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Wang X, Xiang M, Li H, Li X, Mu K, Huang S, Zhang Y, Cheng X, Yang S, Yuan X, Singh RP, Bhavani S, Zeng Q, Wu J, Kang Z, Liu S, Han D. High-density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:152. [PMID: 38850423 DOI: 10.1007/s00122-024-04654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
KEY MESSAGE The durable stripe rust resistance gene Yr30 was fine-mapped to a 610-kb region in which five candidate genes were identified by expression analysis and sequence polymorphisms. The emergence of genetically diverse and more aggressive races of Puccinia striiformis f. sp. tritici (Pst) in the past twenty years has resulted in global stripe rust outbreaks and the rapid breakdown of resistance genes. Yr30 is an adult plant resistance (APR) gene with broad-spectrum effectiveness and its durability. Here, we fine-mapped the YR30 locus to a 0.52-cM interval using 1629 individuals derived from residual heterozygous F5:6 plants in a Yaco"S"/Mingxian169 recombinant inbred line population. This interval corresponded to a 610-kb region in the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 2.1 on chromosome arm 3BS harboring 30 high-confidence genes. Five genes were identified as candidate genes based on functional annotation, expression analysis by RNA-seq and sequence polymorphisms between cultivars with and without Yr30 based on resequencing. Haplotype analysis of the target region identified six haplotypes (YR30_h1-YR30_h6) in a panel of 1215 wheat accessions based on the 660K feature genotyping array. Lines with YR30_h6 displayed more resistance to stripe rust than the other five haplotypes. Near-isogenic lines (NILs) with Yr30 showed a 32.94% higher grain yield than susceptible counterparts when grown in a stripe rust nursery, whereas there was no difference in grain yield under rust-free conditions. These results lay a foundation for map-based cloning Yr30.
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Affiliation(s)
- Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Mingjie Xiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Huaizhou Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiaoxiao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Keqing Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yibo Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiangrui Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shuqing Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xunying Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), 56237, El Batan, Texcoco, Estado de Mexico, Mexico
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan City, 430070, Hubei Province, China
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), 56237, El Batan, Texcoco, Estado de Mexico, Mexico
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Sharma D, Kumari A, Sharma P, Singh A, Sharma A, Mir ZA, Kumar U, Jan S, Parthiban M, Mir RR, Bhati P, Pradhan AK, Yadav A, Mishra DC, Budhlakoti N, Yadav MC, Gaikwad KB, Singh AK, Singh GP, Kumar S. Meta-QTL analysis in wheat: progress, challenges and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:247. [PMID: 37975911 DOI: 10.1007/s00122-023-04490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.
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Affiliation(s)
- Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Anupma Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anshu Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Sofora Jan
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - M Parthiban
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Reyazul Rouf Mir
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Pradeep Bhati
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Anjan Kumar Pradhan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Aakash Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Neeraj Budhlakoti
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh C Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Kiran B Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India.
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Deblieck M, Ordon F, Serfling A. Mapping of prehaustorial resistance against wheat leaf rust in einkorn ( Triticum monococcum), a progenitor of wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1252123. [PMID: 37936932 PMCID: PMC10626456 DOI: 10.3389/fpls.2023.1252123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/25/2023] [Indexed: 11/09/2023]
Abstract
Wheat leaf rust (Puccinia triticina) is one of the most significant fungal diseases of wheat, causing substantial yield losses worldwide. Infestation is currently being reduced by fungicide treatments and mostly vertical resistance. However, these measures often break down when the fungal virulence pattern changes, resulting in a breakdown of vertical resistances. In contrast, the prehaustorial resistance (phr) that occurs in the einkorn-wheat leaf rust interaction is race-independent, characterized by an early defense response of plants during the prehaustorial phase of infestation. Einkorn (Triticum monococcum) is closely related to Triticum urartu as a progenitor of wheat and generally shows a high level of resistance against leaf rust of wheat. Hence, einkorn can serve as a valuable source to improve the level of resistance to the pathogen in future wheat lines. In particular, einkorn accession PI272560 is known to exhibit a hypersensitive prehaustorial effector triggered immune reaction, preventing the infection of P. triticina. Remarkably, this effector-triggered immune reaction turned out to be atypical as it is non-race-specific (horizontal). To genetically dissect the prehaustorial resistance (phr) in PI272560, a biparental F2 population of 182 plants was established after crossing PI272560 with the susceptible T. boeoticum accession 36554. Three genetic maps comprising 2,465 DArT-seq markers were constructed, and a major QTL was detected on chromosome 5A. To locate underlying candidate genes, marker sequences flanking the respective QTL were aligned to the T. urartu reference genome and transcriptome data available from the parental accessions were used. Within the QTL interval of approximately 16.13 million base pairs, the expression of genes under inoculated and non-inoculated conditions was analyzed via a massive analysis of cDNA (MACE). Remarkably, a single gene located 3.4 Mbp from the peak marker within the major QTL was upregulated (20- to 95-fold) after the inoculation in the resistant accession in comparison to the susceptible T. boeoticum accession. This gene belongs to a berberine bridge enzyme-like protein that is suspected to interact on the plant surface with glycoside hydrolases (GH) secreted by the fungus and to induce a hypersensitive defense reaction in the plant after fungal infections.
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Jain N, Shiv A, Sinha N, Singh PK, Prasad P, Balyan HS, Gupta PK. Leaf rust responsive miRNA and their target genes in wheat. Funct Integr Genomics 2022; 23:14. [PMID: 36550370 DOI: 10.1007/s10142-022-00928-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.
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Affiliation(s)
- Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Aalok Shiv
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - P K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Pramod Prasad
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, 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.
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Mapuranga J, Chang J, Zhang L, Zhang N, Yang W. Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions. J Fungi (Basel) 2022; 9:jof9010004. [PMID: 36675825 PMCID: PMC9862911 DOI: 10.3390/jof9010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.
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Mapuranga J, Chang J, Yang W. Combating powdery mildew: Advances in molecular interactions between Blumeria graminis f. sp. tritici and wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1102908. [PMID: 36589137 PMCID: PMC9800938 DOI: 10.3389/fpls.2022.1102908] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Wheat powdery mildew caused by a biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a widespread airborne disease which continues to threaten global wheat production. One of the most chemical-free and cost-effective approaches for the management of wheat powdery mildew is the exploitation of resistant cultivars. Accumulating evidence has reported that more than 100 powdery mildew resistance genes or alleles mapping to 63 different loci (Pm1-Pm68) have been identified from common wheat and its wild relatives, and only a few of them have been cloned so far. However, continuous emergence of new pathogen races with novel degrees of virulence renders wheat resistance genes ineffective. An essential breeding strategy for achieving more durable resistance is the pyramiding of resistance genes into a single genotype. The genetics of host-pathogen interactions integrated with temperature conditions and the interaction between resistance genes and their corresponding pathogen a virulence genes or other resistance genes within the wheat genome determine the expression of resistance genes. Considerable progress has been made in revealing Bgt pathogenesis mechanisms, identification of resistance genes and breeding of wheat powdery mildew resistant cultivars. A detailed understanding of the molecular interactions between wheat and Bgt will facilitate the development of novel and effective approaches for controlling powdery mildew. This review gives a succinct overview of the molecular basis of interactions between wheat and Bgt, and wheat defense mechanisms against Bgt infection. It will also unleash the unsung roles of epigenetic processes, autophagy and silicon in wheat resistance to Bgt.
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