change in expression under drought (relative to normal conditions) in a tolerant cv. named TAM107. These CGs encoded proteins belonging to the following families: NAD-dependent epimerase/dehydratase, protein kinase, NAD(P)-binding domain protein, heat shock protein 70 (Hsp70), glycosyltransferase 2-like, etc. Important MQTLs and CGs identified in the present study should prove useful for future molecular breeding and for the study of molecular basis of drought tolerance in cereals in general and wheat in particular.
Collapse
Affiliation(s)
- Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| |
Collapse
|
28
|
Devi SJSR, Singh K, Umakanth B, Vishalakshi B, Rao KVS, Suneel B, Sharma SK, Kadambari GKM, Prasad MS, Senguttvel P, Syamaladevi DP, Madhav MS. Identification and Characterization of a Large Effect QTL from Oryza glumaepatula Revealed Pi68(t) as Putative Candidate Gene for Rice Blast Resistance. RICE (NEW YORK, N.Y.) 2020; 13:17. [PMID: 32166467 PMCID: PMC7067966 DOI: 10.1186/s12284-020-00378-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/02/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Field resistance is often effective and durable as compared to vertical resistance. The introgression line (INGR15002) derived from O. glumaepatula has proven broad spectrum field resistance for both leaf and neck blast. RESULTS Quantitative Trait Loci (QTL) analysis of INGR15002, led to the identification of two major QTL - qBL3 contributing about 34% and 32% phenotypic variance towards leaf and neck blast resistance, respectively and qBL7 contributing about 25% of phenotypic variance for leaf blast. Further, qBL3 was fine mapped, narrowed down to 300 kb region and a linked SNP maker was identified. By combining mapping with microarray analysis, a candidate gene, Os03g0281466 (malectin-serine threonine kinase), was identified in the fine mapped region and named as Pi68(t). The nucleotide variations in the coding as well as upstream region of the gene was identified through cloning and sequence analysis of Pi68(t) alleles. These significant variations led to the non-synonymous changes in the protein as well as variations (presence/absence) in four important motifs (W-box element; MYC element; TCP element; BIHD1OS) at promoter region those are associated with resistance and susceptible reactions. The effect of qBL3 was validated by its introgression into BPT5204 (susceptible variety) through marker-assisted selection and progeny exhibiting resistance to both leaf and neck blast was identified. Further, the utility of linked markers of Pi68(t) in the blast breeding programs was demonstrated in elite germplasm lines. CONCLUSIONS This is the first report on the identification and characterization of major effect QTL from O. glumaepatula, which led to the identification of a putative candidate gene, Pi68(t), which confers field resistance to leaf as well as neck blast in rice.
Collapse
Affiliation(s)
- S. J. S. Rama Devi
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - Kuldeep Singh
- Department of Plant Breeding and Genetics, P.A.U, Ludhiana, Punjab India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
- School of Agricultural Biotechnology, P.A.U, Ludhiana, Punjab India
| | - B. Umakanth
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - B. Vishalakshi
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | | | - B. Suneel
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - S. K. Sharma
- Plant Pathology Division, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
- Plant Pathology Division, Indian Institute of Rice Research, Hyderabad-30, India
| | | | - M. S. Prasad
- Plant Pathology Division, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, India
| | - P. Senguttvel
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - Divya P. Syamaladevi
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
| | - M. S. Madhav
- Crop Improvement Division, Indian Institute of Rice Research, Hyderabad-30, India
- Crop Improvement Section, IIRR, Hyderabad, 500 030 India
| |
Collapse
|
29
|
GAVHANE DNYANESHWARB, KULWAL PAWANL, KUMBHAR SHAILESHD, JADHAV ASHOKS, SARAWATE CHANDRAKANTD. Cataloguing of blast resistance genes in landraces and breeding lines of rice from India. J Genet 2019. [DOI: 10.1007/s12041-019-1148-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Xiao W, Yang Q, Huang M, Guo T, Liu Y, Wang J, Yang G, Zhou J, Yang J, Zhu X, Chen Z, Wang H. Improvement of rice blast resistance by developing monogenic lines, two-gene pyramids and three-gene pyramid through MAS. RICE (NEW YORK, N.Y.) 2019; 12:78. [PMID: 31686256 PMCID: PMC6828908 DOI: 10.1186/s12284-019-0336-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice production. Development of resistant varieties through pyramiding of resistant (R) genes is considered as an effective strategy to cope with the disease. However, is it really essential to pyramid more R genes in a specific ecological regions? To answer this question, a set of rice improved lines were developed in this study. Afterwards, the blast disease resistance and agronomic traits of the recurrent parent (RP), donor parents (DPs) and improved lines were investigated. RESULTS We developed seven improved lines, comprising three monogenic lines, three two-gene pyramids and one three-gene pyramid, by introgression of R gene(s) into a common genetic background using marker-assisted backcross breeding (MABB). Based on 302 SSR markers, the recurrent genome of the seven improved lines reached a range of 89.1 to 95.5%, with the average genome recovery of 92.9%. The pathogenicity assays inoculated with 32 different blast isolates under artificial conditions showed that the resistance spectrum of all the improved lines was significantly broadened. The assays further showed that the two-gene pyramids and the three-gene pyramid exhibited wider resistance spectrum than the monogenic lines. At natural nurseries, the three monogenic lines still showed high ratios of infected panicles, whereas the two-gene pyramids and the three-gene pyramid showed high level of panicle blast resistance. However, the two-gene pyramid R504 reached the similar resistance effect of the three-gene pyramid R507 considering resistance spectrum under artificial conditions and panicle blast resistance under field conditions. Generally, the improved lines showed comparable agronomic traits compared with the recurrent parent (RP), but the three-gene pyramid showed reduced grain yield per plant. CONCLUSIONS All the improved lines conferred wider resistance spectrum compared with the RP. Yet, the three monogenic lines did not work under field conditions of the two nurseries. Given the similar performances on the main agronomic traits as the RP, the two-gene pyramids have achieved the breeding goals of broad resistance spectrum and effective panicle blast resistance. Whereas, the three-gene pyramid harboring Pi2, Pi46 and Pita seems superfluous considering its reduced yield, although it also showed displayed high level of blast resistance. Thus, rational use of R genes rather than stacking more R genes is recommended to control the disease.
Collapse
Affiliation(s)
- Wuming Xiao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Qiyun Yang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, People's Republic of China
| | - Ming Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jiyong Zhou
- Guangdong Agricultural Technology Extension Station, Guangzhou, 510520, People's Republic of China
| | - Jianyuan Yang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, People's Republic of China
| | - Xiaoyuan Zhu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, People's Republic of China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| |
Collapse
|
31
|
Kalia S, Rathour R. Current status on mapping of genes for resistance to leaf- and neck-blast disease in rice. 3 Biotech 2019; 9:209. [PMID: 31093479 PMCID: PMC6509304 DOI: 10.1007/s13205-019-1738-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 04/29/2019] [Indexed: 12/15/2022] Open
Abstract
Blast disease caused by fungal pathogen Pyricularia oryzae is a major threat to rice productivity worldwide. The rice-blast pathogen can infect both leaves and panicle neck nodes. Nearly, 118 genes for resistance to leaf blast have been identified and 25 of these have been molecularly characterized. A great majority of these genes encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins and are organized into clusters as allelic or tightly linked genes. Compared to ever expanding list of leaf-blast-resistance genes, a few major genes mediating protection to neck blast have been identified. A great majority of the genetic studies conducted with the genotypes differing in the degree of susceptibility/resistance to neck blast have suggested quantitative inheritance for the trait. Several reports on co-localization of gene/QTLs for leaf- and neck-blast resistance in rice genome have suggested the existence of common genes for resistance to both phases of the disease albeit inconsistencies in the genomic positions leaf- and neck-blast-resistance genes in some instances have presented the contrasting scenario. There is a strong evidence to suggest that developmentally regulated expression of many blast-resistance genes is a key determinant deciding their effectiveness against leaf or neck blast. Testing of currently characterized leaf-blast-resistance genes for their reaction to neck blast is required to expand the existing repertoire resistance genes against neck blast. Current developments in the understanding of molecular basis of host-pathogen interactions in rice-blast pathosystem offer novel possibilities for achieving durable resistance to blast through exploitation of natural or genetically engineered loss-of-function alleles of host susceptibility genes.
Collapse
Affiliation(s)
- S. Kalia
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh 176062 India
| | - R. Rathour
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh 176062 India
| |
Collapse
|
32
|
Tonnessen BW, Bossa-Castro AM, Mauleon R, Alexandrov N, Leach JE. Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice. Sci Rep 2019; 9:1536. [PMID: 30733489 PMCID: PMC6367480 DOI: 10.1038/s41598-018-38195-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/18/2018] [Indexed: 12/30/2022] Open
Abstract
Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens (Magnaporthe oryzae, Rhizoctonia solani, and Xanthomonas oryzae pv. oryzae) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, called cis-Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs include cis-elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.
Collapse
Affiliation(s)
| | | | - Ramil Mauleon
- International Rice Research Institute, Manila, Philippines
| | | | - Jan E Leach
- Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
33
|
Wang Z, Ma LY, Cao J, Li YL, Ding LN, Zhu KM, Yang YH, Tan XL. Recent Advances in Mechanisms of Plant Defense to Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2019; 10:1314. [PMID: 31681392 PMCID: PMC6813280 DOI: 10.3389/fpls.2019.01314] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/20/2023]
Abstract
Sclerotinia sclerotiorum (Lib.) de Bary is an unusual pathogen which has the broad host range, diverse infection modes, and potential double feeding lifestyles of both biotroph and necrotroph. It is capable of infecting over 400 plant species found worldwide and more than 60 names have agriculturally been used to refer to diseases caused by this pathogen. Plant defense to S. sclerotiorum is a complex biological process and exhibits a typical quantitative disease resistance (QDR) response. Recent studies using Arabidopsis thaliana and crop plants have obtained new advances in mechanisms used by plants to cope with S. sclerotiorum infection. In this review, we focused on our current understanding on plant defense mechanisms against this pathogen, and set up a model for the defense process including three stages: recognition of this pathogen, signal transduction and defense response. We also have a particular interest in defense signaling mediated by diverse signaling molecules. We highlight the current challenges and unanswered questions in both the defense process and defense signaling. Essentially, we discussed candidate resistance genes newly mapped by using high-throughput experiments in important crops, and classified these potential gene targets into different stages of the defense process, which will broaden our understanding of the genetic architecture underlying quantitative resistance to S. sclerotiorum. We proposed that more powerful mapping population(s) will be required for accurate and reliable QDR gene identification.
Collapse
|
34
|
Jairin J, Vejchasarn P, Somjai T, Srivilai K, Darwell K, Leelagud P, Kawichai R, Kotcharerk J, Suthanthangjai A, Popa N, Lachanthuek S, Chamarerk V. Identification of QTLs for Blast, Bacterial Blight, and Planthopper Resistance Using SNP-Based Linkage Maps from Two Recombinant Inbred Rice Lines. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/ajps.2019.105056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
35
|
In silico Analysis of qBFR4 and qLBL5 in Conferring Quantitative Resistance Against Rice Blast. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.03] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
|
36
|
Hasan MM, Rafii MY, Ismail MR, Mahmood M, Rahim HA, Latif MA, Amirul Alam M, Ahmad F, Malek MA. Genetic analysis of the resistance to rice blast in the BC 2F 1 population derived from MR263 × Pongsu Seribu 1. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1506266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- M. M. Hasan
- Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Selangor, Malaysia
| | - M. Y. Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Selangor, Malaysia
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Selangor, Malaysia
| | - M. R. Ismail
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Selangor, Malaysia
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Selangor, Malaysia
| | - M. Mahmood
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - H. A. Rahim
- Agrotechnology and Bioscience Division, Malaysian Nuclear Agency, Selangor, Malaysia
| | - M. A. Latif
- Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Md. Amirul Alam
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Fahim Ahmad
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Selangor, Malaysia
| | - M. A. Malek
- Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Singh PK, Nag A, Arya P, Kapoor R, Singh A, Jaswal R, Sharma TR. Prospects of Understanding the Molecular Biology of Disease Resistance in Rice. Int J Mol Sci 2018; 19:E1141. [PMID: 29642631 PMCID: PMC5979409 DOI: 10.3390/ijms19041141] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/03/2018] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host-pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.
Collapse
Affiliation(s)
- Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Nag
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Preeti Arya
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Akshay Singh
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute, Mohali 140 306, Punjab, India.
| |
Collapse
|
39
|
Chang HX, Roth MG, Wang D, Cianzio SR, Lightfoot DA, Hartman GL, Chilvers MI. Integration of sudden death syndrome resistance loci in the soybean genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:757-773. [PMID: 29435603 DOI: 10.1007/s00122-018-3063-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 01/19/2018] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Complexity and inconsistencies in resistance mapping publications of soybean sudden death syndrome (SDS) result in interpretation difficulty. This review integrates SDS mapping literature and proposes a new nomenclature system for reproducible SDS resistance loci. Soybean resistance to sudden death syndrome (SDS) is composed of foliar resistance to phytotoxins and root resistance to pathogen invasion. There are more than 80 quantitative trait loci (QTL) and dozens of single nucleotide polymorphisms (SNPs) associated with soybean resistance to SDS. The validity of these QTL and SNPs is questionable because of the complexity in phenotyping methodologies, the disease synergism between SDS and soybean cyst nematode (SCN), the variability from the interactions between soybean genotypes and environments, and the inconsistencies in the QTL nomenclature. This review organizes SDS mapping results and proposes the Rfv (resistance to Fusarium virguliforme) nomenclature based on supporting criteria described in the text. Among ten reproducible loci receiving our Rfv nomenclature, Rfv18-01 is mostly supported by field studies and it co-localizes to the SCN resistance locus rhg1. The possibility that Rfv18-01 is a pleiotropic resistance locus and the concern about Rfv18-01 being confounded with Rhg1 is discussed. On the other hand, Rfv06-01, Rfv06-02, Rfv09-01, Rfv13-01, and Rfv16-01 were identified both by screening soybean leaves against phytotoxic culture filtrates and by evaluating SDS severity in fields. Future phenotyping using leaf- and root-specific resistance screening methodologies may improve the precision of SDS resistance, and advanced genetic studies may further clarify the interactions among soybean genotypes, F. virguliforme, SCN, and environments. The review provides a summary of the SDS resistance literature and proposes a framework for communicating SDS resistance loci for future research considering molecular interactions and genetic breeding for soybean SDS resistance.
Collapse
Affiliation(s)
- Hao-Xun Chang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Mitchell G Roth
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Genetics Program, Michigan State University, East Lansing, MI, USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA.
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- USDA-Agricultural Research Service, Urbana, IL, USA.
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
- Genetics Program, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
40
|
Plissonneau C, Rouxel T, Chèvre A, Van De Wouw AP, Balesdent M. One gene-one name: the AvrLmJ1 avirulence gene of Leptosphaeria maculans is AvrLm5. MOLECULAR PLANT PATHOLOGY 2018; 19:1012-1016. [PMID: 28661570 PMCID: PMC6638039 DOI: 10.1111/mpp.12574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 05/05/2023]
Abstract
Leptosphaeria maculans, the causal agent of blackleg disease, interacts with Brassica napus (oilseed rape, canola) and other Brassica hosts in a gene-for-gene manner. The avirulence gene AvrLmJ1 has been cloned previously and shown to interact with an unidentified Brassica juncea resistance gene. In this study, we show that the AvrLmJ1 gene maps to the same position as the AvrLm5 locus. Furthermore, isolates complemented with the AvrLmJ1 locus confer avirulence towards B. juncea genotypes harbouring Rlm5. These findings demonstrate that AvrLmJ1 is AvrLm5 and highlight the need for shared resources to characterize accurately avirulence and/or resistance genes.
Collapse
Affiliation(s)
- Clémence Plissonneau
- UMR Bioger, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, Thiverval‐GrignonF‐78850France
| | - Thierry Rouxel
- UMR Bioger, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, Thiverval‐GrignonF‐78850France
| | | | | | - Marie‐Hélène Balesdent
- UMR Bioger, INRA, AgroParisTech, Université Paris‐Saclay, Avenue Lucien Brétignières, Thiverval‐GrignonF‐78850France
| |
Collapse
|
41
|
Wu Y, Yu L, Xiao N, Dai Z, Li Y, Pan C, Zhang X, Liu G, Li A. Characterization and evaluation of rice blast resistance of Chinese indica hybrid rice parental lines. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
42
|
Nelson R, Wiesner-Hanks T, Wisser R, Balint-Kurti P. Navigating complexity to breed disease-resistant crops. Nat Rev Genet 2017; 19:21-33. [PMID: 29109524 DOI: 10.1038/nrg.2017.82] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plant diseases are responsible for substantial crop losses each year and pose a threat to global food security and agricultural sustainability. Improving crop resistance to pathogens through breeding is an environmentally sound method for managing disease and minimizing these losses. However, it is challenging to breed varieties with resistance that is effective, stable and broad-spectrum. Recent advances in genetic and genomic technologies have contributed to a better understanding of the complexity of host-pathogen interactions and have identified some of the genes and mechanisms that underlie resistance. This new knowledge is benefiting crop improvement through better-informed breeding strategies that utilize diverse forms of resistance at different scales, from the genome of a single plant to the plant varieties deployed across a region.
Collapse
Affiliation(s)
- Rebecca Nelson
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Tyr Wiesner-Hanks
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Randall Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716, USA
| | - Peter Balint-Kurti
- United States Department of Agriculture Agricultural Research Service (USDA-ARS), Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695-7616, USA
| |
Collapse
|
43
|
Pilet-Nayel ML, Moury B, Caffier V, Montarry J, Kerlan MC, Fournet S, Durel CE, Delourme R. Quantitative Resistance to Plant Pathogens in Pyramiding Strategies for Durable Crop Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:1838. [PMID: 29163575 PMCID: PMC5664368 DOI: 10.3389/fpls.2017.01838] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/10/2017] [Indexed: 05/18/2023]
Abstract
Quantitative resistance has gained interest in plant breeding for pathogen control in low-input cropping systems. Although quantitative resistance frequently has only a partial effect and is difficult to select, it is considered more durable than major resistance (R) genes. With the exponential development of molecular markers over the past 20 years, resistance QTL have been more accurately detected and better integrated into breeding strategies for resistant varieties with increased potential for durability. This review summarizes current knowledge on the genetic inheritance, molecular basis, and durability of quantitative resistance. Based on this knowledge, we discuss how strategies that combine major R genes and QTL in crops can maintain the effectiveness of plant resistance to pathogens. Combining resistance QTL with complementary modes of action appears to be an interesting strategy for breeding effective and potentially durable resistance. Combining quantitative resistance with major R genes has proven to be a valuable approach for extending the effectiveness of major genes. In the plant genomics era, improved tools and methods are becoming available to better integrate quantitative resistance into breeding strategies. Nevertheless, optimal combinations of resistance loci will still have to be identified to preserve resistance effectiveness over time for durable crop protection.
Collapse
Affiliation(s)
- Marie-Laure Pilet-Nayel
- Institute for Genetics, Environment and Plant Protection (INRA), UMR 1349, Leu Rheu, France
- PISOM, UMT INRA-Terres Inovia, Le Rheu, France
| | | | - Valérie Caffier
- Research Institute of Horticulture and Seeds (INRA), UMR 1345, Beaucouzé, France
| | - Josselin Montarry
- Institute for Genetics, Environment and Plant Protection (INRA), UMR 1349, Leu Rheu, France
| | - Marie-Claire Kerlan
- Institute for Genetics, Environment and Plant Protection (INRA), UMR 1349, Leu Rheu, France
| | - Sylvain Fournet
- Institute for Genetics, Environment and Plant Protection (INRA), UMR 1349, Leu Rheu, France
| | - Charles-Eric Durel
- Research Institute of Horticulture and Seeds (INRA), UMR 1345, Beaucouzé, France
| | - Régine Delourme
- Institute for Genetics, Environment and Plant Protection (INRA), UMR 1349, Leu Rheu, France
| |
Collapse
|
44
|
Dong L, Liu S, Xu P, Deng W, Li X, Tharreau D, Li J, Zhou J, Wang Q, Tao D, Yang Q. Fine mapping of Pi57(t) conferring broad spectrum resistance against Magnaporthe oryzae in introgression line IL-E1454 derived from Oryza longistaminata. PLoS One 2017; 12:e0186201. [PMID: 29016662 PMCID: PMC5634632 DOI: 10.1371/journal.pone.0186201] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/27/2017] [Indexed: 01/22/2023] Open
Abstract
Wild species of the genus Oryza are excellent gene pools for improvement of agronomic traits of Asian cultivated rice. The blast resistance gene Pi57(t) in the introgression line IL-E1454 derived from Oryza longistaminata was previously mapped on rice chromosome 12. Inoculation with 322 Magnaporthe oryzae isolates collected from 6 countries indicated that Pi57(t) conferred broad spectrum resistance against M. oryzae. Two mapping populations consisting of 29070 and 10375 F2 plants derived from the crosses of resistant donor IL-E1454 with susceptible parents RD23 and Lijiangxintuanheigu respectively, were used for fine mapping of Pi57(t) locus. Based on genotyping and phenotyping results of recombinants screened from the two crosses, Pi57(t) was finally mapped to a 51.7-kb region flanked by two molecular markers (STS57-320 and STS57-372) on the short arm and close to the centromere of chromosome 12. Six candidate resistance genes were predicted in the target region according to the reference sequence of Nipponbare. These results could facilitate both marker-assisted selection for disease-resistant breeding and gene cloning.
Collapse
Affiliation(s)
- Liying Dong
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Shufang Liu
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Peng Xu
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Kunming, Yunnan, China
| | - Wei Deng
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Xundong Li
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Didier Tharreau
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR BGPI, Montpellier, France
| | - Jing Li
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Jiawu Zhou
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Qun Wang
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Dayun Tao
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- * E-mail: (DT); (QY)
| | - Qinzhong Yang
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- * E-mail: (DT); (QY)
| |
Collapse
|
45
|
Sornkom W, Miki S, Takeuchi S, Abe A, Asano K, Sone T. Fluorescent reporter analysis revealed the timing and localization of AVR-Pia expression, an avirulence effector of Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2017; 18:1138-1149. [PMID: 27528510 PMCID: PMC6638300 DOI: 10.1111/mpp.12468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/20/2016] [Accepted: 08/11/2016] [Indexed: 05/09/2023]
Abstract
In order to facilitate infection, the rice blast pathogen Magnaporthe oryzae secretes an abundance of proteins, including avirulence effectors, to diminish its host's defences. Avirulence effectors are recognized by host resistance proteins and trigger the host's hypersensitive response, which is a rapid and effective form of innate plant immunity. An understanding of the underlying molecular mechanisms of such interactions is crucial for the development of strategies to control disease. However, the expression and secretion of certain effector proteins, such as AVR-Pia, have yet to be reported. Reverse transcription-polymerase chain reaction (RT-PCR) revealed that AVR-Pia was only expressed during infection. Fluorescently labelled AVR-Pia indicated that AVR-Pia expression was induced during appressorial differentiation in the cells of both rice and onion, as well as in a penetration-deficient (Δpls1) mutant capable of developing melanized appressoria, but unable to penetrate host cells, suggesting that AVR-Pia expression is independent of fungal penetration. Using live-cell imaging, we also documented the co-localization of green fluorescent protein (GFP)-labelled AVR-Pia and monomeric red fluorescent protein (mRFP)-labelled PWL2, which indicates that AVR-Pia accumulates in biotrophic interfacial complexes before being delivered to the plant cytosol. Together, these results suggest that AVR-Pia is a cytoplasmic effector that is expressed at the onset of appressorial differentiation and is translocated to the biotrophic interfacial complex, and then into the host's cytoplasm.
Collapse
Affiliation(s)
- Worawan Sornkom
- Graduation School of AgricultureHokkaido University, Kita‐9, Nishi‐9Kita‐kuSapporo060‐8589Japan
| | - Shinsuke Miki
- Graduation School of AgricultureHokkaido University, Kita‐9, Nishi‐9Kita‐kuSapporo060‐8589Japan
| | - Saori Takeuchi
- Graduation School of AgricultureHokkaido University, Kita‐9, Nishi‐9Kita‐kuSapporo060‐8589Japan
| | - Ayumi Abe
- Graduation School of AgricultureHokkaido University, Kita‐9, Nishi‐9Kita‐kuSapporo060‐8589Japan
| | - Kozo Asano
- Graduation School of AgricultureHokkaido University, Kita‐9, Nishi‐9Kita‐kuSapporo060‐8589Japan
| | - Teruo Sone
- Graduation School of AgricultureHokkaido University, Kita‐9, Nishi‐9Kita‐kuSapporo060‐8589Japan
| |
Collapse
|
46
|
Wu Y, Chen Y, Pan C, Xiao N, Yu L, Li Y, Zhang X, Pan X, Chen X, Liang C, Dai Z, Li A. Development and Evaluation of Near-Isogenic Lines with Different Blast Resistance Alleles at the Piz Locus in japonica Rice from the Lower Region of the Yangtze River, China. PLANT DISEASE 2017; 101:1283-1291. [PMID: 30682968 DOI: 10.1094/pdis-12-16-1855-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, threatens rice production in most of the rice-growing areas in China, especially in regions that have grown Oryza sativa subsp. japonica in recent years. The use of resistance genes is the most effective and economical approach for blast control. In our study, a set of six near-isogenic lines (NIL) were developed by introgression of six resistance alleles of the Piz locus (Pi2, Pigm, Pi40, Pi9, Piz, and Pizt) into a blast-susceptible, high-yielding, high-quality japonica '07GY31' via marker-assisted backcross breeding. Artificial inoculation using 144 M. oryzae isolates collected from the lower region of the Yangtze River, China, revealed that most of the NIL, including NIL-Pi2, NIL-Pigm, NIL-Pi40, NIL-Pi9, and NIL-Pizt, exhibited broad-spectrum resistance against rice blast at the seedling stage, with resistance frequencies (RF) of 93.06 to 98.61%. NIL-Piz was an exception, with an RF of 21.53%, which was slightly higher than the recurrent parent 07GY31. NIL-Pi40 and NIL-Pigm had broad-spectrum resistance (RF of 93.33 and 71.67%, respectively) at the heading stage following inoculation of 60 isolates of M. oryzae. Field trials with artificial inoculation at the seedling and heading stage showed that NIL-Pigm and NIL-Pi40 were highly resistant in four locations under high disease pressure. NIL-Pizt showed effective resistance in three locations from Zhejiang and Jiangsu Provinces. This study shows that O. sativa subsp. japonica alleles of the Piz locus confer resistance to M. oryzae, and provides an effective method to enhance seedling and panicle blast resistance in rice plants in the lower region of the Yangtze River, China.
Collapse
Affiliation(s)
- Yunyu Wu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225009, China; and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
| | - Yu Chen
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing; and Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Cunhong Pan
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Ning Xiao
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Ling Yu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Yuhong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Xiaoxiang Zhang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Xuebiao Pan
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou
| | - Xijun Chen
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou
| | - Chengzhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengyuan Dai
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225009, China; and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225009, China; and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
| |
Collapse
|
47
|
Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Latif MA. Marker-assisted introgression of broad-spectrum blast resistance genes into the cultivated MR219 rice variety. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:2810-2818. [PMID: 27778337 DOI: 10.1002/jsfa.8109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/30/2016] [Accepted: 10/20/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND The rice cultivar MR219 is famous for its better yield and long and fine grain quality; however, it is susceptible to blast disease. The main objective of this study was to introgress blast resistance genes into MR219 through marker-assisted selection (MAS). The rice cultivar MR219 was used as the recurrent parent, and Pongsu Seribu 1 was used as the donor. RESULTS Marker-assisted foreground selection was performed using RM6836 and RM8225 to identify plants possessing blast resistance genes. Seventy microsatellite markers were used to estimate recurrent parent genome (RPG) recovery. Our analysis led to the development of 13 improved blast resistant lines with Piz, Pi2 and Pi9 broad-spectrum blast resistance genes and an MR219 genetic background. The RPG recovery of the selected improved lines was up to 97.70% with an average value of 95.98%. Selected improved lines showed a resistance response against the most virulent blast pathogen pathotype, P7.2. The selected improved lines did not express any negative effect on agronomic traits in comparison with MR219. CONCLUSION The research findings of this study will be a conducive approach for the application of different molecular techniques that may result in accelerating the development of new disease-resistant rice varieties, which in turn will match rising demand and food security worldwide. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Gous Miah
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohd Y Rafii
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohd R Ismail
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Adam B Puteh
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Harun A Rahim
- Agrotechnology and Bioscience Division, Malaysian Nuclear Agency, 43000, Kajang, Selangor, Malaysia
| | | |
Collapse
|
48
|
Babasaheb Aglawe S, Bangale U, Sagili Jayasree Satya RD, Balija V, Vijay Pal B, Susheel Kumar S, Pawan Kumar S, Sudhir Kumar, Maddamshetty S, Maganti SM. Identification of novel QTLs conferring field resistance for rice leaf and neck blast from an unique landrace of India. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
49
|
Karre S, Kumar A, Dhokane D, Kushalappa AC. Metabolo-transcriptome profiling of barley reveals induction of chitin elicitor receptor kinase gene (HvCERK1) conferring resistance against Fusarium graminearum. PLANT MOLECULAR BIOLOGY 2017; 93:247-267. [PMID: 27844244 DOI: 10.1007/s11103-016-0559-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/08/2016] [Indexed: 05/25/2023]
Abstract
We report plausible disease resistance mechanisms induced by barley resistant genotype CI89831 against Fusarium head blight (FHB) based on metabolo-transcriptomics approach. We identified HvCERK1 as a candidate gene for FHB resistance, which is functional in resistant genotype CI9831 but non-functional in susceptible cultivars H106-371 and Zhedar-2. For the first time, we were able to show a hierarchy of regulatory genes that regulated downstream biosynthetic genes that eventually produced resistance related metabolites that reinforce the cell walls to contain the pathogen progress in plant. The HvCERK1 can be used for replacing in susceptible commercial cultivars, if non-functional, based on genome editing. Fusarium head blight (FHB) management is a great challenge in barley and wheat production worldwide. Though barley genome sequence and advanced omics technologies are available, till date none of the resistance mechanisms has been clearly deciphered. Hence, this study was aimed at identifying candidate gene(s) and elucidating resistance mechanisms induced by barley resistant genotype CI9831 based on integrated metabolomics and transcriptomics approach. Following Fusarium graminearum infection, we identified accumulation of specific set of induced secondary metabolites, belonging to phenylpropanoid, hydroxycinnamic acid (HCAA) and jasmonic acid pathways, and their biosynthetic genes. In association with these, receptor kinases such as chitin elicitor receptor kinase (HvCERK1) and protein kinases such as MAP kinase 3 (HvMPK3) and MAPK substrate 1 (HvMKS1), and transcription factors such as HvERF1/5, HvNAC42, HvWRKY23 and HvWRKY70 were also found upregulated with high fold change. Polymorphism studies across three barley genotypes confirmed the presence of mutations in HvCERK1 gene in two susceptible genotypes, isolating this gene as a potential candidate for FHB resistance. Further, the silencing of functional HvCERK1 gene in the resistant genotype CI9831, followed by gene expression and metabolite analysis revealed its role as an elicitor recognition receptor that triggered downstream regulatory genes, which in turn, regulated downstream metabolic pathway genes to biosynthesize resistance related (RR) metabolites to contain the pathogen to spikelet infection. A putative model on metabolic pathway regulation is proposed.
Collapse
Affiliation(s)
- Shailesh Karre
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Arun Kumar
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Dhananjay Dhokane
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Ajjamada C Kushalappa
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada.
| |
Collapse
|
50
|
Daware AV, Srivastava R, Singh AK, Parida SK, Tyagi AK. Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:807. [PMID: 28611791 PMCID: PMC5447001 DOI: 10.3389/fpls.2017.00807] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/29/2017] [Indexed: 05/20/2023]
Abstract
Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control) by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information.
Collapse
Affiliation(s)
| | | | - Ashok K. Singh
- Division of Genetics, Indian Agricultural Research InstituteNew Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome ResearchNew Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome ResearchNew Delhi, India
- Department of Plant Molecular Biology, University of Delhi South CampusNew Delhi, India
- *Correspondence: Akhilesh K. Tyagi, Swarup K. Parida, ;
| |
Collapse
|