1
|
Concepcion JS, Noble AD, Thompson AM, Dong Y, Olson EL. Genomic regions influencing the hyperspectral phenome of deoxynivalenol infected wheat. Sci Rep 2024; 14:19340. [PMID: 39164367 PMCID: PMC11336138 DOI: 10.1038/s41598-024-69830-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024] Open
Abstract
The quantitative nature of fusarium head blight (FHB) resistance requires further exploration of the wheat genome to identify regions conferring resistance. In this study, we explored the application of hyperspectral imaging of Fusarium-infected wheat kernels and identified regions of the wheat genome contributing significantly to the accumulation of Deoxynivalenol (DON) mycotoxin. Strong correlations were identified between hyperspectral reflectance values for 204 wavebands in the 397-673 nm range and DON mycotoxin. Dimensionality reduction using principal components was performed for all 204 wavebands and 38 sliding windows across the range of wavebands. The first principal component (PC1) of all 204 wavebands explained 70% of the total variation in waveband reflectance values and was highly correlated with DON mycotoxin. PC1 was used as a phenotype in a genome wide association study and a large effect QTL on chromosome 2D was identified for PC1 of all wavebands as well as nearly all 38 sliding windows. The allele contributing variation in PC1 values also led to a substantial reduction in DON. The 2D polymorphism affecting DON levels localized to the exon of TraesCS2D02G524600 which is upregulated in wheat spike and rachis tissues during FHB infection. This work demonstrates the value of hyperspectral imaging as a correlated trait for investigating the genetic basis of resistance and developing wheat varieties with enhanced resistance to FHB.
Collapse
Affiliation(s)
- Jonathan S Concepcion
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Amanda D Noble
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Addie M Thompson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Eric L Olson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA.
| |
Collapse
|
2
|
Heckmann A, Perochon A, Doohan FM. Genome-wide analysis of salicylic acid and jasmonic acid signalling marker gene families in wheat. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:691-704. [PMID: 38864777 DOI: 10.1111/plb.13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Jasmonic acid (JA) and salicylic acid (SA) phytohormone pathways are important regulators of stress tolerance. Knowledge regarding the diversity, phylogeny and functionality of wheat genes involved in JA and SA response is limited. Using Arabidopsis, rice and wheat genomic and wheat disease transcriptomic data, we deduced the size, phylogenetic diversity and pathogen-responsiveness of seven hormone-responsive gene families, and thus selected 14 candidates as potential hormone responsive gene markers. Gene-specific expression studies assessed the impact of exogenous JA and SA on their transcriptional activation in leaves of two distinct wheat cultivars. RNAseq data were interrogated to assess their disease responsiveness and tissue-specific expression. This study elucidated the number, phylogeny and pathogen-responsiveness of wheat genes from seven families, including 12 TaAOS, 6 TaJAMyb, 256 TaWRKY group III, 85 TaPR1, 205 TaPR2, 76 TaPR3 and 124 TaPR5. This included the first description of the wheat AOS, JAMyb, PR2, PR3 and PR5 gene families. Gene expression studies delineated TaAOS1-5B and TaJAMyb-4A as JA-responsive in leaves, but not significantly responsive to SA treatment, while TaWRKY45-B was a SA- but not a JA-responsive marker. Other candidate genes were either unresponsive or non-specific to SA or JA. Our findings highlight that all seven gene families are greatly expanded in wheat as compared to other plants (up to 7.6-fold expansion), and demonstrate disparity in the response to biotic stress between some homoeologous and paralogous sequences within these families. The SA- and JA-responsive marker genes identified herein will prove useful tools to monitor these signalling pathways in wheat.
Collapse
Affiliation(s)
- A Heckmann
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - A Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - F M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
3
|
Lin J, Ruan S, Guo Q, Zhang Y, Fang M, Li T, Luo G, Tian Z, Zhang Y, Tandayu E, Chen C, Lu J, Ma C, Si H. Comprehensive genome-wide analysis of wheat xylanase inhibitor protein (XIP) genes: unveiling their role in Fusarium head blight resistance and plant immune mechanisms. BMC PLANT BIOLOGY 2024; 24:462. [PMID: 38802731 PMCID: PMC11129392 DOI: 10.1186/s12870-024-05176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.
Collapse
Affiliation(s)
- Juan Lin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Shuang Ruan
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Qi Guo
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Yonglin Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Mengyuan Fang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Tiantian Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Gan Luo
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Zhuangbo Tian
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Yi Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Erwin Tandayu
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Can Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China.
| |
Collapse
|
4
|
Zhang M, Jiang P, Wu Q, Han X, Man J, Sun J, Liang J, Chen J, Zhao Q, Guo Y, An Y, Jia H, Li S, Xu Y. Identification of candidate genes for Fusarium head blight resistance from QTLs using RIL population in wheat. PLANT MOLECULAR BIOLOGY 2024; 114:62. [PMID: 38771394 DOI: 10.1007/s11103-024-01462-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024]
Abstract
Fusarium head blight (FHB) stands out as one of the most devastating wheat diseases and leads to significantly grain yield losses and quality reductions in epidemic years. Exploring quantitative trait loci (QTL) for FHB resistance is a critical step for developing new FHB-resistant varieties. We previously constructed a genetic map of unigenes (UG-Map) according to the physical positions using a set of recombinant-inbred lines (RILs) derived from the cross of 'TN18 × LM6' (TL-RILs). Here, the number of diseased spikelets (NDS) and relative disease index (RDI) for FHB resistance were investigated under four environments using TL-RILs, which were distributed across 13 chromosomes. A number of 36 candidate genes for NDS and RDI from of 19 stable QTLs were identified. The average number of candidate genes per QTL was 1.89, with 14 (73.7%), two (10.5%), and three (15.8%) QTLs including one, two, and 3-10 candidate genes, respectively. Among the 24 candidate genes annotated in the reference genome RefSeq v1.1, the homologous genes of seven candidate genes, including TraesCS4B02G227300 for QNds/Rdi-4BL-4553, TraesCS5B02G303200, TraesCS5B02G303300, TraesCS5B02G303700, TraesCS5B02G303800 and TraesCS5B02G304000 for QNds/Rdi-5BL-9509, and TraesCS7A02G568400 for QNds/Rdi-7AL-14499, were previously reported to be related to FHB resistance in wheat, barely or Brachypodium distachyon. These genes should be closely associated with FHB resistance in wheat. In addition, the homologous genes of five genes, including TraesCS1A02G037600LC for QNds-1AS-2225, TraesCS1D02G017800 and TraesCS1D02G017900 for QNds-1DS-527, TraesCS1D02G018000 for QRdi-1DS-575, and TraesCS4B02G227400 for QNds/Rdi-4BL-4553, were involved in plant defense responses against pathogens. These genes should be likely associated with FHB resistance in wheat.
Collapse
Affiliation(s)
- Mingxia Zhang
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Peng Jiang
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, Nanjing, 210095, China
| | - Qun Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xu Han
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Junxia Man
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Junsheng Sun
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Jinlong Liang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Jingchuan Chen
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Qi Zhao
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Ying Guo
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Yanrong An
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Haiyan Jia
- Applied Plant Genomics Laboratory, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Sishen Li
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China.
| | - Yongyu Xu
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
| |
Collapse
|
5
|
Sun S, Bakkeren G. A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1369299. [PMID: 38681221 PMCID: PMC11046709 DOI: 10.3389/fpls.2024.1369299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/19/2024] [Indexed: 05/01/2024]
Abstract
The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signaling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue of FMOs found in genomes across vascular plants and explore, in depth, 170 wheat TaFMO genes for sequence architecture, cis-acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2 TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.
Collapse
Affiliation(s)
- Sherry Sun
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Center, Summerland, BC, Canada
| |
Collapse
|
6
|
Meng D, Dong X, He X, Pan R, Sun M, Chu Y, Tong Z, Yi X, Fan H, Gao T, Duan J. Effects of wheat varieties, fungicides and application time on Fusarium head blight and deoxynivalenol contamination control in wheat. PEST MANAGEMENT SCIENCE 2023; 79:4784-4794. [PMID: 37471098 DOI: 10.1002/ps.7674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/11/2023] [Accepted: 07/18/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Yield loss and toxin contamination caused by wheat Fusarium head blight (FHB) have always been a worldwide concern. Cultivating disease-resistant varieties and fungicide application are effective measures to control FHB. The comprehensive control technology system for FHB and toxin contamination of wheat in Anhui Province needs further improvement. This study compared the control efficacy of different wheat varieties, fungicides and application times on wheat FHB and deoxynivalenol (DON) contamination, and the dynamic change of DON accumulation after application. RESULTS Among the 93 main wheat varieties in Anhui Province, the disease-resistant and low-toxic wheat variety "Ningmai 26" was more suitable for planting in the central part of Anhui Province. At the same time, "Yangmai 22" was used for subsequent experiments. The field efficacy trials of different fungicides showed that 30% prothioconazole oil dispersion (OD) had the highest control efficacy on FHB and DON contamination, reaching 94.33 and 77.49%, respectively. The study on the optimum application time of prothioconazole showed that the 0-20% flowering stage was the key point of DON control. The survey of the dynamic changes of DON accumulation showed that prothioconazole could significantly reduce the level of DON accumulation while inhibiting the accumulation rate of DON. At the same time, the control fungicide carbendazim increased the level of DON contamination. CONCLUSION This study will provide excellent germplasm resources for cultivating disease-resistant and low-toxic wheat varieties, and provide a theoretical reference for establishing a collaborative prevention and control system of disease control and toxin reduction. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- DanDan Meng
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - Xu Dong
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - XianFang He
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Rui Pan
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
| | - MingNa Sun
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - Yue Chu
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - Zhou Tong
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - XiaoTong Yi
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - Hui Fan
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - TongChun Gao
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| | - JinSheng Duan
- Institute of Plant Protection and Agro-Product Safety, Anhui Academy of Agricultural Sciences, Hefei, China
- Key Laboratory of Agro-Product Safety Risk Evaluation (Hefei), Ministry of Agriculture, Hefei, China
| |
Collapse
|
7
|
Fu K, Wu Q, Jiang N, Hu S, Ye H, Hu Y, Li L, Li T, Sun Z. Identification and Expressional Analysis of siRNAs Responsive to Fusarium graminearum Infection in Wheat. Int J Mol Sci 2023; 24:16005. [PMID: 37958988 PMCID: PMC10650599 DOI: 10.3390/ijms242116005] [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: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The outbreak of Fusarium head blight (FHB) poses a serious threat to wheat production as it leads to both significant yield losses and accumulation of several mycotoxins including deoxynivalenol (DON) in the grains, which are harmful to human and livestock. To date, hundreds of FHB-resistance-related quantitative trait loci (QTLs) have been reported, but only a few of them have been cloned and used for breeding. Small interfering RNAs (siRNA) have been reported in plants to mediate host defense against pathogens, but they have rarely been reported in wheat-FHB interaction. In order to identify the key siRNAs that can potentially be used in the improvement of resistance to FHB, siRNAs from the spikes of an FHB-resistant variety Sumai 3 and an FHB-susceptible variety of Chinese Spring (CS) were sequenced after F. graminearum infection and mock inoculation, respectively. The expression patterns of the siRNAs of interest were analyzed. A total of 4019 siRNAs of high-confidence were identified, with 131 being CS-specific, 309 Sumai 3-specific and 3071 being common in both varieties. More than 87% of these siRNAs were 24 nt in length. An overall down-regulation trend was found for siRNAs in the spikes of both varieties after being infected with F. graminearum. The expression patterns for Triticum aestivum Dicer-like 3 (TaDCL3) that synthesizes 24 nt siRNAs were validated by qRT-PCR, which were positively correlated with those of the siRNAs. A total of 85% of the differentially expressed genes putatively targeted by the siRNAs were significantly up-regulated after infection, showing a negative correlation with the overall down-regulated expression of siRNAs. Interestingly, the majority of the up-regulated genes are annotated as disease resistance. These results suggested that the inhibition of siRNA by F. graminearum up-regulated the disease resistance genes, which were putatively suppressed by siRNAs through RNA-directed DNA methylation (RdDM). Consequently, the resistant capability to F. graminearum infection was enhanced. This study provides novel clues for investigating the function of siRNA in wheat-F. graminearum interaction.
Collapse
Affiliation(s)
- Kai Fu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Qianhui Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Ning Jiang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Sijia Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Ye
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yi Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Lei Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Tao Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhengxi Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
8
|
Haile JK, Sertse D, N’Diaye A, Klymiuk V, Wiebe K, Ruan Y, Chawla HS, Henriquez MA, Wang L, Kutcher HR, Steiner B, Buerstmayr H, Pozniak CJ. Multi-locus genome-wide association studies reveal the genetic architecture of Fusarium head blight resistance in durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1182548. [PMID: 37900749 PMCID: PMC10601657 DOI: 10.3389/fpls.2023.1182548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023]
Abstract
Durum wheat is more susceptible to Fusarium head blight (FHB) than other types or classes of wheat. The disease is one of the most devastating in wheat; it reduces yield and end-use quality and contaminates the grain with fungal mycotoxins such as deoxynivalenol (DON). A panel of 265 Canadian and European durum wheat cultivars, as well as breeding and experimental lines, were tested in artificially inoculated field environments (2019-2022, inclusive) and two greenhouse trials (2019 and 2020). The trials were assessed for FHB severity and incidence, visual rating index, Fusarium-damaged kernels, DON accumulation, anthesis or heading date, maturity date, and plant height. In addition, yellow pigment and protein content were analyzed for the 2020 field season. To capture loci underlying FHB resistance and related traits, GWAS was performed using single-locus and several multi-locus models, employing 13,504 SNPs. Thirty-one QTL significantly associated with one or more FHB-related traits were identified, of which nine were consistent across environments and associated with multiple FHB-related traits. Although many of the QTL were identified in regions previously reported to affect FHB, the QTL QFhb-3B.2, associated with FHB severity, incidence, and DON accumulation, appears to be novel. We developed KASP markers for six FHB-associated QTL that were consistently detected across multiple environments and validated them on the Global Durum Panel (GDP). Analysis of allelic diversity and the frequencies of these revealed that the lines in the GDP harbor between zero and six resistance alleles. This study provides a comprehensive assessment of the genetic basis of FHB resistance and DON accumulation in durum wheat. Accessions with multiple favorable alleles were identified and will be useful genetic resources to improve FHB resistance in durum breeding programs through marker-assisted recurrent selection and gene stacking.
Collapse
Affiliation(s)
- Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Demissew Sertse
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Valentyna Klymiuk
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Krystalee Wiebe
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Harmeet S. Chawla
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Maria-Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Lipu Wang
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Hadley R. Kutcher
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Barbara Steiner
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
9
|
Nasrallah JB. Stop and go signals at the stigma-pollen interface of the Brassicaceae. PLANT PHYSIOLOGY 2023; 193:927-948. [PMID: 37423711 PMCID: PMC10517188 DOI: 10.1093/plphys/kiad301] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/16/2023] [Indexed: 07/11/2023]
Affiliation(s)
- June B Nasrallah
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
10
|
Kirana RP, Michel S, Moreno-Amores J, Prat N, Lemmens M, Buerstmayr M, Buerstmayr H, Steiner B. Pyramiding Fusarium head blight resistance QTL from T. aestivum, T. dicoccum and T. dicoccoides in durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:201. [PMID: 37639019 PMCID: PMC10462738 DOI: 10.1007/s00122-023-04426-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
KEY MESSAGE FHB resistance of durum wheat was improved by introgression of Fhb1 and resistance genes from emmer wheat and by selection against adverse alleles of elite durum wheat. Durum wheat is particularly susceptible to Fusarium head blight (FHB) and breeding for resistance is impeded by the low genetic variation within the elite gene pool. To extend the genetic basis for FHB resistance in durum wheat, we analyzed 603 durum wheat lines from crosses of elite durum wheat with resistance donors carrying resistance alleles derived from Triticum aestivum, T. dicoccum and T. dicoccoides. The lines were phenotyped for FHB resistance, anthesis date, and plant height in artificially inoculated disease nurseries over 5 years. A broad variation was found for all traits, while anthesis date and plant height strongly influenced FHB severities. To correct for spurious associations, we adjusted FHB scorings for temperature fluctuations during the anthesis period and included plant height as a covariate in the analysis. This resulted in the detection of seven quantitative trait loci (QTL) affecting FHB severities. The hexaploid wheat-derived Fhb1 QTL was most significant on reducing FHB severities, highlighting its successful introgression into several durum wheat backgrounds. For two QTL on chromosomes 1B and 2B, the resistance alleles originated from the T. dicoccum line Td161 and T. dicoccoides accessions Mt. Hermon#22 and Mt. Gerizim#36, respectively. The other four QTL featured unfavorable alleles derived from elite durum wheat that increased FHB severities, with a particularly negative effect on chromosome 6A that simultaneously affected plant height and anthesis date. Therefore, in addition to pyramiding resistance genes, selecting against adverse alleles present in elite durum wheat could be a promising avenue in breeding FHB-resistant durum wheat.
Collapse
Affiliation(s)
- Rizky Pasthika Kirana
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
- Laboratory of Plant Breeding, Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sebastian Michel
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Jose Moreno-Amores
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Noemie Prat
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Marc Lemmens
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Maria Buerstmayr
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Hermann Buerstmayr
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria
| | - Barbara Steiner
- University of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, Konrad-Lorenz-Straße 20, 3430, Tulln, Austria.
| |
Collapse
|
11
|
Cabral AL, Ruan Y, Cuthbert RD, Li L, Zhang W, Boyle K, Berraies S, Henriquez MA, Burt A, Kumar S, Fobert P, Piche I, Bokore FE, Meyer B, Sangha J, Knox RE. Multi-locus genome-wide association study of fusarium head blight in relation to days to anthesis and plant height in a spring wheat association panel. FRONTIERS IN PLANT SCIENCE 2023; 14:1166282. [PMID: 37457352 PMCID: PMC10346453 DOI: 10.3389/fpls.2023.1166282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/03/2023] [Indexed: 07/18/2023]
Abstract
Fusarium head blight (FHB) is a highly destructive fungal disease of wheat to which host resistance is quantitatively inherited and largely influenced by the environment. Resistance to FHB has been associated with taller height and later maturity; however, a further understanding of these relationships is needed. An association mapping panel (AMP) of 192 predominantly Canadian spring wheat was genotyped with the wheat 90K single-nucleotide polymorphism (SNP) array. The AMP was assessed for FHB incidence (INC), severity (SEV) and index (IND), days to anthesis (DTA), and plant height (PLHT) between 2015 and 2017 at three Canadian FHB-inoculated nurseries. Seven multi-environment trial (MET) datasets were deployed in a genome-wide association study (GWAS) using a single-locus mixed linear model (MLM) and a multi-locus random SNP-effect mixed linear model (mrMLM). MLM detected four quantitative trait nucleotides (QTNs) for INC on chromosomes 2D and 3D and for SEV and IND on chromosome 3B. Further, mrMLM identified 291 QTNs: 50 (INC), 72 (SEV), 90 (IND), 41 (DTA), and 38 (PLHT). At two or more environments, 17 QTNs for FHB, DTA, and PLHT were detected. Of these 17, 12 QTNs were pleiotropic for FHB traits, DTA, and PLHT on chromosomes 1A, 1D, 2D, 3B, 5A, 6B, 7A, and 7B; two QTNs for DTA were detected on chromosomes 1B and 7A; and three PLHT QTNs were located on chromosomes 4B and 6B. The 1B DTA QTN and the three pleiotropic QTNs on chromosomes 1A, 3B, and 6B are potentially identical to corresponding quantitative trait loci (QTLs) in durum wheat. Further, the 3B pleiotropic QTN for FHB INC, SEV, and IND co-locates with TraesCS3B02G024900 within the Fhb1 region on chromosome 3B and is ~3 Mb from a cloned Fhb1 candidate gene TaHRC. While the PLHT QTN on chromosome 6B is putatively novel, the 1B DTA QTN co-locates with a disease resistance protein located ~10 Mb from a Flowering Locus T1-like gene TaFT3-B1, and the 7A DTA QTN is ~5 Mb away from a maturity QTL QMat.dms-7A.3 of another study. GWAS and QTN candidate genes enabled the characterization of FHB resistance in relation to DTA and PLHT. This approach should eventually generate additional and reliable trait-specific markers for breeding selection, in addition to providing useful information for FHB trait discovery.
Collapse
Affiliation(s)
- Adrian L. Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard D. Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Lin Li
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Wentao Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada
| | - Samia Berraies
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Andrew Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Pierre Fobert
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Isabelle Piche
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Firdissa E. Bokore
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Jatinder Sangha
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron E. Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| |
Collapse
|
12
|
Li G, Yuan Y, Zhou J, Cheng R, Chen R, Luo X, Shi J, Wang H, Xu B, Duan Y, Zhong J, Wang X, Kong Z, Jia H, Ma Z. FHB resistance conferred by Fhb1 is under inhibitory regulation of two genetic loci in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:134. [PMID: 37217699 DOI: 10.1007/s00122-023-04380-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE Two loci inhibiting Fhb1 resistance to Fusarium head blight were identified through genome-wide association mapping and validated in biparental populations. Fhb1 confers Fusarium head blight (FHB) resistance by limiting fungal spread within spikes in wheat (type II resistance). However, not all lines with Fhb1 display the expected resistance. To identify genetic factors regulating Fhb1 effect, a genome-wide association study for type II resistance was first performed with 72 Fhb1-carrying lines using the Illumina 90 K iSelect SNP chip. Of 84 significant marker-trait associations detected, more than half were repeatedly detected in at least two environments, with the SNPs distributed in one region on chromosome 5B and one on chromosome 6A. This result was validated in a collection of 111 lines with Fhb1 and 301 lines without Fhb1. We found that these two loci caused significant resistance variations solely among lines with Fhb1 by compromising the resistance. In1, the inhibitory gene on chromosome 5B, was in close linkage with Xwgrb3860 in a recombinant inbred line population derived from Nanda2419 × Wangshuibai and a double haploid (DH) population derived from R-43 (Fhb1 near isogenic line) × Biansui7 (with Fhb1 and In1); and In2, the inhibitory gene on chromosome 6A, was mapped to the Xwgrb4113-Xwgrb4034 interval using a DH population derived from R-43 × PH8901 (with Fhb1 and In2). In1 and In2 are present in all wheat-growing areas worldwide. Their frequencies in China's modern cultivars are high but have significantly decreased in comparison with landraces. These findings are of great significance for FHB resistance breeding using Fhb1.
Collapse
Affiliation(s)
- Guoqiang Li
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China.
| | - Yang Yuan
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Jiyang Zhou
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- College of Life Science and Technology, Xinjiang University, Urumqi, 830046, Xinjiang, China
| | - Rui Cheng
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Ruitong Chen
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Xianmin Luo
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Jinxing Shi
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Heyu Wang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Boyang Xu
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Youyu Duan
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Jinkun Zhong
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Xin Wang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Zhongxin Kong
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Haiyan Jia
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China.
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, Jiangsu, China.
| |
Collapse
|
13
|
Fanelli G, Kuzmanović L, Giovenali G, Tundo S, Mandalà G, Rinalducci S, Ceoloni C. Untargeted Metabolomics Reveals a Multi-Faceted Resistance Response to Fusarium Head Blight Mediated by the Thinopyrum elongatum Fhb7E Locus Transferred via Chromosome Engineering into Wheat. Cells 2023; 12:1113. [PMID: 37190021 PMCID: PMC10136595 DOI: 10.3390/cells12081113] [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: 02/27/2023] [Revised: 04/04/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
The Thinopyrum elongatum Fhb7E locus has been proven to confer outstanding resistance to Fusarium Head Blight (FHB) when transferred into wheat, minimizing yield loss and mycotoxin accumulation in grains. Despite their biological relevance and breeding implications, the molecular mechanisms underlying the resistant phenotype associated with Fhb7E have not been fully uncovered. To gain a broader understanding of processes involved in this complex plant-pathogen interaction, we analysed via untargeted metabolomics durum wheat (DW) rachises and grains upon spike inoculation with Fusarium graminearum (Fg) and water. The employment of DW near-isogenic recombinant lines carrying or lacking the Th. elongatum chromosome 7E region including Fhb7E on their 7AL arm, allowed clear-cut distinction between differentially accumulated disease-related metabolites. Besides confirming the rachis as key site of the main metabolic shift in plant response to FHB, and the upregulation of defence pathways (aromatic amino acid, phenylpropanoid, terpenoid) leading to antioxidants and lignin accumulation, novel insights were revealed. Fhb7E conferred constitutive and early-induced defence response, in which specific importance of polyamine biosynthesis, glutathione and vitamin B6 metabolisms, along with presence of multiple routes for deoxynivalenol detoxification, was highlighted. The results suggested Fhb7E to correspond to a compound locus, triggering a multi-faceted plant response to Fg, effectively limiting Fg growth and mycotoxin production.
Collapse
Affiliation(s)
- Giuseppina Fanelli
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy; (G.F.)
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (L.K.); (G.G.); (G.M.)
| | - Ljiljana Kuzmanović
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (L.K.); (G.G.); (G.M.)
| | - Gloria Giovenali
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (L.K.); (G.G.); (G.M.)
| | - Silvio Tundo
- Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy; (S.T.)
| | - Giulia Mandalà
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (L.K.); (G.G.); (G.M.)
| | - Sara Rinalducci
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy; (G.F.)
| | - Carla Ceoloni
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (L.K.); (G.G.); (G.M.)
| |
Collapse
|
14
|
Vranic M, Perochon A, Benbow H, Doohan FM. Comprehensive analysis of pathogen-responsive wheat NAC transcription factors: new candidates for crop improvement. G3 (BETHESDA, MD.) 2022; 12:jkac247. [PMID: 36130261 PMCID: PMC9635653 DOI: 10.1093/g3journal/jkac247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/03/2022] [Indexed: 11/26/2022]
Abstract
Wheat NAC (TaNAC) transcription factors are important regulators of stress responses and developmental processes. This study proposes a new TaNAC nomenclature and identified defense-associated TaNACs based on the analysis of RNA-sequencing datasets of wheat tissue infected with major fungal pathogens. A total of 146 TaNACs were pathogen-responsive, of which 52 were orthologous with functionally characterized defense-associated NACs from barley, rice, and Arabidopsis, as deduced via phylogenetic analysis. Next, we focused on the phylogenetic relationship of the pathogen-responsive TaNACs and their expression profiles in healthy and diseased tissues. Three subfamilies ("a," "e," and "f") were significantly enriched in pathogen-responsive TaNACs, of which the majority were responsive to at least 2 pathogens (universal pathogen response). Uncharacterized TaNACs from subfamily "a" enriched with defense-associated NACs are promising candidates for functional characterization in pathogen defense. In general, pathogen-responsive TaNACs were expressed in at least 2 healthy organs. Lastly, we showed that the wheat NAM domain is significantly divergent in sequence in subfamilies "f," "g," and "h" based on HMMER and motif analysis. New protein motifs were identified in both the N- and C-terminal parts of TaNACs. Three of those identified in the C-terminal part were linked to pathogen responsiveness of the TaNACs and 2 were linked to expression in grain tissue. Future studies should benefit from this comprehensive in silico analysis of pathogen-responsive TaNACs as a basis for selecting the most promising candidates for functional validation and crop improvement.
Collapse
Affiliation(s)
- Monika Vranic
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
| | - Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
| | - Harriet Benbow
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
15
|
Wu L, He X, He Y, Jiang P, Xu K, Zhang X, Singh PK. Genetic sources and loci for Fusarium head blight resistance in bread wheat. Front Genet 2022; 13:988264. [PMID: 36246592 PMCID: PMC9561102 DOI: 10.3389/fgene.2022.988264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Fusarium head blight (FHB) of wheat is an important disease worldwide, affecting the yield, end-use quality and threatening food safety. Genetic resources or stable loci for FHB resistance are still limited in breeding programs. A panel of 265 bread wheat accessions from China, CIMMYT-Mexico and other countries was screened for FHB resistance under 5 field experiments in Mexico and China, and a genome-wide association analysis was performed to identify QTLs associated with FHB resistance. The major locus Fhb1 was significantly associated with FHB severity and Deoxynivalenol content in grains. FHB screening experiments in multiple environments showed that Fhb1-harbouring accessions Sumai3, Sumai5, Ningmai9, Yangmai18 and Tokai66 had low FHB index, disease severity and DON content in grains in response to different Fusarium species and ecological conditions in Mexico and China. Accessions Klein Don Enrique, Chuko and Yumai34 did not have Fhb1 but still showed good FHB resistance and low mycotoxin accumulation. Sixteen loci associated with FHB resistance or DON content in grains were identified on chromosomes 1A, 1B, 2B, 3A, 3D, 4B, 4D, 5A, 5B, 7A, and 7B in multiple environments, explaining phenotypic variation of 4.43–10.49%. The sources with good FHB resistance reported here could be used in breeding programs for resistance improvement in Mexico and China, and the significant loci could be further studied and introgressed for resistance improvement against FHB and mycotoxin accumulation in grains.
Collapse
Affiliation(s)
- Lei Wu
- CIMMYT-JAAS Joint Center for Wheat Diseases, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Yi He
- CIMMYT-JAAS Joint Center for Wheat Diseases, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Peng Jiang
- CIMMYT-JAAS Joint Center for Wheat Diseases, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kaijie Xu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xu Zhang
- CIMMYT-JAAS Joint Center for Wheat Diseases, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Xu Zhang, ; Pawan K. Singh,
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- *Correspondence: Xu Zhang, ; Pawan K. Singh,
| |
Collapse
|
16
|
Seidl B, Rehak K, Bueschl C, Parich A, Buathong R, Wolf B, Doppler M, Mitterbauer R, Adam G, Khewkhom N, Wiesenberger G, Schuhmacher R. Gramiketides, Novel Polyketide Derivatives of Fusarium graminearum, Are Produced during the Infection of Wheat. J Fungi (Basel) 2022; 8:1030. [PMID: 36294594 PMCID: PMC9605136 DOI: 10.3390/jof8101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
The plant pathogen Fusarium graminearum is a proficient producer of mycotoxins and other in part still unknown secondary metabolites, some of which might act as virulence factors on wheat. The PKS15 gene is expressed only in planta, so far hampering the identification of an associated metabolite. Here we combined the activation of silent gene clusters by chromatin manipulation (kmt6) with blocking the metabolic flow into the competing biosynthesis of the two major mycotoxins deoxynivalenol and zearalenone. Using an untargeted metabolomics approach, two closely related metabolites were found in triple mutants (kmt6 tri5 pks4,13) deficient in production of the major mycotoxins deoxynivalenol and zearalenone, but not in strains with an additional deletion in PKS15 (kmt6 tri5 pks4,13 pks15). Characterization of the metabolites, by LC-HRMS/MS in combination with a stable isotope-assisted tracer approach, revealed that they are likely hybrid polyketides comprising a polyketide part consisting of malonate-derived acetate units and a structurally deviating part. We propose the names gramiketide A and B for the two metabolites. In a biological experiment, both gramiketides were formed during infection of wheat ears with wild-type but not with pks15 mutants. The formation of the two gramiketides during infection correlated with that of the well-known virulence factor deoxynivalenol, suggesting that they might play a role in virulence.
Collapse
Affiliation(s)
- Bernhard Seidl
- Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Katrin Rehak
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 24, 3430 Tulln, Austria
| | - Christoph Bueschl
- Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Alexandra Parich
- Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Raveevatoo Buathong
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Ngamwongwan Road, Lat Yao, Chatuchak, Bangkok 10900, Thailand
| | - Bernhard Wolf
- Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Maria Doppler
- Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
- Core Facility Bioactive Molecules: Screening and Analysis, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | - Rudolf Mitterbauer
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 24, 3430 Tulln, Austria
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 24, 3430 Tulln, Austria
| | - Netnapis Khewkhom
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Ngamwongwan Road, Lat Yao, Chatuchak, Bangkok 10900, Thailand
| | - Gerlinde Wiesenberger
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 24, 3430 Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology IFA-Tulln, Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| |
Collapse
|
17
|
Comparison of Antifungal Activity of Bacillus Strains against Fusarium graminearum In Vitro and In Planta. PLANTS 2022; 11:plants11151999. [PMID: 35956478 PMCID: PMC9370729 DOI: 10.3390/plants11151999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/30/2022]
Abstract
Fusarium graminearum (Fg) causes Fusarium head blight (FHB) disease in wheat and barley. This pathogen produces mycotoxins including deoxynivalenol (DON), the T-2 and fumorisin B1. Translocation of the mycotoxins in grains causes important losses in yields and contributes to serious health problems in humans and livestock. We tested the Bacillus strains, two commercial, QST713 (Serenade®) and FZB24 (TAEGRO®) and one non-commercial strain EU07 as microbial biological control agents against the F. graminearum strain Fg-K1-4 both in vitro and in planta. The EU07 strain showed better performance in suppressing the growth of Fg-K1-4. Cell-free bacterial cultures displayed significant antagonistic activity on Fg-K1-4. Remarkably, heat and proteinase K treatment of bacterial broths did not reduce the antagonistic activity of Bacillus cultures. DON assays showed that Bacillus strain was not affected by the presence of DON in the media. Leaf and head infection assays using Brachypodium distachyon (Bd-21) indicated that EU07 inhibits Fg-K1-4 growth in vivo and promotes plant growth. Overall, the EU07 strain performed better, indicating that it could be explored for the molecular investigations and protection of cereal crops against FHB disease.
Collapse
|
18
|
Buerstmayr M, Buerstmayr H. The effect of the Rht1 haplotype on Fusarium head blight resistance in relation to type and level of background resistance and in combination with Fhb1 and Qfhs.ifa-5A. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1985-1996. [PMID: 35396946 PMCID: PMC9205817 DOI: 10.1007/s00122-022-04088-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The effect of the Rht1-genes on FHB resistance depends on anther extrusion and level of background resistance. Qfhs.ifa-5A increases resistance and anther extrusion as efficiently as semi-dwarfing alleles decrease it. The semi-dwarfing reduced height alleles Rht-D1b and Rht-B1b have been deployed in modern wheat cultivars throughout the world, but they increase susceptibility to Fusarium head blight (FHB). Here, we investigated the impact of the Rht1 genes on anther retention (AR) in relation to FHB resistance using four different sets of near-isogenic lines (NILs) with contrasting levels and types of background FHB resistance. NILs were evaluated for FHB severity, plant height and AR in three greenhouse and three field trials using artificial spray inoculation. Rht-B1b and Rht-D1b alleles increased AR and FHB susceptibility in all genetic backgrounds. The magnitude of the effects differed between NIL groups. Increased FHB susceptibility largely followed increased AR. Differences in FHB susceptibility between tall and dwarf haplotypes were largest in the NIL group with the highest changes in AR. In the most resistant NIL group, dwarfed lines had only slightly higher AR than tall lines and maintained good resistance, while both tall and dwarf lines had high levels of retained anthers in the most susceptible NIL group. We further investigated the effect of the major Fusarium resistance QTL Fhb1 and Qfhs.ifa-5A in combination with the Rht1 genes. Qfhs.ifa-5A enhanced anther extrusion in tall as well as semi-dwarf haplotypes, whereas Fhb1 did not affect AR. Qfhs.ifa-5A supported FHB resistance more efficiently than Fhb1 in lines that were more responsive to AR, while both Fhb1 and Qfhs.ifa-5A were equally efficient in NILs that had high background resistance and low response to AR.
Collapse
Affiliation(s)
- Maria Buerstmayr
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, 3430, Tulln, Austria.
| | - Hermann Buerstmayr
- Department of Agrobiotechnology, Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences Vienna, Konrad Lorenz Str. 20, 3430, Tulln, Austria
| |
Collapse
|
19
|
Saini DK, Chahal A, Pal N, Srivastava P, Gupta PK. Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:11. [PMID: 37309411 PMCID: PMC10248701 DOI: 10.1007/s11032-022-01282-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
In wheat, meta-QTLs (MQTLs) and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103 QTLs; fusarium head blight (FHB), 184 QTLs; karnal bunt (KB), 66 QTLs; and loose smut (LS), 14 QTLs. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed candidate genes (DECGs). Among the DECGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping and cloning of MDR genes and marker-assisted breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01282-z.
Collapse
Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttrakhand-263145 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| |
Collapse
|
20
|
Song P, Zhang L, Wu L, Hu H, Liu Q, Li D, Hu P, Zhou F, Bu R, Wei Q, Yu Y, Guan Y, Chen E, Su X, Huang Z, Qiao M, Ru Z, Li C. A Ricin B-Like Lectin Protein Physically Interacts with TaPFT and Is Involved in Resistance to Fusarium Head Blight in Wheat. PHYTOPATHOLOGY 2021; 111:2309-2316. [PMID: 34058858 DOI: 10.1094/phyto-11-20-0506-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium head blight (FHB), mainly caused by Fusarium graminearum, has become one of the most serious diseases that damage wheat. The TaPFT (pore-forming toxin-like) and TaHRC (histidine-rich calcium-binding protein) genes at the quantitative trait locus Fhb1 were identified to confer resistance to FHB in the wheat cultivar Sumai 3. In this study, a wheat ricin B-like lectin gene (designated TaRBL) that interacted with TaPFT was isolated by a yeast two-hybrid screen of a wheat cDNA library. A yeast two-hybrid and bimolecular fluorescence complementation study further verified that TaRBL interacted with TaPFT but not with TaHRC. Gene expression studies showed that upon F. graminearum infection, TaRBL expression was upregulated in resistant cultivars but downregulated in susceptible cultivars. Furthermore, knockdown of TaRBL expression by barley stripe mosaic virus-induced gene silencing significantly reduced the resistance of wheat to FHB in both the resistant cultivar Sumai 3 and the susceptible cultivar Jimai 22. Thus, we conclude that TaRBL encodes a ricin B-like lectin protein that interacts with TaPFT and is involved in resistance to FHB in wheat.
Collapse
Affiliation(s)
- Puwen Song
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lufan Zhang
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Liuliu Wu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Haiyan Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qili Liu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Dongxiao Li
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ping Hu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Feng Zhou
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Ruifang Bu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Qichao Wei
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yongang Yu
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yuanyuan Guan
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Eryong Chen
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaojia Su
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhongwen Huang
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Mei Qiao
- College of Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Zhengang Ru
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Chengwei Li
- College of Life Science and Technology, Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| |
Collapse
|
21
|
Hadizadeh Esfahani A, Maß J, Hallab A, Schuldt BM, Nevarez D, Usadel B, Ott MC, Buer B, Schuppert A. Plant PhysioSpace: a robust tool to compare stress response across plant species. PLANT PHYSIOLOGY 2021; 187:1795-1811. [PMID: 34734276 PMCID: PMC8566309 DOI: 10.1093/plphys/kiab325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023]
Abstract
Generalization of transcriptomics results can be achieved by comparison across experiments. This generalization is based on integration of interrelated transcriptomics studies into a compendium. Such a focus on the bigger picture enables both characterizations of the fate of an organism and distinction between generic and specific responses. Numerous methods for analyzing transcriptomics datasets exist. Yet, most of these methods focus on gene-wise dimension reduction to obtain marker genes and gene sets for, for example, pathway analysis. Relying only on isolated biological modules might result in missing important confounders and relevant contexts. We developed a method called Plant PhysioSpace, which enables researchers to compute experimental conditions across species and platforms without a priori reducing the reference information to specific gene sets. Plant PhysioSpace extracts physiologically relevant signatures from a reference dataset (i.e. a collection of public datasets) by integrating and transforming heterogeneous reference gene expression data into a set of physiology-specific patterns. New experimental data can be mapped to these patterns, resulting in similarity scores between the acquired data and the extracted compendium. Because of its robustness against platform bias and noise, Plant PhysioSpace can function as an inter-species or cross-platform similarity measure. We have demonstrated its success in translating stress responses between different species and platforms, including single-cell technologies. We have also implemented two R packages, one software and one data package, and a Shiny web application to facilitate access to our method and precomputed models.
Collapse
Affiliation(s)
- Ali Hadizadeh Esfahani
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52074, Germany
| | - Janina Maß
- IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Asis Hallab
- IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich 52425, Germany
| | | | - David Nevarez
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52074, Germany
| | - Björn Usadel
- IBG-4: Bioinformatics, Forschungszentrum Jülich, Jülich 52425, Germany
| | | | - Benjamin Buer
- Crop Science Division, Bayer AG, Monheim am Rhein 40789, Germany
| | - Andreas Schuppert
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen 52074, Germany
| |
Collapse
|
22
|
Malla KB, Thapa G, Doohan FM. Mitochondrial phosphate transporter and methyltransferase genes contribute to Fusarium head blight Type II disease resistance and grain development in wheat. PLoS One 2021; 16:e0258726. [PMID: 34648604 PMCID: PMC8516198 DOI: 10.1371/journal.pone.0258726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Fusarium head blight (FHB) is an economically important disease of wheat that results in yield loss and grain contaminated with fungal mycotoxins that are harmful to human and animal health. Herein we characterised two wheat genes involved in the FHB response in wheat: a wheat mitochondrial phosphate transporter (TaMPT) and a methyltransferase (TaSAM). Wheat has three sub-genomes (A, B, and D) and gene expression studies demonstrated that TaMPT and TaSAM homoeologs were differentially expressed in response to FHB infection and the mycotoxigenic Fusarium virulence factor deoxynivalenol (DON) in FHB resistant wheat cv. CM82036 and susceptible cv. Remus. Virus-induced gene silencing (VIGS) of either TaMPT or TaSAM enhanced the susceptibility of cv. CM82036 to FHB disease, reducing disease spread (Type II disease resistance). VIGS of TaMPT and TaSAM significantly reduced grain number and grain weight. This indicates TaSAM and TaMPT genes also contribute to grain development in wheat and adds to the increasing body of evidence linking FHB resistance genes to grain development. Hence, Fusarium responsive genes TaSAM and TaMPT warrant further study to determine their potential to enhance both disease resistance and grain development in wheat.
Collapse
Affiliation(s)
- Keshav B. Malla
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
| | - Ganesh Thapa
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
| | - Fiona M. Doohan
- UCD Earth Institute, UCD Institute of Food and Health and UCD School of Biology and Environmental Sciences, UCD Science Centre East, University College Dublin, Belfield, Dublin, Ireland
| |
Collapse
|
23
|
Zhang Y, Li A, Zhu S, Li L, He X, Sun Z, Li T. Basal Rachis Internode Injection: A Novel Inoculation Method to Evaluate Wheat Resistance to Fusarium Head Blight. PHYTOPATHOLOGY 2021; 111:1670-1674. [PMID: 33599531 DOI: 10.1094/phyto-11-20-0488-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium head blight (FHB) is one of the most destructive fungal diseases of wheat. However, difficulties in reliably phenotyping of this disease have greatly hindered the understanding of the mechanism of wheat-pathogen interaction and genetic improvement of FHB resistance. Here we report a novel inoculation method called basal rachis internode injection (BRII), in which inoculum is injected into the basal internode of a rachis instead of a floret, as is done in single floret inoculation (SFI). One of the prominent advantages of BRII over SFI and other traditional methods lies in its independence from the moisture-maintaining system that is necessary for all existing methods, making it insensitive to environmental humidity and hence cost-effective. Another unique feature of BRII is that this method produces nearly clear-cut reaction types, by which FHB resistance can be treated as a qualitative trait because generally no FHB symptoms appear on the spikelets of resistant genotypes. In addition, BRII outperformed SFI with a higher infection rate and better goodness of fit with known FHB resistance and quantitative trait locus components in a panel of 15 genotypes, as well as two populations of recombinant inbred lines segregating in Fhb1. Note that BRII and SFI methods are not mutually exclusive but rather complementary because each method has its own advantages in differentiating FHB resistance between genotypes. Combining these two methods would significantly improve the reliability and consistency of FHB phenotyping in wheat.
Collapse
Affiliation(s)
- Yuhui Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in Jiangsu/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Aiai Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in Jiangsu/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing 100176, China
| | - Suqin Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in Jiangsu/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Lei Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in Jiangsu/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico DF, Mexico
| | - Zhengxi Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in Jiangsu/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Tao Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Collaborative Innovation of Modern Crops and Food Crops in Jiangsu/Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
24
|
Liu Y, Han N, Wang S, Chen C, Lu J, Riaz MW, Si H, Sun G, Ma C. Genome-Wide Identification of Triticum aestivum Xylanase Inhibitor Gene Family and Inhibitory Effects of XI-2 Subfamily Proteins on Fusarium graminearum GH11 Xylanase. FRONTIERS IN PLANT SCIENCE 2021; 12:665501. [PMID: 34381472 PMCID: PMC8350787 DOI: 10.3389/fpls.2021.665501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/21/2021] [Indexed: 06/13/2023]
Abstract
Triticum aestivum xylanase inhibitor (TaXI) gene plays an important role in plant defense. Recently, TaXI-III inhibitor has been shown to play a dual role in wheat resistance to Fusarium graminearum infection. Thus, identifying the members of the TaXI gene family and clarifying its role in wheat resistance to stresses are essential for wheat resistance breeding. However, to date, no comprehensive research on TaXIs in wheat (Triticum aestivum L.) has been conducted. In this study, a total of 277 TaXI genes, including six genes that we cloned, were identified from the recently released wheat genome database (IWGSC RefSeq v1.1), which were unevenly located on 21 chromosomes of wheat. Phylogenetic analysis divided these genes into six subfamilies, all the six genes we cloned belonged to XI-2 subfamily. The exon/intron structure of most TaXI genes and the conserved motifs of proteins in the same subfamily are similar. The TaXI gene family contains 92 homologous gene pairs or clusters, 63 and 193 genes were identified as tandem replication and segmentally duplicated genes, respectively. Analysis of the cis-acting elements in the promoter of TaXI genes showed that they are involved in wheat growth, hormone-mediated signal transduction, and response to biotic and abiotic stresses. RNA-seq data analysis revealed that TaXI genes exhibited expression preference or specificity in different organs and developmental stages, as well as in diverse stress responses, which can be regulated or induced by a variety of plant hormones and stresses. In addition, the qRT-PCR data and heterologous expression analysis of six TaXI genes revealed that the genes of XI-2 subfamily have double inhibitory effect on GH11 xylanase of F. graminearum, suggesting their potential important roles in wheat resistance to F. graminearum infection. The outcomes of this study not only enhance our understanding of the TaXI gene family in wheat, but also help us to screen more candidate genes for further exploring resistance mechanism in wheat.
Collapse
Affiliation(s)
- Yang Liu
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Nannan Han
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Sheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Can Chen
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Muhammad Waheed Riaz
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Genlou Sun
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Biology Department, Saint Mary’s University, Halifax, NS, Canada
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
- National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei, China
- Anhui Key Laboratory of Crop Biology, Hefei, China
| |
Collapse
|
25
|
Buerstmayr M, Wagner C, Nosenko T, Omony J, Steiner B, Nussbaumer T, Mayer KFX, Buerstmayr H. Fusarium head blight resistance in European winter wheat: insights from genome-wide transcriptome analysis. BMC Genomics 2021; 22:470. [PMID: 34167474 PMCID: PMC8228913 DOI: 10.1186/s12864-021-07800-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Resistance to FHB is quantitatively controlled by the combined effects of many small to medium effect QTL. Flowering traits, especially the extent of extruded anthers, are strongly associated with FHB resistance. Results To characterize the genetic basis of FHB resistance, we generated and analyzed phenotypic and gene expression data on the response to Fusarium graminearum (Fg) infection in 96 European winter wheat genotypes, including several lines containing introgressions from the highly resistant Asian cultivar Sumai3. The 96 lines represented a broad range in FHB resistance and were assigned to sub-groups based on their phenotypic FHB severity score. Comparative analyses were conducted to connect sub-group-specific expression profiles in response to Fg infection with FHB resistance level. Collectively, over 12,300 wheat genes were Fusarium responsive. The core set of genes induced in response to Fg was common across different resistance groups, indicating that the activation of basal defense response mechanisms was largely independent of the resistance level of the wheat line. Fg-induced genes tended to have higher expression levels in more susceptible genotypes. Compared to the more susceptible non-Sumai3 lines, the Sumai3-derivatives demonstrated higher constitutive expression of genes associated with cell wall and plant-type secondary cell wall biogenesis and higher constitutive and Fg-induced expression of genes involved in terpene metabolism. Gene expression analysis of the FHB QTL Qfhs.ifa-5A identified a constitutively expressed gene encoding a stress response NST1-like protein (TraesCS5A01G211300LC) as a candidate gene for FHB resistance. NST1 genes are key regulators of secondary cell wall biosynthesis in anther endothecium cells. Whether the stress response NST1-like gene affects anther extrusion, thereby affecting FHB resistance, needs further investigation. Conclusion Induced and preexisting cell wall components and terpene metabolites contribute to resistance and limit fungal colonization early on. In contrast, excessive gene expression directs plant defense response towards programmed cell death which favors necrotrophic growth of the Fg pathogen and could thus lead to increased fungal colonization. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07800-1.
Collapse
Affiliation(s)
- Maria Buerstmayr
- University of Natural Resources and Life Sciences, Austria, Department of Agrobiotechnology - IFA Tulln, Institute of Biotechnology in Plant Production, Konrad Lorenz Str 20, Tulln, Austria.
| | - Christian Wagner
- University of Natural Resources and Life Sciences, Austria, Department of Agrobiotechnology - IFA Tulln, Institute of Biotechnology in Plant Production, Konrad Lorenz Str 20, Tulln, Austria
| | - Tetyana Nosenko
- Helmholtz Zentrum München, Germany, PGSB Plant Genome and Systems Biology, German Research Center for Environmental Health, Neuherberg, Germany.,Helmholtz Zentrum München, Germany, Research Unit Environmental Simulation (EUS) at the Institute of Biochemical Plant Pathology (BIOP), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Jimmy Omony
- Helmholtz Zentrum München, Germany, PGSB Plant Genome and Systems Biology, German Research Center for Environmental Health, Neuherberg, Germany.,Helmholtz Zentrum München, Germany, Institut für Asthma- und Allergieprävention (IAP), Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Munich, Germany
| | - Barbara Steiner
- University of Natural Resources and Life Sciences, Austria, Department of Agrobiotechnology - IFA Tulln, Institute of Biotechnology in Plant Production, Konrad Lorenz Str 20, Tulln, Austria
| | - Thomas Nussbaumer
- Helmholtz Zentrum München, Germany, Institute of Network Biology (INET), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,Helmholtz Zentrum München, Germany, Institute of Environmental Medicine UNIKA-T, Technical University and Helmholtz Zentrum München, Augsburg, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Germany, PGSB Plant Genome and Systems Biology, German Research Center for Environmental Health, Neuherberg, Germany
| | - Hermann Buerstmayr
- University of Natural Resources and Life Sciences, Austria, Department of Agrobiotechnology - IFA Tulln, Institute of Biotechnology in Plant Production, Konrad Lorenz Str 20, Tulln, Austria
| |
Collapse
|
26
|
Wang R, Hua C, Hu Y, Li L, Sun Z, Li T. Two Different Inoculation Methods Unveiled the Relative Independence of DON Accumulation in Wheat Kernels from Disease Severity on Spike after Infection by Fusarium Head Blight. Toxins (Basel) 2021; 13:toxins13050353. [PMID: 34069221 PMCID: PMC8156083 DOI: 10.3390/toxins13050353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/08/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
Fusarium head blight (FHB) causes wheat yield loss and mycotoxin (deoxynivalenol, DON) accumulation in wheat kernel. Developing wheat cultivars with overall resistance to both FHB spread within a spike and DON accumulation in kernels is crucial for ensuring food security and food safety. Here, two relatively novel inoculation methods, bilateral floret inoculation (BFI) and basal rachis internode injection (BRII), were simultaneously employed to evaluate disease severity and DON content in kernels in a segregating population of recombinant inbred lines (RILs) developed from Ning 7840 (carrying Fhb1) and Clark (without Fhb1). Under both inoculation methods, four contrasting combinations of disease severity and DON content were identified: high severity/high DON (HSHD), high severity/low DON (HSLD), low severity/high DON (LSHD) and low severity/low DON (LSLD). Unexpectedly, the BRII method clearly indicated that disease severity was not necessarily relevant to DON concentration. The effects of Fhb1 on disease severity, and on DON concentrations, agreed very well across the two methods. Several lines carrying Fhb1 showed extremely higher severity and (or) DON content under both inoculation methods. The “Mahalanobis distance” (MD) method was used to rate overall resistance of a line by inclusion of both disease severity and DON content over both methods to select LSLD lines.
Collapse
Affiliation(s)
| | | | | | | | | | - Tao Li
- Correspondence: ; Tel.: +86-514-8797-7806
| |
Collapse
|
27
|
Perochon A, Benbow HR, Ślęczka-Brady K, Malla KB, Doohan FM. Analysis of the chromosomal clustering of Fusarium-responsive wheat genes uncovers new players in the defence against head blight disease. Sci Rep 2021; 11:7446. [PMID: 33811222 PMCID: PMC8018971 DOI: 10.1038/s41598-021-86362-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
There is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium-responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non-metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin-like proteins. 20 of the FRGCs encode nonhomologous, non-metabolic genes (including defence-related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium-responsive genes, five of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specific traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease.
Collapse
Affiliation(s)
- Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Harriet R Benbow
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Katarzyna Ślęczka-Brady
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Keshav B Malla
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fiona M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin 4, Ireland.
| |
Collapse
|
28
|
Xie Y, Ravet K, Pearce S. Extensive structural variation in the Bowman-Birk inhibitor family in common wheat (Triticum aestivum L.). BMC Genomics 2021; 22:218. [PMID: 33765923 PMCID: PMC7995804 DOI: 10.1186/s12864-021-07475-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bowman-Birk inhibitors (BBI) are a family of serine-type protease inhibitors that modulate endogenous plant proteolytic activities during different phases of development. They also inhibit exogenous proteases as a component of plant defense mechanisms, and their overexpression can confer resistance to phytophagous herbivores and multiple fungal and bacterial pathogens. Dicot BBIs are multifunctional, with a "double-headed" structure containing two separate inhibitory loops that can bind and inhibit trypsin and chymotrypsin proteases simultaneously. By contrast, monocot BBIs have a non-functional chymotrypsin inhibitory loop, although they have undergone internal duplication events giving rise to proteins with multiple BBI domains. RESULTS We used a Hidden Markov Model (HMM) profile-based search to identify 57 BBI genes in the common wheat (Triticum aestivum L.) genome. The BBI genes are unevenly distributed, with large gene clusters in the telomeric regions of homoeologous group 1 and 3 chromosomes that likely arose through a series of tandem gene duplication events. The genomes of wheat progenitors also contain contiguous clusters of BBI genes, suggesting this family underwent expansion before the domestication of common wheat. However, the BBI gene family varied in size among different cultivars, showing this family remains dynamic. Because of these expansions, the BBI gene family is larger in wheat than other monocots such as maize, rice and Brachypodium. We found BBI proteins in common wheat with intragenic homologous duplications of cysteine-rich functional domains, including one protein with four functional BBI domains. This diversification may expand the spectrum of target substrates. Expression profiling suggests that some wheat BBI proteins may be involved in regulating endogenous proteases during grain development, while others were induced in response to biotic and abiotic stresses, suggesting a role in plant defense. CONCLUSIONS Genome-wide characterization reveals that the BBI gene family in wheat is subject to a high rate of homologous tandem duplication and deletion events, giving rise to a diverse set of encoded proteins. This information will facilitate the functional characterization of individual wheat BBI genes to determine their role in wheat development and stress responses, and their potential application in breeding.
Collapse
Affiliation(s)
- Yucong Xie
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Karl Ravet
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| |
Collapse
|
29
|
Shimizu KK, Copetti D, Okada M, Wicker T, Tameshige T, Hatakeyama M, Shimizu-Inatsugi R, Aquino C, Nishimura K, Kobayashi F, Murata K, Kuo T, Delorean E, Poland J, Haberer G, Spannagl M, Mayer KFX, Gutierrez-Gonzalez J, Muehlbauer GJ, Monat C, Himmelbach A, Padmarasu S, Mascher M, Walkowiak S, Nakazaki T, Ban T, Kawaura K, Tsuji H, Pozniak C, Stein N, Sese J, Nasuda S, Handa H. De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes. PLANT & CELL PHYSIOLOGY 2021; 62:8-27. [PMID: 33244607 PMCID: PMC7991897 DOI: 10.1093/pcp/pcaa152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 05/08/2023]
Abstract
Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.
Collapse
Affiliation(s)
- Kentaro K Shimizu
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Environmental Systems Science, Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Moeko Okada
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Department of Biology, Faculty of Science, Niigata University, Niigata, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
| | - Fuminori Kobayashi
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba, Japan
| | - Kazuki Murata
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tony Kuo
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- University of Guelph, Centre for Biodiversity Genomics, Guelph, ON, Canada
| | - Emily Delorean
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Georg Haberer
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Weihenstephan, Germany
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
| | - Cecile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sean Walkowiak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Canadian Grain Commission, Grain Research Laboratory, Winnipeg, MB, Canada
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Department of Crop Science, Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Humanome Lab, Inc, Tokyo, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hirokazu Handa
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba, Japan
- Laboratoty of Plant Breeding, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| |
Collapse
|
30
|
Soni N, Altartouri B, Hegde N, Duggavathi R, Nazarian-Firouzabadi F, Kushalappa AC. TaNAC032 transcription factor regulates lignin-biosynthetic genes to combat Fusarium head blight in wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110820. [PMID: 33568310 DOI: 10.1016/j.plantsci.2021.110820] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Fusarium head blight (FHB) is a destructive disease affecting cereal crops globally due to mycotoxin contamination of grains that reduce yield and quality. Among hundreds of QTLs identified for resistance, the QTL-Fhb1 is of significant interest even today, for its major contribution to FHB resistance. Previously, QTL-Fhb1 dissection based on a combined metabolo-genomics approach, identified a few potential resistance genes, including a NAC like transcription factor for FHB resistance. Sequencing and phylogenetic analysis confirmed NAC to be the wheat TaNAC032. Also, the quantitative RT-PCR studies revealed a greater induced expression of TaNAC032 in resistant NIL in comparison to susceptible NIL upon Fusarium graminearum (Fg) infection. The virus-induced gene silencing (VIGS) based functional validation of TaNAC032 in resistant NIL confirmed increased disease severity and fungal biomass. Metabolic profiling revealed low abundances of resistance-related (RR) metabolites in TaNAC032 silenced NIL-R compared to non-silenced. Silenced plants showed decreased transcript abundances of RR metabolite biosynthetic genes associated with a reduction in total lignin content in rachis, confirming the regulatory role of TaNAC032 in wheat in response to Fg infection. If TaNA032 is mutated in an FHB susceptible cultivar, it can be edited to enhance FHB resistance.
Collapse
Affiliation(s)
- Nancy Soni
- Plant Science Department, McGill University, Quebec, Canada
| | - Bara Altartouri
- Department of Biological Sciences, Université de Montréal, Quebec, Canada
| | - Niranjan Hegde
- Plant Science Department, McGill University, Quebec, Canada
| | - Raj Duggavathi
- Animal Science Department, McGill University, Quebec, Canada
| | | | | |
Collapse
|
31
|
Zakieh M, Gaikpa DS, Leiva Sandoval F, Alamrani M, Henriksson T, Odilbekov F, Chawade A. Characterizing Winter Wheat Germplasm for Fusarium Head Blight Resistance Under Accelerated Growth Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:705006. [PMID: 34512690 PMCID: PMC8425451 DOI: 10.3389/fpls.2021.705006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/02/2021] [Indexed: 05/16/2023]
Abstract
Fusarium head blight (FHB) is one of the economically important diseases of wheat as it causes severe yield loss and reduces grain quality. In winter wheat, due to its vernalization requirement, it takes an exceptionally long time for plants to reach the heading stage, thereby prolonging the time it takes for characterizing germplasm for FHB resistance. Therefore, in this work, we developed a protocol to evaluate winter wheat germplasm for FHB resistance under accelerated growth conditions. The protocol reduces the time required for plants to begin heading while avoiding any visible symptoms of stress on plants. The protocol was tested on 432 genotypes obtained from a breeding program and a genebank. The mean area under disease progress curve for FHB was 225.13 in the breeding set and 195.53 in the genebank set, indicating that the germplasm from the genebank set had higher resistance to FHB. In total, 10 quantitative trait loci (QTL) for FHB severity were identified by association mapping. Of these, nine QTL were identified in the combined set comprising both genebank and breeding sets, while two QTL each were identified in the breeding set and genebank set, respectively, when analyzed separately. Some QTLs overlapped between the three datasets. The results reveal that the protocol for FHB evaluation integrating accelerated growth conditions is an efficient approach for FHB resistance breeding in winter wheat and can be even applied to spring wheat after minor modifications.
Collapse
Affiliation(s)
- Mustafa Zakieh
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - David S. Gaikpa
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | | - Marwan Alamrani
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | | - Firuz Odilbekov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
- Lantmännen Lantbruk, Svalöv, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
- *Correspondence: Aakash Chawade,
| |
Collapse
|
32
|
Sallam AH, Manan F, Bajgain P, Martin M, Szinyei T, Conley E, Brown-Guedira G, Muehlbauer GJ, Anderson JA, Steffenson BJ. Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat. THE PLANT GENOME 2020; 13:e20051. [PMID: 33217209 DOI: 10.1002/tpg2.20051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome-wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA-ARS wheat (Triticum aestivum L.) core collection by developing the Spring Wheat Multiparent Introgression Population (SWMIP). To develop this population, twenty-five core parents were crossed and backcrossed to the Minnesota spring wheat cultivar RB07. The NAM population and 26 founder parents were genotyped using genotyping-by-sequencing and phenotyped for heading date, height, test weight, and grain protein content. After quality control, 20,312 markers with physical map positions were generated for 2,038 recombinant inbred lines (RILs). The number of RILs in each family varied between 58 and 96. Three GWAS models were utilized for quantitative trait loci (QTL) detection and accounted for known family stratification, genetic kinship, and both covariates. GWAS was performed on the whole population and also by bootstrap sampling of an equal number of RILs from each family. Greater power of QTL detection was achieved by treating families equally through bootstrapping. In total 16, 15, 12, and 13 marker-trait associations (MTAs) were identified for heading date, height, test weight, and grain protein content, respectively. Some of these MTAs were coincident with major genes known to control the traits, but others were novel and contributed by the wheat core parents. The SWMIP will be a valuable source of genetic variation for spring wheat breeding.
Collapse
Affiliation(s)
- Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Fazal Manan
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Matthew Martin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tamas Szinyei
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Emily Conley
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| |
Collapse
|
33
|
Identification of novel QTLs for late leaf spot resistance and validation of a major rust QTL in peanut ( Arachis hypogaea L.). 3 Biotech 2020; 10:458. [PMID: 33088655 DOI: 10.1007/s13205-020-02446-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022] Open
Abstract
Co-occurrence of two devastating foliar-fungal diseases of peanut, viz., late leaf spot (LLS), and rust may cause heavy yield loss besides adversely affecting the quality of kernel and fodder. This study reports the mapping of seven novel stress-related candidate EST-SSRs in a region having major QTLs for LLS and rust diseases using an F2 mapping population (GJG17 × GPBD4) consisting of 328 individuals. The parental polymorphism using 1311 SSRs revealed 84 SSRs (6.4%) as polymorphic and of these 70 SSRs could be mapped on 14 linkage groups (LG). QTL analysis has identified a common QTL (LLSQTL1/RustQTL) for LLS and rust diseases in the map interval of 1.41 cM on A03 chromosome, explaining 47.45% and 70.52% phenotypic variations, respectively. Another major QTL for LLS (LLSQTL1), explaining a 29.06% phenotypic variation was also found on LG_A03. A major rust QTL has been validated which was found harboring R-gene and resistance-related genes having a role in inducing hypersensitive response (HR). Further, 23 linked SSRs including seven novel EST-SSRs were also validated in 177 diverse Indian groundnut genotypes. Twelve genotypes resistant to both LLS and rust were found carrying the common (rust and LLS) QTL region, LLS QTL region, and surrounding regions. These identified and validated candidate EST-SSR markers would be of great use for the peanut breeding groups working for the improvement of foliar-fungal disease resistance.
Collapse
|
34
|
Thambugala D, Brûlé-Babel AL, Blackwell BA, Fedak G, Foster AJ, MacEachern D, Gilbert J, Henriquez MA, Martin RA, McCallum BD, Spaner D, Iqbal M, Pozniak CJ, N'Diaye A, McCartney CA. Genetic analyses of native Fusarium head blight resistance in two spring wheat populations identifies QTL near the B1, Ppd-D1, Rht-1, Vrn-1, Fhb1, Fhb2, and Fhb5 loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2775-2796. [PMID: 32556394 DOI: 10.1007/s00122-020-03631-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
QTL analyses of two bi-parental mapping populations with AC Barrie as a parent revealed numerous FHB-resistance QTL unique to each population and uncovered novel variation near Fhb1. Fusarium head blight (FHB) is a destructive disease of wheat worldwide, leading to severe yield and quality losses. The genetic basis of native FHB resistance was examined in two populations: a recombinant inbred line population from the cross Cutler/AC Barrie and a doubled haploid (DH) population from the cross AC Barrie/Reeder. Numerous QTL were detected among the two mapping populations with many being cross-specific. Photoperiod insensitivity at Ppd-D1 and dwarfing at Rht-B1 and Rht-D1 was associated with increased FHB susceptibility. Anthesis date QTL at or near the Vrn-A1 and Vrn-B1 loci co-located with major FHB-resistance QTL in the AC Barrie/Reeder population. The loci were epistatic for both traits, such that DH lines with both late alleles were considerably later to anthesis and had reduced FHB symptoms (i.e., responsible for the epistatic interaction). Interestingly, AC Barrie contributed FHB resistance near the Fhb1 locus in the Cutler population and susceptibility in the Reeder population. Analyses of the Fhb1 candidate genes PFT and TaHRC confirmed that AC Barrie, Cutler, and Reeder do not carry the Sumai-3 Fhb1 gene. Resistance QTL were also detected at the expected locations of Fhb2 and Fhb5. The native FHB-resistance QTL detected near Fhb1, Fhb2, and Fhb5 do not appear to be as effective as Fhb1, Fhb2, and Fhb5 from Sumai-3. The presence of awns segregated at the B1 awn inhibitor locus in both populations, but was only associated with FHB resistance in the Cutler/AC Barrie population suggesting linkage caused the association rather than pleiotropy.
Collapse
Affiliation(s)
- Dinushika Thambugala
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Anita L Brûlé-Babel
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Barbara A Blackwell
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Adam J Foster
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PEI, C1A 4N6, Canada
| | - Dan MacEachern
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PEI, C1A 4N6, Canada
| | - Jeannie Gilbert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Richard A Martin
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PEI, C1A 4N6, Canada
| | - Brent D McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Dean Spaner
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Iqbal
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
| |
Collapse
|
35
|
Badouin H, Velt A, Gindraud F, Flutre T, Dumas V, Vautrin S, Marande W, Corbi J, Sallet E, Ganofsky J, Santoni S, Guyot D, Ricciardelli E, Jepsen K, Käfer J, Berges H, Duchêne E, Picard F, Hugueney P, Tavares R, Bacilieri R, Rustenholz C, Marais GAB. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biol 2020; 21:223. [PMID: 32892750 PMCID: PMC7487632 DOI: 10.1186/s13059-020-02131-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.
Collapse
Affiliation(s)
- Hélène Badouin
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
| | - Amandine Velt
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - François Gindraud
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Timothée Flutre
- GQE-Le Moulon, INRAE, Univ. Paris-Sud, CNRS, AgroParisTech, Univ. Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Vincent Dumas
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Sonia Vautrin
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Jonathan Corbi
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Jérémy Ganofsky
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Santoni
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kristen Jepsen
- IGM Genomics Center, University of California, San Diego, La Jolla, CA, USA
| | - Jos Käfer
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Hélène Berges
- INRAE, Centre National de Ressources Génomiques Végétales, F-31326, Castanet-Tolosan, France
| | - Eric Duchêne
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Franck Picard
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Philippe Hugueney
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France
| | - Raquel Tavares
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Roberto Bacilieri
- INRAE, UMR AGAP, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Camille Rustenholz
- Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000, Colmar, France.
| | - Gabriel A B Marais
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France.
| |
Collapse
|
36
|
Carmack WJ, Clark A, Dong Y, Brown-Guedira G, Van Sanford D. Optical Sorter-Based Selection Effectively Identifies Soft Red Winter Wheat Breeding Lines With Fhb1 and Enhances FHB Resistance in Lines With and Without Fhb1. FRONTIERS IN PLANT SCIENCE 2020; 11:1318. [PMID: 32983207 PMCID: PMC7479218 DOI: 10.3389/fpls.2020.01318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Previous results from our lab have shown that using an optical sorter to identify Fusarium head blight (FHB) resistant breeding lines was effective at reducing the toxin deoxynivalenol (DON) and FHB-associated kernel damage. In this paper we quantified the proportion of desirable genotypes at FHB resistance QTL in lines from three selection cycles of optical sorting. Breeding lines were genotyped at loci on chromosomes 3BS, 2DL, and 5A using the following DNA markers: TaHRC, CFD233, and GWM304. TaHRC is a KASP marker for Fhb1, a major FHB resistance QTL on chromosome 3BS. CFD233 is an SSR marker for Qfhs.nau-2DL on chromosome 2DL. GWM304 is an SSR marker for Qfhs.ifa-5A on chromosome 5A. Sorter selection was effective at identifying lines that had the resistant genotype at TaHRC; in other words, the sorter was able to identify lines with resistance alleles at Fhb1. The sorter was less effective at selecting for the resistant genotype at CFD233 and GWM304. However, the proportion of lines with resistant genotypes at GWM304 did increase with additional sorter selection, just not to the degree that was observed for the Fhb1-associated marker. The proportion of lines with resistant alleles at CFD233 did not show a consistent trend. In addition to increasing the proportion of lines with Fhb1 and Qfhs.ifa-5A each selection cycle, optical sorter-based mass selection enhanced FHB resistance in different marker genotype combinations evaluated in this study. For example, there were net reductions in DON and kernel damage after two cycles of sorter selection in 15X110601S07002, a line with Fhb1, with Qfhs.nau-2DL, and with Qfhs.ifa-5A; final C3 DON levels were 63% of the resistant check (KY02C-3005-25). Kernel damage was also reduced in 15X110601A08221 a line without Fhb1, without Qfhs.nau-2DL, and without Qfhs.ifa-5A. Our findings suggest the increased resistance observed in different marker genotype combinations was conferred by QTL other than Fhb1, QFhs.nau-2DL, and Qfhs.ifa-5, and validate our previous results that the optical sorter is effective at selecting FHB-resistant breeding material.
Collapse
Affiliation(s)
- W. Jesse Carmack
- Department of Plant and Soil Science, University of Kentucky, Lexington, KY, United States
| | - Anthony Clark
- Department of Plant and Soil Science, University of Kentucky, Lexington, KY, United States
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Gina Brown-Guedira
- Plant Science Research Unit, USDA-Agricultural Research Service, Raleigh, NC, United States
| | - David Van Sanford
- Department of Plant and Soil Science, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
37
|
Zhao L, Abdelsalam NR, Xu Y, Chen MS, Feng Y, Kong L, Bai G. Identification of two novel Hessian fly resistance genes H35 and H36 in a hard winter wheat line SD06165. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2343-2353. [PMID: 32436021 DOI: 10.1007/s00122-020-03602-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/01/2020] [Indexed: 05/19/2023]
Abstract
Two new Hessian fly resistance QTLs (H35 and H36) and tightly linked SNP markers were identified in a US hard winter wheat SD06165. Hessian fly (HF), Mayetiola destructor (Say), is one of the most destructive pests in wheat (Triticum aestivum L.) worldwide. Growing resistant cultivars is the most effective approach to minimize Hessian fly damage. To identify new quantitative trait loci (QTLs) for HF resistance, a recombinant inbred line population was developed by crossing HF resistant wheat line SD06165 to a susceptible line OK05312. The population was genotyped with 1709 single-nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing and phenotyped for HF resistance in greenhouses. Two novel QTLs for HF resistance were identified from SD06165. The major QTL, designated as H35, was closely linked to SNP marker SDOKSNP7679 on chromosome 3BS that explained 23.8% and 36.0% of the phenotypic variations; the minor QTL, designated as H36, was flanked by SNP markers SDOKSNP1618 and SDOKSNP8089 on chromosome 7AS and explained 8.5% and 13.1% of the phenotypic variation in the two experiments. Significant interaction was detected between the two QTLs. Seventeen SNPs that tightly link to H35 and eight SNPs that tightly link to H36 were converted to kompetitive allele specific polymerase chain reaction markers for selecting these QTLs in breeding programs.
Collapse
Affiliation(s)
- Lanfei Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agriculture University, Taian, 271018, Shandong, China
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Nader Ragab Abdelsalam
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
- Agricultural Botany Department, Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Yunfeng Xu
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Ming-Shun Chen
- Hard Winter Wheat Genetics Research Unit, USDA, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Yi Feng
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
- College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agriculture University, Taian, 271018, Shandong, China
| | - Guihua Bai
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA.
- Hard Winter Wheat Genetics Research Unit, USDA, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA.
| |
Collapse
|
38
|
Gong X, He X, Zhang Y, Li L, Sun Z, Bai G, Singh PK, Li T. Development of an Evaluation System for Fusarium Resistance in Wheat Grains and Its Application in Assessment of the Corresponding Effects of Fhb1. PLANT DISEASE 2020; 104:2210-2216. [PMID: 32511047 DOI: 10.1094/pdis-12-19-2584-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Fusarium head blight (FHB) caused by Fusarium species is a globally important wheat disease. Host resistance to FHB is composed of multiple mechanisms, including resistance to initial infection (type I), disease spread (type II), toxin accumulation (type III), kernel infection (type IV), and yield loss (type V), of which the last three have been less studied. Traditionally, the Fusarium-damaged kernel rate (FDK; percentage of Fusarium-infected grains) from point- or spray-inoculated experiments was used as the parameter for type IV resistance, which may be problematic because of the influence of type II resistance. Here we propose a new definition for type IV resistance: that is, the resistance against Fusarium infection expressed in wheat grains that have the same chance in contact with the pathogen, under favorable temperature and humidity for infection. Fhb1 confers strong type II resistance, leading to significantly reduced FHB severity and FDK. To investigate the role of Fhb1 in type IV resistance, a pair of near-isogenic lines, R22W (Fhb1 carrier, resistant in terms of type II resistance) and S22V (non-Fhb1, susceptible), along with eight wheat genotypes differing at Fhb1 were inoculated at different grain development stages with Fusarium macrospores both in vivo and in vitro. The in vivo experiments with all florets inoculated demonstrated a significant reduction in thousand kernel weight (TKW) in inoculated grains, regardless of their Fhb1 status and developmental stages. Surprisingly, R22W showed more TKW reduction than S22V, which was supported by the scanning electron microscopy observation that confirmed the more severe degradation of starch granules in R22W grains. The in vitro experiments demonstrated that grains from both R22W and S22V promoted fungal colonization, but no significant difference was found between the two lines. In summary, our results indicated that the proposed type IV evaluation system is effective in determining different grain resistance levels, providing novel tools for FHB resistance breeding. The finding that Fhb1 is not associated with type IV resistance enriches our understanding of this gene.
Collapse
Affiliation(s)
- Xuan Gong
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico DF, Mexico
| | - Yuhui Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Lei Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Zhengxi Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Guihua Bai
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, U.S.A
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico DF, Mexico
| | - Tao Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
39
|
Ghimire B, Sapkota S, Bahri BA, Martinez-Espinoza AD, Buck JW, Mergoum M. Fusarium Head Blight and Rust Diseases in Soft Red Winter Wheat in the Southeast United States: State of the Art, Challenges and Future Perspective for Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:1080. [PMID: 32765563 PMCID: PMC7378807 DOI: 10.3389/fpls.2020.01080] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/30/2020] [Indexed: 05/21/2023]
Abstract
Among the biotic constraints to wheat (Triticum aestivum L.) production, fusarium head blight (FHB), caused by Fusarium graminearum, leaf rust (LR), caused by Puccinia triticina, and stripe rust (SR) caused by Puccinia striiformis are problematic fungal diseases worldwide. Each can significantly reduce grain yield while FHB causes additional food and feed safety concerns due to mycotoxin contamination of grain. Genetic resistance is the most effective and sustainable approach for managing wheat diseases. In the past 20 years, over 500 quantitative trait loci (QTLs) conferring small to moderate effects for the different FHB resistance types have been reported in wheat. Similarly, 79 Lr-genes and more than 200 QTLs and 82 Yr-genes and 140 QTLs have been reported for seedling and adult plant LR and SR resistance, respectively. Most QTLs conferring rust resistance are race-specific generally conforming to a classical gene-for-gene interaction while resistance to FHB exhibits complex polygenic inheritance with several genetic loci contributing to one resistance type. Identification and deployment of additional genes/QTLs associated with FHB and rust resistance can expedite wheat breeding through marker-assisted and/or genomic selection to combine small-effect QTL in the gene pool. LR disease has been present in the southeast United States for decades while SR and FHB have become increasingly problematic in the past 20 years, with FHB arguably due to increased corn acreage in the region. Currently, QTLs on chromosome 1B from Jamestown, 1A, 1B, 2A, 2B, 2D, 4A, 5A, and 6A from W14, Ning7840, Ernie, Bess, Massey, NC-Neuse, and Truman, and 3B (Fhb1) from Sumai 3 for FHB resistance, Lr9, Lr10, Lr18, Lr24, Lr37, LrA2K, and Lr2K38 genes for LR resistance, and Yr17 and YrR61 for SR resistance have been extensively deployed in southeast wheat breeding programs. This review aims to disclose the current status of FHB, LR, and SR diseases, summarize the genetics of resistance and breeding efforts for the deployment of FHB and rust resistance QTL on soft red winter wheat cultivars, and present breeding strategies to achieve sustainable management of these diseases in the southeast US.
Collapse
Affiliation(s)
- Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Suraj Sapkota
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Bochra A. Bahri
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | | | - James W. Buck
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, United States
| |
Collapse
|
40
|
Isidro-Sánchez J, D'Arcy Cusack K, Verheecke-Vaessen C, Kahla A, Bekele W, Doohan F, Magan N, Medina A. Genome-wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.). THE PLANT GENOME 2020; 13:e20023. [PMID: 33016604 DOI: 10.1002/tpg2.20023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
Fusarium langsethiae is a symptomless pathogen of oat panicles that produces T-2 and HT-2 mycotoxins, two of the most potent trichothecenes produced by Fusarium fungi in cereals. In the last few years, the levels of these mycotoxin in oat grain has increased and the European commission have already recommended a maximum level for of 1000 μg kg-1 for unprocessed oat for human consumption. The optimal and most sustainable way of combating infection and mycotoxin contamination is by releasing resistant oat varieties. Here the objective was to determine if we could identify any genomic loci associated with either the accumulation of F. langsethiae DNA or mycotoxins in the grain. In each of two years, field trials were conducted wherein 190 spring oat varieties were inoculated with a mixture of three isolate of the pathogen. Mycotoxins were quantified using liquid chromatography-tandem mass spectrometry. Varieties were genotyped using 16,863 genotyping by sequencing markers. Genome-wide association studies associated 5 SNPs in the linkage group Mr06 with T-2 + HT-2 mycotoxin accumulation. Markers were highly correlated, and a single QTL was identified. The marker avgbs_6K_95238.1 mapped within genes showing similarity to lipase, lipase-like or lipase precursor mRNA sequences and zinc-finger proteins. These regions have previously been shown to confer a significant increase in resistance to Fusarium species.
Collapse
Affiliation(s)
- Julio Isidro-Sánchez
- UCD Agriculture & Food Science, College of Health and Agriculture Science, University College Dublin, Belfield, Dublin, 4, Ireland
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Kane D'Arcy Cusack
- UCD Agriculture & Food Science, College of Health and Agriculture Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Carol Verheecke-Vaessen
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Amal Kahla
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Wubishet Bekele
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Fiona Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Naresh Magan
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Angel Medina
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| |
Collapse
|
41
|
Paudel B, Zhuang Y, Galla A, Dahal S, Qiu Y, Ma A, Raihan T, Yen Y. WFhb1-1 plays an important role in resistance against Fusarium head blight in wheat. Sci Rep 2020; 10:7794. [PMID: 32385328 PMCID: PMC7210279 DOI: 10.1038/s41598-020-64777-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 04/17/2020] [Indexed: 01/14/2023] Open
Abstract
Fusarium head blight (FHB) is a severe disease of wheat (Triticum aestivum L.). Qfhb1 is the most important quantitative trait locus (QTL) for FHB resistance. We previously identified wheat gene WFhb1-1 (aka WFhb1-c1) as a candidate for FHB resistance gene. Here we report that WFhb1-1 has been cloned. The gene (GenBank # KU304333.1) consists of a single exon, encoding a putative membrane protein of 127 amino acids. WFhb1-1 protein produced in Pichia pastoris inhibits growth of both F. graminearum and P. pastoris in culture. Western Blotting with anti- WFhb1-1 antibody revealed a significant decrease (p < 0.01) in WFhb1-1 accumulation, 12 hours post Fusarium inoculation in non-Qfhb1-carrier wheat but not in Qfhb1-carrier wheat. Overexpressing WFhb1-1 in non-Qfhb1-carrier wheat led to a significant decrease (p < 0.01) in Fusarium-damaged rachis rate, Fusarium-diseased kernel rate and DON content in harvested kernels, while silencing WFhb1-1 in Qfhb1-carrier wheat resulted in a significant increase (p < 0.01) in FHB severity. Therefore, WFhb1-1 is an important FHB resistance gene with a potential antifungal function and probably a key functional component of Qfhb1 in wheat. A model regarding how WFhb1-1 functions in FHB resistance/susceptibility is hypothesized and discussed.
Collapse
Affiliation(s)
- Bimal Paudel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Yongbin Zhuang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.,College of Agronomy, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Aravind Galla
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.,Department of Entomology, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Subha Dahal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Yinjie Qiu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.,Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Anjun Ma
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.,Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Tajbir Raihan
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
| |
Collapse
|
42
|
Ma Z, Xie Q, Li G, Jia H, Zhou J, Kong Z, Li N, Yuan Y. Germplasms, genetics and genomics for better control of disastrous wheat Fusarium head blight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1541-1568. [PMID: 31900498 DOI: 10.1007/s00122-019-03525-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/23/2019] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB), or scab, for its devastating nature to wheat production and food security, has stimulated worldwide attention. Multidisciplinary efforts have been made to fight against FHB for a long time, but the great progress has been achieved only in the genomics era of the past 20 years, particularly in the areas of resistance gene/QTL discovery, resistance mechanism elucidation and molecular breeding for better resistance. This review includes the following nine main sections, (1) FHB incidence, epidemic and impact, (2) causal Fusarium species, distribution and virulence, (3) types of host resistance to FHB, (4) germplasm exploitation for FHB resistance, (5) genetic control of FHB resistance, (6) fine mapping of Fhb1, Fhb2, Fhb4 and Fhb5, (7) cloning of Fhb1, (8) omics-based gene discovery and resistance mechanism study and (9) breeding for better FHB resistance. The advancements that have been made are outstanding and exciting; however, judged by the complicated nature of resistance to hemi-biotrophic pathogens like Fusarium species and lack of immune germplasm, it is still a long way to go to overcome FHB.
Collapse
Affiliation(s)
- Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Quan Xie
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Guoqiang Li
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Haiyan Jia
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jiyang Zhou
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhongxin Kong
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Na Li
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yang Yuan
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| |
Collapse
|
43
|
Hao Y, Rasheed A, Zhu Z, Wulff BBH, He Z. Harnessing Wheat Fhb1 for Fusarium Resistance. TRENDS IN PLANT SCIENCE 2020; 25:1-3. [PMID: 31679993 DOI: 10.1016/j.tplants.2019.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/30/2019] [Accepted: 10/10/2019] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, is an economically devastating disease of wheat worldwide. Fhb1, a widely used genetic source of FHB resistance, originated in East Asia. The recent cloning of Fhb1 opens a new avenue to improve FHB resistance in wheat and potentially other crops.
Collapse
Affiliation(s)
- Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; International Maize and Wheat Improvement Centre (CIMMYT), c/o CAAS, 12 Zhongguancun South Street, Beijing 100081, China; Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Zhanwang Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
| | | | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; International Maize and Wheat Improvement Centre (CIMMYT), c/o CAAS, 12 Zhongguancun South Street, Beijing 100081, China.
| |
Collapse
|
44
|
Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. THE NEW PHYTOLOGIST 2020; 225:511-529. [PMID: 31418861 DOI: 10.1111/nph.16122] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 05/21/2023]
Abstract
Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning important traits is of great importance. MADS-box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC-type MADS-box genes. Homoeolog retention is significantly above the average genome-wide retention rate for wheat genes, indicating that many MIKC-type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily-specific expression pattern, indicating broad conservation of function of MIKC-type genes during wheat evolution. We also found extensive expansion of some MIKC-type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC-type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC-type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.
Collapse
Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Alice Kennedy
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sirui Pan
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Lars S Jermiin
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| |
Collapse
|
45
|
Sari E, Cabral AL, Polley B, Tan Y, Hsueh E, Konkin DJ, Knox RE, Ruan Y, Fobert PR. Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat. BMC Genomics 2019; 20:925. [PMID: 31795948 PMCID: PMC6891979 DOI: 10.1186/s12864-019-6161-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Fusarium head blight (FHB) resistance in the durum wheat breeding gene pool is rarely reported. Triticum turgidum ssp. carthlicum line Blackbird is a tetraploid relative of durum wheat that offers partial FHB resistance. Resistance QTL were identified for the durum wheat cv. Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B in a previous study. The objective of this study was to identify the defense mechanisms underlying the resistance of Blackbird and report candidate regulator defense genes and single nucleotide polymorphism (SNP) markers within these genes for high-resolution mapping of resistance QTL reported for the durum wheat cv. Strongfield/Blackbird population. RESULTS Gene network analysis identified five networks significantly (P < 0.05) associated with the resistance to FHB spread (Type II FHB resistance) one of which showed significant correlation with both plant height and relative maturity traits. Two gene networks showed subtle differences between Fusarium graminearum-inoculated and mock-inoculated plants, supporting their involvement in constitutive defense. The candidate regulator genes have been implicated in various layers of plant defense including pathogen recognition (mainly Nucleotide-binding Leucine-rich Repeat proteins), signaling pathways including the abscisic acid and mitogen activated protein (MAP) kinase, and downstream defense genes activation including transcription factors (mostly with dual roles in defense and development), and cell death regulator and cell wall reinforcement genes. The expression of five candidate genes measured by quantitative real-time PCR was correlated with that of RNA-seq, corroborating the technical and analytical accuracy of RNA-sequencing. CONCLUSIONS Gene network analysis allowed identification of candidate regulator genes and genes associated with constitutive resistance, those that will not be detected using traditional differential expression analysis. This study also shed light on the association of developmental traits with FHB resistance and partially explained the co-localization of FHB resistance with plant height and maturity QTL reported in several previous studies. It also allowed the identification of candidate hub genes within the interval of three previously reported FHB resistance QTL for the Strongfield/Blackbird population and associated SNPs for future high resolution mapping studies.
Collapse
Affiliation(s)
- Ehsan Sari
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada.
| | - Adrian L Cabral
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Brittany Polley
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Yifang Tan
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Emma Hsueh
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Pierre R Fobert
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| |
Collapse
|
46
|
Foroud NA, Baines D, Gagkaeva TY, Thakor N, Badea A, Steiner B, Bürstmayr M, Bürstmayr H. Trichothecenes in Cereal Grains - An Update. Toxins (Basel) 2019; 11:E634. [PMID: 31683661 PMCID: PMC6891312 DOI: 10.3390/toxins11110634] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023] Open
Abstract
Trichothecenes are sesquiterpenoid mycotoxins produced by fungi from the order Hypocreales, including members of the Fusarium genus that infect cereal grain crops. Different trichothecene-producing Fusarium species and strains have different trichothecene chemotypes belonging to the Type A and B class. These fungi cause a disease of small grain cereals, called Fusarium head blight, and their toxins contaminate host tissues. As potent inhibitors of eukaryotic protein synthesis, trichothecenes pose a health risk to human and animal consumers of infected cereal grains. In 2009, Foroud and Eudes published a review of trichothecenes in cereal grains for human consumption. As an update to this review, the work herein provides a comprehensive and multi-disciplinary review of the Fusarium trichothecenes covering topics in chemistry and biochemistry, pathogen biology, trichothecene toxicity, molecular mechanisms of resistance or detoxification, genetics of resistance and breeding strategies to reduce their contamination of wheat and barley.
Collapse
Affiliation(s)
- Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada.
| | - Danica Baines
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada.
| | - Tatiana Y Gagkaeva
- Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant Protection (VIZR), St. Petersburg, Pushkin 196608, Russia.
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.
| | - Ana Badea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB R7A 5Y3, Canada.
| | - Barbara Steiner
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria.
| | - Maria Bürstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria.
| | - Hermann Bürstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln 3430, Austria.
| |
Collapse
|
47
|
Doppler M, Kluger B, Bueschl C, Steiner B, Buerstmayr H, Lemmens M, Krska R, Adam G, Schuhmacher R. Stable Isotope-Assisted Plant Metabolomics: Investigation of Phenylalanine-Related Metabolic Response in Wheat Upon Treatment With the Fusarium Virulence Factor Deoxynivalenol. FRONTIERS IN PLANT SCIENCE 2019; 10:1137. [PMID: 31736983 PMCID: PMC6831647 DOI: 10.3389/fpls.2019.01137] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/20/2019] [Indexed: 05/03/2023]
Abstract
The major Fusarium mycotoxin deoxynivalenol (DON) is a virulence factor in wheat and has also been shown to induce defense responses in host plant tissue. In this study, global and tracer labeling with 13C were combined to annotate the overall metabolome of wheat spikes and to evaluate the response of phenylalanine-related pathways upon treatment with DON. At anthesis, spikes of resistant and susceptible cultivars as well as two related near isogenic wheat lines (NILs) differing in the presence/absence of the major resistance QTL Fhb1 were treated with 1 mg DON or water (control), and samples were collected at 0, 12, 24, 48, and 96 h after treatment (hat). A total of 172 Phe-derived wheat constituents were detected with our untargeted approach employing 13C-labeled phenylalanine and subsequently annotated as flavonoids, lignans, coumarins, benzoic acid derivatives, hydroxycinnamic acid amides (HCAAs), as well as peptides. Ninety-six hours after the DON treatment, up to 30% of the metabolites biosynthesized from Phe showed significantly increased levels compared to the control samples. Major metabolic changes included the formation of precursors of compounds implicated in cell wall reinforcement and presumed antifungal compounds. In addition, also dipeptides, which presumably are products of proteolytic degradation of truncated proteins generated in the presence of the toxin, were significantly more abundant upon DON treatment. An in-depth comparison of the two NILs with correlation clustering of time course profiles revealed some 70 DON-responsive Phe derivatives. While several flavonoids had constitutively different abundance levels between the two NILs differing in resistance, other Phe-derived metabolites such as HCAAs and hydroxycinnamoyl quinates were affected differently in the two NILs after treatment with DON. Our results suggest a strong activation of the general phenylpropanoid pathway and that coumaroyl-CoA is mainly diverted towards HCAAs in the presence of Fhb1, whereas the metabolic route to monolignol(-conjugates), lignans, and lignin seems to be favored in the absence of the Fhb1 resistance quantitative trait loci.
Collapse
Affiliation(s)
- Maria Doppler
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Bernhard Kluger
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Christoph Bueschl
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Barbara Steiner
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Hermann Buerstmayr
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Marc Lemmens
- Department of Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Rudolf Krska
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
- School of Biological Sciences, Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| | - Rainer Schuhmacher
- Department of Agrobiotechnology (IFA-Tulln), Institute of Bioanalytics and Agro-Metabolomics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln, Austria
| |
Collapse
|
48
|
Yeast two-hybrid screening for proteins that interact with PFT in wheat. Sci Rep 2019; 9:15521. [PMID: 31664150 PMCID: PMC6820867 DOI: 10.1038/s41598-019-52030-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022] Open
Abstract
Fusarium head blight (FHB) is a devastating disease of wheat worldwide. Fhb1 is the most consistently reported quantitative trait locus (QTL) for FHB resistance breeding. A pore-forming toxin-like (PFT) gene at Fhb1 was first cloned by map-based cloning and found to confer FHB resistance in wheat. Proteins often interact with each other to execute their functions. Characterization of the proteins interacting with PFT might therefore provide information on the molecular mechanisms of PFT functions. In this study, a high-quality yeast two-hybrid (Y2H) library using RNA extracted from Fusarium graminearum (Fg)-infected wheat spikes of Sumai 3 was constructed. The agglutinin domains of PFT exhibited no self-activation and toxicity to yeast cells and were used as bait to screen the Y2H library. Twenty-three proteins that interact with PFT were obtained, which were mainly involved in the ubiquitination process, clathrin coat assembly, the oxidation-reduction process, and protein phosphorylation. The expression pattern of these interacting genes was analyzed by quantitative real-time PCR. This study clarifies the protein interactions of PFT and raises a regulatory network for PFT regarding FHB resistance in wheat.
Collapse
|
49
|
Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family in Triticum aestivum. G3-GENES GENOMES GENETICS 2019; 9:2709-2722. [PMID: 31227524 PMCID: PMC6686943 DOI: 10.1534/g3.119.400444] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The serine protease inhibitor (serpin) gene family is the largest family of protease inhibitors. Serine protease inhibitors have an active, but under-characterized, role in grain development and defense against pathogen attack in cereal crops. By exploiting publicly available genomic, transcriptomic and proteomic data for wheat (Triticum aestivum), we have identified and annotated the entire ’serpinome’ of wheat and constructed a high-quality and robust phylogenetic tree of the gene family, identifying paralogous and homeologous clades from the hexaploid wheat genome, including the Serpin-Z group that have been well characterized in barley. Using publicly available RNAseq data (http://www.wheat-expression.com/), expression profiles of the wheat serpins were explored across a variety of tissues from the developing grain, spikelet and spike. We show that the SERPIN-Z clade, among others, are highly expressed during grain development, and that there is homeologous and paralogous functional redundancy in this gene family. Further to their role in grain development, serpins play an important but under-explored role in response to fungal pathogens. Using 13 RNAseq datasets of wheat tissues infected by fungal pathogens, we identified 37 serpins with a significant disease response. The majority of the disease-responsive serpins were upregulated by Fusarium graminearum, a destructive fungal pathogen that attacks the spike and developing grain of wheat. As serpins are ubiquitous in wheat grain, the genes encoding serpins may be linked to grain development, with their disease response a result of pleiotropy.
Collapse
|
50
|
Liu Y, Salsman E, Fiedler JD, Hegstad JB, Green A, Mergoum M, Zhong S, Li X. Genetic Mapping and Prediction Analysis of FHB Resistance in a Hard Red Spring Wheat Breeding Population. FRONTIERS IN PLANT SCIENCE 2019; 10:1007. [PMID: 31447872 PMCID: PMC6691880 DOI: 10.3389/fpls.2019.01007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/18/2019] [Indexed: 05/23/2023]
Abstract
Fusarium head blight (FHB) is one of the most destructive diseases in wheat worldwide. Breeding for FHB resistance is hampered by its complex genetic architecture, large genotype by environment interaction, and high cost of phenotype screening. Genomic selection (GS) is a powerful tool to enhance improvement of complex traits such as FHB resistance. The objectives of this study were to (1) investigate the genetic architecture of FHB resistance in a North Dakota State University (NDSU) hard red spring wheat breeding population, (2) test if the major QTL Fhb1 and Fhb5 play an important role in this breeding population; and (3) assess the potential of GS to enhance breeding efficiency of FHB resistance. A total of 439 elite spring wheat breeding lines from six breeding cycles were genotyped using genotyping-by-sequencing (GBS) and 102,147 SNP markers were obtained. Evaluation of FHB severity was conducted in 10 unbalanced field trials across multiple years and locations. One QTL for FHB resistance was identified and located on chromosome arm 1AL, explaining 5.3% of total phenotypic variation. The major type II resistance QTL Fhb1 only explained 3.1% of total phenotypic variation and the QTL Fhb5 was not significantly associated with FHB resistance in this breeding population. Our results suggest that integration of many genes with medium/minor effects in this breeding population should provide stable FHB resistance. Genomic prediction accuracies of 0.22-0.44 were obtained when predicting over breeding cycles in this study, indicating the potential of GS to enhance the improvement of FHB resistance.
Collapse
Affiliation(s)
- Yuan Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Evan Salsman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Jason D. Fiedler
- Biosciences Research Laboratory, USDA-ARS Genotyping Laboratory, Fargo, ND, United States
| | - Justin B. Hegstad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Andrew Green
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA, United States
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| |
Collapse
|