1
|
Makhoul M, Schlichtermann RH, Ugwuanyi S, Weber SE, Voss-Fels KP, Stahl A, Zetzsche H, Wittkop B, Snowdon RJ, Obermeier C. Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:125. [PMID: 38727862 PMCID: PMC11087350 DOI: 10.1007/s00122-024-04634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/20/2024] [Indexed: 05/13/2024]
Abstract
KEY MESSAGE PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.
Collapse
Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | - Samson Ugwuanyi
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sven E Weber
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Kai P Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
| |
Collapse
|
2
|
Wang Y, Gao M, Jiang Y, Huang W, Zhao X, Zhu W, Li H, Wang Y, Zeng J, Wu D, Wei Y, Zhou Y, Zheng Y, Zhang P, Chen G, Kang H. Identification of candidate genes for adult plant stripe rust resistance transferred from Aegilops ventricosa 2N vS into wheat via fine mapping and transcriptome analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:116. [PMID: 38698276 DOI: 10.1007/s00122-024-04620-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
KEY MESSAGE An adult plant gene for resistance to stripe rust was narrowed down to the proximal one-third of the 2NvS segment translocated from Aegilops ventricosa to wheat chromosome arm 2AS, and based on the gene expression analysis, two candidate genes were identified showing a stronger response at the adult plant stage compared to the seedling stage. The 2NvS translocation from Aegilops ventricosa, known for its resistance to various diseases, has been pivotal in global wheat breeding for more than three decades. Here, we identified an adult plant resistance (APR) gene in the 2NvS segment in wheat line K13-868. Through fine mapping in a segregating near-isogenic line (NIL) derived population of 6389 plants, the candidate region for the APR gene was narrowed down to between 19.36 Mb and 33 Mb in the Jagger reference genome. Transcriptome analysis in NILs strongly suggested that this APR gene conferred resistance to stripe rust by triggering plant innate immune responses. Based on the gene expression analysis, two disease resistance-associated genes within the candidate region, TraesJAG2A03G00588940 and TraesJAG2A03G00590140, exhibited a stronger response to Puccinia striiformis f. sp. tritici (Pst) infection at the adult plant stage than at the seedling stage, indicating that they could be potential candidates for the resistance gene. Additionally, we developed a co-dominant InDel marker, InDel_31.05, for detecting this APR gene. Applying this marker showed that over one-half of the wheat varieties approved in 2021 and 2022 in Sichuan province, China, carry this gene. Agronomic trait evaluation of NILs indicated that the 2NvS segment effectively mitigated the negative effects of stripe rust on yield without affecting other important agronomic traits. This study provided valuable insights for cloning and breeding through the utilization of the APR gene present in the 2NvS segment.
Collapse
Affiliation(s)
- Yuqi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Mengru Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wuzhou Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xin Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW, 2570, Australia.
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| |
Collapse
|
3
|
Adhikari L, Raupp J, Wu S, Koo DH, Friebe B, Poland J. Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1268370. [PMID: 37915516 PMCID: PMC10616851 DOI: 10.3389/fpls.2023.1268370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023]
Abstract
Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.
Collapse
Affiliation(s)
- Laxman Adhikari
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Shuangye Wu
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| |
Collapse
|
4
|
Cruppe G, Lemes da Silva C, Lollato RP, Fritz AK, Kuhnem P, D Cruz C, Calderon L, Valent B. QTL Pyramiding Provides Marginal Improvement in 2N vS-Based Wheat Blast Resistance. PLANT DISEASE 2023; 107:2407-2416. [PMID: 36691278 DOI: 10.1094/pdis-09-22-2030-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Wheat blast, caused by the fungus Magnaporthe oryzae Triticum pathotype (MoT), is a devastating disease affecting South America, Bangladesh, and Zambia. Resistance to wheat blast has strongly relied on the 2NvS translocation; however, newer MoT isolates have increased aggressiveness, threatening the 2NvS translocation's effectiveness and durability. To identify genomic regions associated with wheat blast resistance, we performed a quantitative trait loci (QTL) mapping study using 187 double-haploid (DH) lines from a cross between the Brazilian wheat cultivars 'TBIO Alvorada' and 'TBIO Sossego', which are moderately resistant and susceptible to blast, respectively. The DH population was evaluated in a greenhouse in Brazil and Bolivia, and field conditions in Bolivia. Contrasting models best explained the relationship between traits evaluated according to differences in disease levels and the presence of the 2NvS. A large effect-locus, derived from 'TBIO Sossego', was identified on chromosome 2AS, which was confirmed to be 2NvS translocation and explained 33.5 to 82.4% of the phenotypic variance. Additional significant loci were identified on 5AL, 1DS, 4DS, 5DL, and 6DL chromosome arms with phenotypic variance <6%, but they were not consistent across trait-environment combinations. QTL pyramiding analyses showed that some specific loci had an additive effect when combined with the 2NvS, suggesting that stacking multiple loci may be an effective strategy to help manage wheat blast. The markers associated with the 2NvS can be used as dominant diagnostic markers for this alien translocation. Additional characterization of these loci using a broader set of MoT isolates is critical to validate their effectiveness against current MoT populations.
Collapse
Affiliation(s)
- Giovana Cruppe
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | | | - Romulo P Lollato
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Allan K Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Paulo Kuhnem
- Biotrigo Genetica, Passo Fundo, Rio Grande do Sul 99052, Brazil
| | - Christian D Cruz
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Lidia Calderon
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| |
Collapse
|
5
|
Guo X, Shi Q, Liu Y, Su H, Zhang J, Wang M, Wang C, Wang J, Zhang K, Fu S, Hu X, Jing D, Wang Z, Li J, Zhang P, Liu C, Han F. Systemic development of wheat-Thinopyrum elongatum translocation lines and their deployment in wheat breeding for Fusarium head blight resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1475-1489. [PMID: 36919201 DOI: 10.1111/tpj.16190] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/09/2023] [Accepted: 03/07/2023] [Indexed: 06/17/2023]
Abstract
Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is one of the most destructive diseases of wheat (Triticum aestivum) around the world. FHB causes significant yield losses and reduces grain quality. The lack of resistance resources is a major bottleneck for wheat FHB resistance breeding. As a wheat relative, Thinopyrum elongatum contains many genes that can be used for wheat improvement. Although the novel gene Fhb-7EL was mapped on chromosome 7EL of Th. elongatum, successful transfer of the FHB resistance gene into commercial wheat varieties has not been reported. In this study, we developed 836 wheat-Th. elongatum translocation lines of various types by irradiating the pollen of the wheat-Th. elongatum addition line CS-7EL at the flowering stage, among which 81 were identified as resistant to FHB. By backcrossing the FHB-resistant lines with the main cultivar Jimai 22, three wheat-Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, were successfully applied in wheat breeding without yield penalty. Combining karyotype and phenotype analyses, we mapped the Fhb-7EL gene to the distal end of chromosome 7EL. Five molecular markers linked with the FHB resistance interval were developed, which facilitates molecular marker-assisted breeding. Altogether, we successfully applied alien chromatin with FHB resistance from Th. elongatum in wheat breeding without yield penalty. These newly developed FHB-resistant wheat-Th. elongatum translocation lines, Zhongke 1878, Zhongke 166, and Zhongke 545, can be used as novel resistance resources for wheat breeding.
Collapse
Affiliation(s)
- Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life Sciences, Linyi University, Linyi, China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Mian Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chunhui Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Kaibiao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shulan Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xiaojun Hu
- Laboratory of Plant Chromosome Biology and Genomic Breeding, School of Life Sciences, Linyi University, Linyi, China
| | - Donglin Jing
- Xingtai Academy of Agricultural Sciences, Xingtai, China
| | - Zhen Wang
- Nanyang Academy of Agricultural Sciences, Nanyang, China
| | - Jinbang Li
- Nanyang Academy of Agricultural Sciences, Nanyang, China
| | - Pingzhi Zhang
- Institute of Crop Sciences, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
6
|
Li Y, Liu L, Wang M, Ruff T, See DR, Hu X, Chen X. Characterization and Molecular Mapping of a Gene Conferring High-Temperature Adult-Plant Resistance to Stripe Rust Originally from Aegilops ventricosa. PLANT DISEASE 2023; 107:431-442. [PMID: 35852900 DOI: 10.1094/pdis-06-22-1419-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wheat near-isogenic line AvSYr17NIL carrying Yr17, originally from Aegilops ventricosa for all-stage resistance to Puccinia striiformis f. sp. tritici, also shows nonrace-specific, high-temperature adult-plant (HTAP) resistance to the stripe rust pathogen. To separate and identify the HTAP resistance gene, seeds of AvSYr17NIL were treated with ethyl methanesulfonate. Mutant lines with only HTAP resistance were obtained, and one of the lines, M1225, was crossed with the susceptible recurrent parent Avocet S (AvS). Field responses of the F2 plants and F3 lines, together with the parents, were recorded at the adult-plant stage in Pullman and Mount Vernon, WA under natural P. striiformis f. sp. tritici infection. The parents and the F4 population were phenotyped with a Yr17-virulent P. striiformis f. sp. tritici race in the adult-plant stage under the high-temperature profile in the greenhouse. The phenotypic results were confirmed by testing the F5 population in the field under natural P. striiformis f. sp. tritici infection. The F2 data indicated a single recessive gene, temporarily named YrM1225, for HTAP resistance. The F4 lines were genotyped with Kompetitive allele-specific PCR markers converted from single-nucleotide polymorphism markers polymorphic between M1225 and AvS. The HTAP resistance gene was mapped on the short arm of chromosome 2A in an interval of 7.5 centimorgans using both linkage and quantitative trait locus mapping approaches. The separation of the HTAP resistance gene from Yr17 should improve the understanding and utilization of the different types of resistance.
Collapse
Affiliation(s)
- Yuxiang Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Lu Liu
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Travis Ruff
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Deven R See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- United States Department of Agriculture Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, U.S.A
| | - Xiaoping Hu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- United States Department of Agriculture Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, U.S.A
| |
Collapse
|
7
|
Multiomics Based Association Mapping in Wheat Reveals Genetic Architecture of Quality and Allergenic Related Proteins. Int J Mol Sci 2023; 24:ijms24021485. [PMID: 36674997 PMCID: PMC9866442 DOI: 10.3390/ijms24021485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Wheat is an important staple crop since its proteins contribute to human and animal nutrition and are important for its end-use quality. However, wheat proteins can also cause adverse human reactions for a large number of people. We performed a genome wide association study (GWAS) on 114 proteins quantified by LC-MS-based proteomics and expressed in an environmentally stable manner in 148 wheat cultivars with a heritability > 0.6. For 54 proteins, we detected quantitative trait loci (QTL) that exceeded the Bonferroni-corrected significance threshold and explained 17.3−84.5% of the genotypic variance. Proteins in the same family often clustered at a very close chromosomal position or the potential homeolog. Major QTLs were found for four well-known glutenin and gliadin subunits, and the QTL segregation pattern in the protein encoding the high molecular weight glutenin subunit Dx5 could be confirmed by SDS gel-electrophoresis. For nine potential allergenic proteins, large QTLs could be identified, and their measured allele frequencies open the possibility to select for low protein abundance by markers as long as their relevance for human health has been conclusively demonstrated. A potential allergen was introduced in the beginning of 1980s that may be linked to the cluster of resistance genes introgressed on chromosome 2AS from Triticum ventricosum. The reported sequence information for the 54 major QTLs can be used to design efficient markers for future wheat breeding.
Collapse
|
8
|
Mohi-Ud-Din M, Rohman MM, Alam MA, Hasanuzzaman M, Islam T. Wheat variety carrying 2N vS chromosomal segment provides yield advantage through lowering terminal heat-induced oxidative stress. PROTOPLASMA 2023; 260:63-76. [PMID: 35397668 DOI: 10.1007/s00709-022-01759-w] [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: 01/08/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
A 2NvS chromosomal segment carrying bread wheat variety, BARI Gom 33 ('BG33'), showed tolerance to terminal heat stress and higher yield over a heat-tolerant non-2NvS BARI Gom 26 ('BG26') and a heat-susceptible Pavon 76 ('Pavon'). This study aimed to ascertain the potential of the 2NvS 'BG33' in terminal heat-induced oxidative stress tolerance compared to non-2NvS 'BG26' and heat-susceptible 'Pavon' under two heat regimes at the reproductive stages viz. control (optimum sowing time) and heat stress (late sowing). We found that both 'BG26' and 'BG33' showed significantly higher tolerance to oxidative stress by limiting the generation of reactive oxygen species (ROS), methylglyoxal under heat stress. During terminal heat stress, both 'BG33' and 'BG26' exhibited greater cellular homeostasis than heat-susceptible 'Pavon', which was maintained by the increased accumulation of osmolytes, nonenzymatic antioxidants, and enzymes associated with ROS scavenging, ascorbate-glutathione cycle, and glyoxalase system. Lesser cellular damage in 'BG26' and 'BG33' was eventually imitated in a smaller reduction in grain yield (15 and 12%, respectively) than in 'Pavon', which had a 33% reduction owing to heat stress. Collectively, our findings revealed that the chromosomal segment 2NvS provides yield advantage to 'BG33' under terminal heat stress by lowering oxidative damage. As 2NvS translocation contains multiple nucleotide-binding domain leucine-rich repeat containing, cytochrome P450, and other gene families associated with plant stress tolerance, further studies are warranted to dissect the underlying molecular mechanisms associated with higher heat stress tolerance of 2NvS carrying 'BG33'.
Collapse
Affiliation(s)
- Mohammed Mohi-Ud-Din
- Department of Crop Botany, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - Md Motiar Rohman
- Plant Breeding Division, Bangladesh Agricultural Research Institute, Gazipur, 1701, Bangladesh
| | - Md Ashraful Alam
- Bangladesh Wheat and Maize Research Institute (BWMRI), Dinajpur, 5200, Bangladesh
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh.
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| |
Collapse
|
9
|
Wu J, Xu D, Fu L, Wu L, Hao W, Li J, Dong Y, Wang F, Wu Y, He Z, Si H, Ma C, Xia X. Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2665-2673. [PMID: 35986759 DOI: 10.1007/s00122-022-04140-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/23/2022] [Indexed: 05/26/2023]
Abstract
A stripe rust resistance gene YrZM175 in Chinese wheat cultivar Zhongmai 175 was mapped to a genomic interval of 636.4 kb on chromosome arm 2AL, and a candidate gene was predicted. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is a worldwide wheat disease that causes large losses in production. Fine mapping and cloning of resistance genes are important for accurate marker-assisted breeding. Here, we report the fine mapping and candidate gene analysis of stripe rust resistance gene YrZM175 in a Chinese wheat cultivar Zhongmai 175. Fifteen F1, 7,325 F2 plants and 117 F2:3 lines derived from cross Avocet S/Zhongmai 175 were inoculated with PST race CYR32 at the seedling stage in a greenhouse, and F2:3 lines were also evaluated for stripe rust reaction in the field using mixed PST races. Bulked segregant RNA-seq (BSR-seq) analyses revealed 13 SNPs in the region 762.50-768.52 Mb on chromosome arm 2AL. By genome mining, we identified SNPs and InDels between the parents and contrasting bulks and mapped YrZM175 to a 0.72-cM, 636.4-kb interval spanned by YrZM175-InD1 and YrZM175-InD2 (763,452,916-764,089,317 bp) including two putative disease resistance genes based on IWGSC RefSeq v1.0. Collinearity analysis indicated similar target genomic intervals in Chinese Spring, Aegilops tauschii (2D: 647.7-650.5 Mb), Triticum urartu (2A: 750.7-752.3 Mb), Triticum dicoccoides (2A: 771.0-774.5 Mb), Triticum turgidum (2B: 784.7-788.2 Mb), and Triticum aestivum cv. Aikang 58 (2A: 776.3-778.9 Mb) and Jagger (2A: 789.3-791.7 Mb). Through collinearity analysis, sequence alignments of resistant and susceptible parents and gene expression level analysis, we predicted TRITD2Bv1G264480 from Triticum turgidum to be a candidate gene for map-based cloning of YrZM175. A gene-specific marker for TRITD2Bv1G264480 co-segregated with the resistance gene. Molecular marker analysis and stripe rust response data revealed that YrZM175 was different from genes Yr1, Yr17, Yr32, and YrJ22 located on chromosome 2A. Fine mapping of YrZM175 lays a solid foundation for functional gene analysis and marker-assisted selection for improved stripe rust resistance in wheat.
Collapse
Affiliation(s)
- Jingchun Wu
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong province, China
| | - Luping Fu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, Jiangsu province, China
- Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Jiangsu province, Yangzhou, 225009, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610011, Sichuan province, China
| | - Weihao Hao
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
| | - Jihu Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong province, China
| | - Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Fengju Wang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuying Wu
- College of Agronomy, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, 450002, Henan province, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Centre (CIMMYT) China Office c/o, CAAS, Beijing, 100081, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China.
| | - Xianchun Xia
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China.
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| |
Collapse
|
10
|
Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat Genet 2022; 54:1544-1552. [DOI: 10.1038/s41588-022-01189-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 08/18/2022] [Indexed: 11/06/2022]
|
11
|
Wu J, Xu D, Fu L, Wu L, Hao W, Li J, Dong Y, Wang F, Wu Y, He Z, Si H, Ma C, Xia X. Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3485-3496. [PMID: 35986759 DOI: 10.1007/s00122-022-04195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
A stripe rust resistance gene YrZM175 in Chinese wheat cultivar Zhongmai 175 was mapped to a genomic interval of 636.4 kb on chromosome arm 2AL, and a candidate gene was predicted. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is a worldwide wheat disease that causes large losses in production. Fine mapping and cloning of resistance genes are important for accurate marker-assisted breeding. Here, we report the fine mapping and candidate gene analysis of stripe rust resistance gene YrZM175 in a Chinese wheat cultivar Zhongmai 175. Fifteen F1, 7,325 F2 plants and 117 F2:3 lines derived from cross Avocet S/Zhongmai 175 were inoculated with PST race CYR32 at the seedling stage in a greenhouse, and F2:3 lines were also evaluated for stripe rust reaction in the field using mixed PST races. Bulked segregant RNA-seq (BSR-seq) analyses revealed 13 SNPs in the region 762.50-768.52 Mb on chromosome arm 2AL. By genome mining, we identified SNPs and InDels between the parents and contrasting bulks and mapped YrZM175 to a 0.72-cM, 636.4-kb interval spanned by YrZM175-InD1 and YrZM175-InD2 (763,452,916-764,089,317 bp) including two putative disease resistance genes based on IWGSC RefSeq v1.0. Collinearity analysis indicated similar target genomic intervals in Chinese Spring, Aegilops tauschii (2D: 647.7-650.5 Mb), Triticum urartu (2A: 750.7-752.3 Mb), Triticum dicoccoides (2A: 771.0-774.5 Mb), Triticum turgidum (2B: 784.7-788.2 Mb), and Triticum aestivum cv. Aikang 58 (2A: 776.3-778.9 Mb) and Jagger (2A: 789.3-791.7 Mb). Through collinearity analysis, sequence alignments of resistant and susceptible parents and gene expression level analysis, we predicted TRITD2Bv1G264480 from Triticum turgidum to be a candidate gene for map-based cloning of YrZM175. A gene-specific marker for TRITD2Bv1G264480 co-segregated with the resistance gene. Molecular marker analysis and stripe rust response data revealed that YrZM175 was different from genes Yr1, Yr17, Yr32, and YrJ22 located on chromosome 2A. Fine mapping of YrZM175 lays a solid foundation for functional gene analysis and marker-assisted selection for improved stripe rust resistance in wheat.
Collapse
Affiliation(s)
- Jingchun Wu
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong province, China
| | - Luping Fu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, Jiangsu province, China
- Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Jiangsu province, Yangzhou, 225009, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610011, Sichuan province, China
| | - Weihao Hao
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
| | - Jihu Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong province, China
| | - Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Fengju Wang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuying Wu
- College of Agronomy, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, 450002, Henan province, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Centre (CIMMYT) China Office c/o, CAAS, Beijing, 100081, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China.
| | - Xianchun Xia
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China.
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| |
Collapse
|
12
|
Hossain MM. Wheat blast: A review from a genetic and genomic perspective. Front Microbiol 2022; 13:983243. [PMID: 36160203 PMCID: PMC9493272 DOI: 10.3389/fmicb.2022.983243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/12/2022] [Indexed: 12/11/2022] Open
Abstract
The newly emerged wheat blast fungus Magnaporthe oryzae Triticum (MoT) is a severe threat to global wheat production. The fungus is a distinct, exceptionally diverse lineage of the M. oryzae, causing rice blast disease. Genome-based approaches employing MoT-specific markers are used to detect MoT field isolates. Sequencing the whole genome indicates the presence of core chromosome and mini-chromosome sequences that harbor effector genes and undergo divergent evolutionary routes. Significant genetic and pathotype diversity within the fungus population gives ample potential for evolutionary change. Identifying and refining genetic markers allows for tracking genomic regions with stable blast resistance. Introgression of quantitative and R gene resistance into popular cultivars is crucial to controlling disease in areas where the pathogen population is diverse and well established. Novel approaches such as CRISPR/Cas-9 genome editing could generate resistant varieties in wheat within a short time. This chapter provides an extensive summary of the genetic and genomic aspects of the wheat blast fungus MoT and offers an essential resource for wheat blast research in the affected areas.
Collapse
|
13
|
Navia-Urrutia M, Mosquera G, Ellsworth R, Farman M, Trick HN, Valent B. Effector Genes in Magnaporthe oryzae Triticum as Potential Targets for Incorporating Blast Resistance in Wheat. PLANT DISEASE 2022; 106:1700-1712. [PMID: 34931892 DOI: 10.1094/pdis-10-21-2209-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Wheat blast (WB), caused by Magnaporthe oryzae Triticum pathotype, recently emerged as a destructive disease that threatens global wheat production. Because few sources of genetic resistance have been identified in wheat, genetic transformation of wheat with rice blast resistance genes could expand resistance to WB. We evaluated the presence/absence of homologs of rice blast effector genes in Triticum isolates with the aim of identifying avirulence genes in field populations whose cognate rice resistance genes could potentially confer resistance to WB. We also assessed presence of the wheat pathogen AVR-Rmg8 gene and identified new alleles. A total of 102 isolates collected in Brazil, Bolivia, and Paraguay from 1986 to 2018 were evaluated by PCR using 21 pairs of gene-specific primers. Effector gene composition was highly variable, with homologs to AvrPiz-t, AVR-Pi9, AVR-Pi54, and ACE1 showing the highest amplification frequencies (>94%). We identified Triticum isolates with a functional AvrPiz-t homolog that triggers Piz-t-mediated resistance in the rice pathosystem and produced transgenic wheat plants expressing the rice Piz-t gene. Seedlings and heads of the transgenic lines were challenged with isolate T25 carrying functional AvrPiz-t. Although slight decreases in the percentage of diseased spikelets and leaf area infected were observed in two transgenic lines, our results indicated that Piz-t did not confer useful WB resistance. Monitoring of avirulence genes in populations is fundamental to identifying effective resistance genes for incorporation into wheat by conventional breeding or transgenesis. Based on avirulence gene distributions, rice resistance genes Pi9 and Pi54 might be candidates for future studies.
Collapse
Affiliation(s)
- Monica Navia-Urrutia
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Gloria Mosquera
- Rice Pathology, International Center for Tropical Agriculture, Palmira, 763537, Colombia
| | - Rebekah Ellsworth
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| |
Collapse
|
14
|
Xue S, Hu S, Chen X, Ma Y, Lu M, Bai S, Wang X, Sun T, Wang Y, Wan H, An X, Li S. Fine mapping of Pm58 from Aegilops tauschii conferring powdery mildew resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1657-1669. [PMID: 35234985 DOI: 10.1007/s00122-022-04061-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/11/2022] [Indexed: 05/26/2023]
Abstract
The powdery mildew resistance gene Pm58 was traced to a 141.3-kb interval with the co-segregating marker Xkasp68500 in wheat breeding. Pm58 is a powdery mildew resistance gene identified in Aegilops tauschii accession TA1662 and effective in a common wheat background. To finely map Pm58, an F2 population of 676 plants derived from the cross T093 × TA1662 was used for recombinant screening. We obtained 13 recombinants that occurred between the flanking markers Xhnu670 and Xhnu186. Genotyping and phenotyping these recombinant F2:3 families delimited Pm58 to a 0.22-cM interval (Xsts20220-Xkasp61553) on chromosome arm 2DS. The region carrying the Pm58 locus was approximately 141.3-kb, which contained eight annotated genes according to the reference genome sequence of Ae. tauschii AL8/78. Haplotype analysis of 178 Ae. tauschii accessions using the candidate gene-specific markers identified a disease resistance gene AET2Gv20068500 as a candidate for Pm58. Comparative mapping of the Pm58-containing interval revealed two presence/absence variations (PAVs) between AL8/78 and common wheat Chinese Spring. PAV-1 resides in the 3'-end of AET2Gv20068500. The majority of 158 common wheat cultivars (84.8%) displayed the absence of a 14.1-kb fragment in the PAV-1 region, which was confirmed by aligning the targeted genome sequences of the other sequenced Ae. tauschii accessions and common wheat cultivars. A co-segregating marker Xkasp68500 developed from AET2Gv20068500 can distinguish TA1662 from all randomly selected common wheat cultivars and will be instrumental for tracking Pm58 in breeding programs.
Collapse
Affiliation(s)
- Shulin Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China.
| | - Shanshan Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Xian Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Yuyu Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Mingxue Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Xintian Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Tiepeng Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Yingxue Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Xia An
- Zibo Academy of Agricultural Sciences, Zibo, 255000, Shandong, China
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China.
| |
Collapse
|
15
|
Khan H, Wani SH, Bhardwaj SC, Rani K, Bishnoi SK, Singh GP. Wheat spike blast: genetic interventions for effective management. Mol Biol Rep 2022; 49:5483-5494. [PMID: 35478296 DOI: 10.1007/s11033-022-07356-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/05/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The fundamental concepts of the genetics, race classification and epidemiology of the Wheat spike blast causing fungus Magnaporthe oryzae pathotype Triticum (MoT) are still evolving despite of its discovery in 1985 in Brazil for the first time. The fungus seems to defy the research progress that is being made globally by continuously evolving into pathotypes which have already overcome the much celebrated 2NS resistance in wheat lines as well as few of the initially effective fungicides. The compartmentalized i.e. two speed genome of the MoT, conferring the fungus an evolutionary advantage, has emerged as a challenge for the wheat spike blast researchers complicating its already difficult management. The airborne fungus with a range of alternative hosts is finding new geographical niches situated on different continents and is a matter of great apprehension among the nations whose food security is primarily dependent on wheat. The wheat blast outbreak in Bangladesh during 2016 was attributed to an isolate from Latin America escaping through a seed import consignment while the latest Zambian outbreak is still to be studied in detail regarding its origin and entry. The challenges in dealing wheat spike blast are not only on the level of genetics and epidemiology alone but also on the levels of policy making regarding international seed movement and research collaborations. The present review deals with these issues mainly concerning the effective management and controlling the international spread of this deadly disease of wheat, with a particular reference to India. We describe the origin, taxonomy, epidemiology and symptomology of MoT and briefly highlight its impact and management practices from different countries. We also discuss the advances in genomics and genome editing technologies that can be used to develop elite wheat genotypes resistant against different stains of wheat spike blast.
Collapse
Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, 132001, Karnal, Haryana, India.
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, 192101, Khudwani, J & K, India
| | - Subhash Chander Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, 171 002, Shimla, Himachal Pradesh, India
| | - Kirti Rani
- ICAR-Directorate of Groundnut Research (DGR), 362001, Junagadh, Gujarat, India
| | - Santosh Kumar Bishnoi
- ICAR- Indian Institute of Wheat and Barley Research, Seed & Research Farm, 125001, Hisar, Haryana, India
| | | |
Collapse
|
16
|
Identification of Genomic Regions and Sources for Wheat Blast Resistance through GWAS in Indian Wheat Genotypes. Genes (Basel) 2022; 13:genes13040596. [PMID: 35456402 PMCID: PMC9025667 DOI: 10.3390/genes13040596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/20/2022] Open
Abstract
Wheat blast (WB) is a devastating fungal disease that has recently spread to Bangladesh and poses a threat to the wheat production in India, which is the second-largest wheat producing country in the world. In this study, 350 Indian wheat genotypes were evaluated for WB resistance in 12 field experiments in three different locations, namely Jashore in Bangladesh and Quirusillas and Okinawa in Bolivia. Single nucleotide polymorphisms (SNPs) across the genome were obtained using DArTseq® technology, and 7554 filtered SNP markers were selected for a genome-wide association study (GWAS). All the three GWAS approaches used identified the 2NS translocation as the only major source of resistance, explaining up to 32% of the phenotypic variation. Additional marker-trait associations were located on chromosomes 2B, 3B, 4D, 5A and 7A, and the combined effect of three SNPs (2B_180938790, 7A_752501634 and 5A_618682953) showed better resistance, indicating their additive effects on WB resistance. Among the 298 bread wheat genotypes, 89 (29.9%) carried the 2NS translocation, the majority of which (60 genotypes) were CIMMYT introductions, and 29 were from India. The 2NS carriers with a grand mean WB index of 6.6 showed higher blast resistance compared to the non-2NS genotypes with a mean index of 46.5. Of the 52 durum wheats, only one genotype, HI 8819, had the 2NS translocation and was the most resistant, with a grand mean WB index of 0.93. Our study suggests that the 2NS translocation is the only major resistance source in the Indian wheat panel analysed and emphasizes the urgent need to identify novel non-2NS resistance sources and genomic regions.
Collapse
|
17
|
Mondaini A, Rosyara U, Sehgal D, Dreisigacker S. Selection signatures in the CIMMYT International Elite Spring and Semi-arid Wheat Yield Trials. THE PLANT GENOME 2022; 15:e20165. [PMID: 34750999 DOI: 10.1002/tpg2.20165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
The International Maize and Wheat Improvement Center (CIMMYT) annually distributes advanced wheat (Triticum aestivum L.) breeding lines to collaborators worldwide through the International Wheat Improvement Network. Lines are disseminated through international nurseries, including the Elite Spring Wheat Yield Trial (ESWYT) targeted to optimal (irrigated and high production) wheat production areas and the Semi-arid Wheat Yield Trial (SAWYT) targeted to low rainfall environments. A total of 2,184 wheat lines that formed the ESWYT and SAWYT since 1979 and 1992, respectively, were genotyped using genotyping-by-sequencing to explore trends of genetic diversity and selection footprints associated with continuous crop improvement and adaptation. Due to a small population size of each trial, adjacent year trials were pooled into subpopulations. Population structure was evaluated using discriminant analysis of principal components and fixation index. High levels of admixture within and across the ESWYT and SAWYT subpopulations were revealed, indicating that the entire genetic diversity in the overall CIMMYT germplasm pool is harnessed to target core traits to individual mega-environments. Genome wide scans of deviations of minor allele frequencies at each marker identified large linkage blocks in several chromosomes. The scans also revealed that 9.8 and 2.0% of the SNP markers could be associated to selection signatures over time and to environmental adaptation (significant deviations between ESWYT and SAWYT), respectively. Several known genes and previously identified haplotypes associated with grain yield in more recent CIMMYT elite germplasm did fall into genomic regions with directional selection.
Collapse
Affiliation(s)
- Alexandre Mondaini
- Institute of Plant Breeding, Seed Science and Population Genetics, Univ. of Hohenheim, Fruhwirthstrasse 21, Stuttgart, 70593, Germany
- current address: Univ. of Hong Kong, 21 Sassoon Rd, Pok Fu Lam, Hong Kong
| | - Umesh Rosyara
- International Maize and Wheat Improvement Center (CIMMYT), Global Wheat Program, Km45 Carretera Mexico-Veracruz, Texcoco, Edo. de México, 56237, México
- current address: BASF, 26 Davis Dr., Research Triangle, NC, 27709, USA
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Global Wheat Program, Km45 Carretera Mexico-Veracruz, Texcoco, Edo. de México, 56237, México
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Global Wheat Program, Km45 Carretera Mexico-Veracruz, Texcoco, Edo. de México, 56237, México
| |
Collapse
|
18
|
Rauf Y, Bajgain P, Rouse MN, Khanzada KA, Bhavani S, Huerta-Espino J, Singh RP, Imtiaz M, Anderson JA. Molecular Characterization of Genomic Regions for Adult Plant Resistance to Stem Rust in a Spring Wheat Mapping Population. PLANT DISEASE 2022; 106:439-450. [PMID: 34353123 DOI: 10.1094/pdis-03-21-0672-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line 'Copio'. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent 'Apav' with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping using 762 genotyping-by-sequencing markers identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37, and Yr17. Three quantitative trait loci (QTLs) were mapped on chromosomes 2B, two QTLs on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D, and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27 to 39% less stem rust coefficient of infection in all field environments compared with RILs with none of these genes, and this gene combination was most effective in the U.S. environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.
Collapse
Affiliation(s)
- Yahya Rauf
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Matthew N Rouse
- Cereal Disease Lab, United States Department of Agriculture, St. Paul, MN 55108, U.S.A
| | - Khalil A Khanzada
- Cereal Disease Research Institute, Pakistan Agricultural Research Council, University of Karachi 75270, Pakistan
| | - Sridhar Bhavani
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Julio Huerta-Espino
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Ravi P Singh
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Muhammad Imtiaz
- Global Wheat Program, International Maize and Wheat Improvement Center, National Agricultural Research Center, Islamabad 44000, Pakistan
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| |
Collapse
|
19
|
Juliana P, He X, Marza F, Islam R, Anwar B, Poland J, Shrestha S, Singh GP, Chawade A, Joshi AK, Singh RP, Singh PK. Genomic Selection for Wheat Blast in a Diversity Panel, Breeding Panel and Full-Sibs Panel. FRONTIERS IN PLANT SCIENCE 2022; 12:745379. [PMID: 35069614 PMCID: PMC8782147 DOI: 10.3389/fpls.2021.745379] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Wheat blast is an emerging threat to wheat production, due to its recent migration to South Asia and Sub-Saharan Africa. Because genomic selection (GS) has emerged as a promising breeding strategy, the key objective of this study was to evaluate it for wheat blast phenotyped at precision phenotyping platforms in Quirusillas (Bolivia), Okinawa (Bolivia) and Jashore (Bangladesh) using three panels: (i) a diversity panel comprising 172 diverse spring wheat genotypes, (ii) a breeding panel comprising 248 elite breeding lines, and (iii) a full-sibs panel comprising 298 full-sibs. We evaluated two genomic prediction models (the genomic best linear unbiased prediction or GBLUP model and the Bayes B model) and compared the genomic prediction accuracies with accuracies from a fixed effects model (with selected blast-associated markers as fixed effects), a GBLUP + fixed effects model and a pedigree relationships-based model (ABLUP). On average, across all the panels and environments analyzed, the GBLUP + fixed effects model (0.63 ± 0.13) and the fixed effects model (0.62 ± 0.13) gave the highest prediction accuracies, followed by the Bayes B (0.59 ± 0.11), GBLUP (0.55 ± 0.1), and ABLUP (0.48 ± 0.06) models. The high prediction accuracies from the fixed effects model resulted from the markers tagging the 2NS translocation that had a large effect on blast in all the panels. This implies that in environments where the 2NS translocation-based blast resistance is effective, genotyping one to few markers tagging the translocation is sufficient to predict the blast response and genome-wide markers may not be needed. We also observed that marker-assisted selection (MAS) based on a few blast-associated markers outperformed GS as it selected the highest mean percentage (88.5%) of lines also selected by phenotypic selection and discarded the highest mean percentage of lines (91.8%) also discarded by phenotypic selection, across all panels. In conclusion, while this study demonstrates that MAS might be a powerful strategy to select for the 2NS translocation-based blast resistance, we emphasize that further efforts to use genomic tools to identify non-2NS translocation-based blast resistance are critical.
Collapse
Affiliation(s)
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico
| | - Felix Marza
- Instituto Nacional de Innovación Agropecuaria y Forestal (INIAF), La Paz, Bolivia
| | - Rabiul Islam
- Bangladesh Wheat and Maize Research Institute (BWMRI), Dinajpur, Bangladesh
| | - Babul Anwar
- Bangladesh Wheat and Maize Research Institute (BWMRI), Dinajpur, Bangladesh
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Gyanendra P. Singh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Arun K. Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, India
- CIMMYT-India, New Delhi, India
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico
| |
Collapse
|
20
|
King J, Grewal S, Othmeni M, Coombes B, Yang CY, Walter N, Ashling S, Scholefield D, Walker J, Hubbart-Edwards S, Hall A, King IP. Introgression of the Triticum timopheevii Genome Into Wheat Detected by Chromosome-Specific Kompetitive Allele Specific PCR Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:919519. [PMID: 35720607 PMCID: PMC9198554 DOI: 10.3389/fpls.2022.919519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/12/2022] [Indexed: 05/08/2023]
Abstract
Triticum timopheevii (2n = 28, A t A t GG) is a tetraploid wild relative species with great potential to increase the genetic diversity of hexaploid wheat Triticum aestivum (2n = 42, AABBDD) for various important agronomic traits. A breeding scheme that propagated advanced backcrossed populations of wheat-T. timopheevii introgression lines through further backcrossing and self-fertilisation resulted in the generation of 99 introgression lines (ILs) that carried 309 homozygous segments from the A t and G subgenomes of T. timopheevii. These introgressions contained 89 and 74 unique segments from the A t and G subgenomes, respectively. These overlapping segments covered 98.9% of the T. timopheevii genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all T. timopheevii chromosomes via varying sized segments except for chromosomes 3A t , 4G, and 6G. Homozygous ILs contained between one and eight of these introgressions with an average of three per introgression line. These homozygous introgressions were detected through the development of a set of 480 chromosome-specific Kompetitive allele specific PCR (KASP) markers that are well-distributed across the wheat genome. Of these, 149 were developed in this study based on single nucleotide polymorphisms (SNPs) discovered through whole genome sequencing of T. timopheevii. A majority of these KASP markers were also found to be T. timopheevii subgenome specific with 182 detecting A t subgenome and 275 detecting G subgenome segments. These markers showed that 98% of the A t segments had recombined with the A genome of wheat and 74% of the G genome segments had recombined with the B genome of wheat with the rest recombining with the D genome of wheat. These results were validated through multi-colour in situ hybridisation analysis. Together these homozygous wheat-T. timopheevii ILs and chromosome-specific KASP markers provide an invaluable resource to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change.
Collapse
Affiliation(s)
- Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- Surbhi Grewal,
| | - Manel Othmeni
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nicola Walter
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jack Walker
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Ian Phillip King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| |
Collapse
|
21
|
Genetic dissection for head blast resistance in wheat using two mapping populations. Heredity (Edinb) 2021; 128:402-410. [PMID: 34880420 PMCID: PMC9177698 DOI: 10.1038/s41437-021-00480-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/11/2022] Open
Abstract
Wheat head blast is a dangerous fungal disease in South America and has recently spread to Bangladesh and Zambia, threatening wheat production in those regions. Host resistance as an economical and environment-friendly management strategy has been heavily relied on, and understanding the resistance loci in the wheat genome is very helpful to resistance breeding. In the current study, two recombinant inbred line (RIL) populations, Alondra/Milan (with 296 RILs) and Caninde#2/Milan-S (with 254 RILs and Milan-S being a susceptible variant of Milan), were used for mapping QTL associated with head blast resistance in field experiments. Phenotyping was conducted in Quirusillas and Okinawa, Bolivia, and in Jashore, Bangladesh, during the 2017–18 and 2018–19 cropping cycles. The DArTseq® technology was employed to genotype the lines, along with four STS markers in the 2NS region. A QTL with consistent major effects was mapped on the 2NS/2AS translocation region in both populations, explaining phenotypic variation from 16.7 to 79.4% across experiments. Additional QTL were detected on chromosomes 2DL, 7AL, and 7DS in the Alondra/Milan population, and 2BS, 4AL, 5AS, 5DL, 7AS, and 7AL in the Caninde#2/Milan-S population, all showing phenotypic effects <10%. The results corroborated the important role of the 2NS/2AS translocation on WB resistance and identified a few novel QTL for possible deployment in wheat breeding. The low phenotypic effects of the non-2NS QTL warrantee further investigation for novel QTL with higher and more stable effects against WB, to alleviate the heavy reliance on 2NS-based resistance.
Collapse
|
22
|
Roy C, Juliana P, Kabir MR, Roy KK, Gahtyari NC, Marza F, He X, Singh GP, Chawade A, Joshi AK, Singh PK. New Genotypes and Genomic Regions for Resistance to Wheat Blast in South Asian Germplasm. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122693. [PMID: 34961165 PMCID: PMC8708018 DOI: 10.3390/plants10122693] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 05/12/2023]
Abstract
Wheat blast (WB) disease, since its first identification in Bangladesh in 2016, is now an established serious threat to wheat production in South Asia. There is a need for sound knowledge about resistance sources and associated genomic regions to assist breeding programs. Hence, a panel of genotypes from India and Bangladesh was evaluated for wheat blast resistance and a genome-wide association study (GWAS) was performed. Disease evaluation was done during five crop seasons-at precision phenotyping platform (PPPs) for wheat blast disease at Jashore (2018-19), Quirusillas (2018-19 and 2019-20) and Okinawa (2019 and 2020). Single nucleotide polymorphisms (SNP) across the genome were obtained using DArTseq genotyping-by-sequencing platform, and in total 5713 filtered markers were used. GWAS revealed 40 significant markers associated with WB resistance, of which 33 (82.5%) were in the 2NS/2AS chromosome segment and one each on seven chromosomes (3B, 3D, 4A, 5A, 5D, 6A and 6B). The 2NS markers contributed significantly in most of the environments, explaining an average of 33.4% of the phenotypic variation. Overall, 22.4% of the germplasm carried 2NS/2AS segment. So far, 2NS translocation is the only effective WB resistance source being used in the breeding programs of South Asia. Nevertheless, the identification of non-2NS/2AS genomic regions for WB resistance provides a hope to broaden and diversify resistance for this disease in years to come.
Collapse
Affiliation(s)
- Chandan Roy
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Sabour 813210, India;
| | - Philomin Juliana
- BISA/CIMMYT-India, NASC Complex, DPS Marg, New Delhi 110012, India; (P.J.); (A.K.J.)
| | - Muhammad R. Kabir
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur 5200, Bangladesh; (M.R.K.); (K.K.R.)
| | - Krishna K. Roy
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur 5200, Bangladesh; (M.R.K.); (K.K.R.)
| | - Navin C. Gahtyari
- ICAR–Vivekanand Parvatiya Krishi Anushandhan Sansthan, Almora 263601, India;
| | - Felix Marza
- Instituto Nacional de Innovación Agropecuaria y Forestal (INIAF), La Paz, Bolivia;
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico DF 06600, Mexico;
| | - Gyanendra P. Singh
- ICAR—Indian Institute of Wheat and Barley Research, Karnal, Maharaja Agarsain Marg, P.O. Box 158, Karnal 132001, India;
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, Sweden;
| | - Arun K. Joshi
- BISA/CIMMYT-India, NASC Complex, DPS Marg, New Delhi 110012, India; (P.J.); (A.K.J.)
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico DF 06600, Mexico;
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico DF 06600, Mexico;
- Correspondence:
| |
Collapse
|
23
|
Jordan KW, Bradbury PJ, Miller ZR, Nyine M, He F, Fraser M, Anderson J, Mason E, Katz A, Pearce S, Carter AH, Prather S, Pumphrey M, Chen J, Cook J, Liu S, Rudd JC, Wang Z, Chu C, Ibrahim AMH, Turkus J, Olson E, Nagarajan R, Carver B, Yan L, Taagen E, Sorrells M, Ward B, Ren J, Akhunova A, Bai G, Bowden R, Fiedler J, Faris J, Dubcovsky J, Guttieri M, Brown-Guedira G, Buckler E, Jannink JL, Akhunov ED. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. G3-GENES GENOMES GENETICS 2021; 12:6423995. [PMID: 34751373 PMCID: PMC9210282 DOI: 10.1093/g3journal/jkab390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/21/2021] [Indexed: 12/04/2022]
Abstract
To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value < 2 × 10−14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.
Collapse
Affiliation(s)
- Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Peter J Bradbury
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Zachary R Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Moses Nyine
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Max Fraser
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jim Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Esten Mason
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80521, USA
| | - Arron H Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Samuel Prather
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, 83210, USA
| | - Jason Cook
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Shuyu Liu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jackie C Rudd
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Zhen Wang
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Chenggen Chu
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Amir M H Ibrahim
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX, 79106, USA
| | - Jonathan Turkus
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Eric Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Ragupathi Nagarajan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Brett Carver
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74075, USA
| | - Ellie Taagen
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Mark Sorrells
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Brian Ward
- USDA-ARS, Plant Science Research Unit, Raleigh, NC, 27695, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Integrative Genomics Facility, Kansas State University, Manhattan, KS, 66506 USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Robert Bowden
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | - Jason Fiedler
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Justin Faris
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, 58102, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - Mary Guttieri
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66502, USA
| | | | - Ed Buckler
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Jean-Luc Jannink
- USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY, 14853, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| |
Collapse
|
24
|
Ghanbarnia K, Gourlie R, Amundsen E, Aboukhaddour R. The Changing Virulence of Stripe Rust in Canada from 1984 to 2017. PHYTOPATHOLOGY 2021; 111:1840-1850. [PMID: 33673753 DOI: 10.1094/phyto-10-20-0469-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is an important wheat disease worldwide. In this study, the P. striiformis f. sp. tritici population in Canada, representing a time period from 1984 to 2017, was analyzed for virulence diversity and geographical distribution. Virulence of 140 P. striiformis f. sp. tritici isolates was evaluated on 17 near-isogenic wheat lines in the 'Avocet S' background, each containing a single resistance gene along with an 18th line 'Tyee'. Seedlings were inoculated with a urediniospore/talc mixture and infection types were evaluated on a scale of 0 to 9. In total, 89 races were identified with various combinations of defeated Yr genes. Clear changes in pathogen virulence have been observed through time that are confirmed by clustering algorithms. The results showed that the tested P. striiformis f. sp. tritici isolates remained avirulent on Yr1, Yr5, and Yr15, and have very low frequency of virulence on Yr76, but had high frequencies of virulence on Yr6, Yr7, Yr8, Yr9, Yr17, Yr43, Yr44, YrTr1, and YrExp2. P. striiformis f. sp. tritici virulence spiked on Yr7, Yr8, and Yr9 for the first time in 2000, and on Yr10 and Yr27 in 2010. Overall, the predominant races in Canada were very similar to those reported in the United States (PSTv-37, PSTv-41, and PSTv-52), which indicates long-distance migration of P. striiformis f. sp. tritici from the United States to Canada. Sixty-four races had unique virulence combinations that had not been previously reported in the United States, which suggested that evolution of virulence/avirulence for host resistance by mutation at local scale, is possible. Analysis of diversity between Canadian isolates and races from the United States since 2010 showed that the P. striiformis f. sp. tritici population in western Canada is similar to that in the western states of the United States, and that the population in eastern Canada is similar to the eastern and/or central regions of the United States, supporting the hypothesis that specific P. striiformis f. sp. tritici populations in North America travel through different wind trajectories.
Collapse
Affiliation(s)
- Kaveh Ghanbarnia
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Ryan Gourlie
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Eric Amundsen
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| |
Collapse
|
25
|
Sharma S, Schulthess AW, Bassi FM, Badaeva ED, Neumann K, Graner A, Özkan H, Werner P, Knüpffer H, Kilian B. Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm. BIOLOGY 2021; 10:982. [PMID: 34681081 PMCID: PMC8533267 DOI: 10.3390/biology10100982] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/02/2022]
Abstract
Wheat (Triticum sp.) is one of the world's most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.
Collapse
Affiliation(s)
- Shivali Sharma
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco;
| | - Ekaterina D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey;
| | - Peter Werner
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| |
Collapse
|
26
|
Singh PK, Gahtyari NC, Roy C, Roy KK, He X, Tembo B, Xu K, Juliana P, Sonder K, Kabir MR, Chawade A. Wheat Blast: A Disease Spreading by Intercontinental Jumps and Its Management Strategies. FRONTIERS IN PLANT SCIENCE 2021; 12:710707. [PMID: 34367228 PMCID: PMC8343232 DOI: 10.3389/fpls.2021.710707] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/24/2021] [Indexed: 05/26/2023]
Abstract
Wheat blast (WB) caused by Magnaporthe oryzae pathotype Triticum (MoT) is an important fungal disease in tropical and subtropical wheat production regions. The disease was initially identified in Brazil in 1985, and it subsequently spread to some major wheat-producing areas of the country as well as several South American countries such as Bolivia, Paraguay, and Argentina. In recent years, WB has been introduced to Bangladesh and Zambia via international wheat trade, threatening wheat production in South Asia and Southern Africa with the possible further spreading in these two continents. Resistance source is mostly limited to 2NS carriers, which are being eroded by newly emerged MoT isolates, demonstrating an urgent need for identification and utilization of non-2NS resistance sources. Fungicides are also being heavily relied on to manage WB that resulted in increasing fungal resistance, which should be addressed by utilization of new fungicides or rotating different fungicides. Additionally, quarantine measures, cultural practices, non-fungicidal chemical treatment, disease forecasting, biocontrol etc., are also effective components of integrated WB management, which could be used in combination with varietal resistance and fungicides to obtain reasonable management of this disease.
Collapse
Affiliation(s)
- Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Navin C. Gahtyari
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan (VPKAS), Almora, India
| | - Chandan Roy
- Department of Plant Breeding and Genetics, BAC, Bihar Agricultural University, Sabour, India
| | - Krishna K. Roy
- Bangladesh Wheat and Maize Research Institute (BWMRI), Dinajpur, Bangladesh
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - B. Tembo
- Zambia Agricultural Research Institute (ZARI), Chilanga, Zambia
| | - Kaijie Xu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Kai Sonder
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Muhammad R. Kabir
- Bangladesh Wheat and Maize Research Institute (BWMRI), Dinajpur, Bangladesh
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| |
Collapse
|
27
|
Fernández-Campos M, Huang YT, Jahanshahi MR, Wang T, Jin J, Telenko DEP, Góngora-Canul C, Cruz CD. Wheat Spike Blast Image Classification Using Deep Convolutional Neural Networks. FRONTIERS IN PLANT SCIENCE 2021; 12:673505. [PMID: 34220894 PMCID: PMC8248543 DOI: 10.3389/fpls.2021.673505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/10/2021] [Indexed: 05/21/2023]
Abstract
Wheat blast is a threat to global wheat production, and limited blast-resistant cultivars are available. The current estimations of wheat spike blast severity rely on human assessments, but this technique could have limitations. Reliable visual disease estimations paired with Red Green Blue (RGB) images of wheat spike blast can be used to train deep convolutional neural networks (CNN) for disease severity (DS) classification. Inter-rater agreement analysis was used to measure the reliability of who collected and classified data obtained under controlled conditions. We then trained CNN models to classify wheat spike blast severity. Inter-rater agreement analysis showed high accuracy and low bias before model training. Results showed that the CNN models trained provide a promising approach to classify images in the three wheat blast severity categories. However, the models trained on non-matured and matured spikes images showing the highest precision, recall, and F1 score when classifying the images. The high classification accuracy could serve as a basis to facilitate wheat spike blast phenotyping in the future.
Collapse
Affiliation(s)
| | - Yu-Ting Huang
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN, United States
| | - Mohammad R. Jahanshahi
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN, United States
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, United States
| | - Tao Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, United States
| | - Jian Jin
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, United States
| | - Darcy E. P. Telenko
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Carlos Góngora-Canul
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Tecnológico Nacional de México/IT Conkal, Conkal, Yucatán, Mexico
| | - C. D. Cruz
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| |
Collapse
|
28
|
Guo H, Du Q, Xie Y, Xiong H, Zhao L, Gu J, Zhao S, Song X, Islam T, Liu L. Identification of Rice Blast Loss-of-Function Mutant Alleles in the Wheat Genome as a New Strategy for Wheat Blast Resistance Breeding. Front Genet 2021; 12:623419. [PMID: 34093638 PMCID: PMC8170139 DOI: 10.3389/fgene.2021.623419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Blast is caused by the host-specific lineages of the fungus Magnaporthe oryzae and is the most important destructive disease in major crop plants, including rice and wheat. The first wheat blast outbreak that occurred in Bangladesh in 2016 and the recent epidemic in Zambia were caused by the M. oryzae Triticum (MoT) pathotype, a fungal lineage belonging to M. oryzae. Although a few reported wheat cultivars show modest resistance to MoT, the patterns of genetic variation and diversity of this pathotype make it crucial to identify additional lines of resistant wheat germplasm. Nearly 40 rice blast resistant and susceptible genes have so far been cloned. Here, we used BLAST analysis to locate two rice blast susceptible genes in the wheat reference genome, bsr-d1 and bsr-k1, and identified six identical homologous genes located on subgenomes A, B, and D. We uncovered a total of 171 single nucleotide polymorphisms (SNPs) in an ethyl methanesulfonate (EMS)-induced population, with mutation densities ranging from 1/1107.1 to 1/230.7 kb through Targeting Induced Local Lesions IN Genomes (TILLING) by sequencing. These included 81 SNPs located in exonic and promoter regions, and 13 coding alleles that are predicted to have severe effects on protein function, including two pre-mature mutants that might affect wheat blast resistance. The loss-of-function alleles identified in this study provide insights into new wheat blast resistant lines, which represent a valuable breeding resource.
Collapse
Affiliation(s)
- Huijun Guo
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qidi Du
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yongdun Xie
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiyun Song
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Luxiang Liu
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
29
|
He X, Juliana P, Kabir MR, Roy KK, Islam R, Marza F, Peterson G, Singh GP, Chawade A, Joshi AK, Singh RP, Singh PK. Screening and Mapping for Head Blast Resistance in a Panel of CIMMYT and South Asian Bread Wheat Germplasm. Front Genet 2021; 12:679162. [PMID: 34054928 PMCID: PMC8155635 DOI: 10.3389/fgene.2021.679162] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/21/2021] [Indexed: 01/26/2023] Open
Abstract
Wheat blast (WB) is a destructive disease in South America and its first outbreak in Bangladesh in 2016 posed a great risk to food security of South Asian countries. A genome wide association study (GWAS) was conducted on a diverse panel of 184 wheat genotypes from South Asia and CIMMYT. Phenotyping was conducted in eight field experiments in Bolivia and Bangladesh and a greenhouse experiment in the United States. Genotypic data included 11,401 SNP markers of the Illumina Infinium 15K BeadChip and four additional STS markers on the 2NS/2AS translocation region. Accessions with stable WB resistance across experiments were identified, which were all 2NS carriers. Nevertheless, a dozen moderately resistant 2AS lines were identified, exhibiting big variation among experiments. Significant marker-trait associations (MTA) were detected on chromosomes 1BS, 2AS, 6BS, and 7BL; but only MTAs on 2AS at the 2NS/2AS translocation region were consistently significant across experiments. The resistant accessions identified in this study could be used in production in South Asian countries as a preemptive strategy to prevent WB outbreak.
Collapse
Affiliation(s)
- Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Muhammad R Kabir
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Bangladesh
| | - Krishna K Roy
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Bangladesh
| | - Rabiul Islam
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Bangladesh
| | - Felix Marza
- Instituto Nacional de Innovación Agropecuaria y Forestal (INIAF), La Paz, Bolivia
| | - Gary Peterson
- United States Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MD, United States
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| |
Collapse
|
30
|
Adonina IG, Timonova EM, Salina EA. Introgressive Hybridization of Common Wheat: Results and Prospects. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421030029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
31
|
Identification of Fusarium head blight resistance loci in two Brazilian wheat mapping populations. PLoS One 2021; 16:e0248184. [PMID: 33684152 PMCID: PMC7939358 DOI: 10.1371/journal.pone.0248184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/19/2021] [Indexed: 11/19/2022] Open
Abstract
Fusarium head blight (FHB) is a disease of wheat (Triticum aestivum L.) that causes major yield losses in South America, as well as many other wheat growing regions around the world. FHB results in low quality, contaminated grain due to the production of mycotoxins such as deoxynivalenol (DON). In Brazil, FHB outbreaks are increasing in frequency and are currently controlled by fungicides which are costly and potentially harmful to the wider environment. To identify the genetic basis of resistance to FHB in Brazilian wheat, two mapping populations (Anahuac 75 × BR 18-Terena and BR 18-Terena × BRS 179) segregating for FHB resistance were phenotyped and quantitative trait loci (QTL) analysis was undertaken to identify genomic regions associated with FHB-related traits. A total of 14 QTL associated with FHB visual symptoms were identified, each of which explained 3.7–17.3% of the phenotypic variance. Two of these QTL were stable across environments. This suggests FHB resistance in Anahuac 75, BR 18-Terena and BRS 179 is controlled by multiple genetic loci that confer relatively minor differences in resistance. A major, novel QTL associated with DON accumulation was also identified on chromosome 4B (17.8% of the phenotypic variance), as well as a major QTL associated with thousand-grain weight on chromosome 6B (16.8% phenotypic variance). These QTL could be useful breeding targets, when pyramided with major sources of resistance such as Fhb1, to improve grain quality and reduce the reliance on fungicides in Brazil and other countries affected by FHB.
Collapse
|
32
|
Dadshani S, Mathew B, Ballvora A, Mason AS, Léon J. Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach. Sci Rep 2021; 11:5527. [PMID: 33750919 PMCID: PMC7970893 DOI: 10.1038/s41598-021-85226-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/25/2021] [Indexed: 01/31/2023] Open
Abstract
Marker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, "Cardos" (registered in 1998) which was the first among the panel to contain this translocation. A "selective sweep" for this important translocation region on chromosome 2AS was found, putatively linked to plant response to biotic stress factors. Our approach helps in overcoming the drawbacks of incorrectly anchored markers on the wheat reference assembly and facilitates detection of selective sweeps for important agronomic traits.
Collapse
Affiliation(s)
- Said Dadshani
- Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of Bonn, Bonn, Germany.
| | - Boby Mathew
- Bayer CropScience, Monheim am Rhein, Germany
| | - Agim Ballvora
- Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of Bonn, Bonn, Germany
| | - Annaliese S Mason
- Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of Bonn, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, University of Bonn, Bonn, Germany.
| |
Collapse
|
33
|
Introgression and genetic mapping of leaf rust and stripe rust resistance in Aegilops triuncialis. J Genet 2021. [DOI: 10.1007/s12041-020-01253-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
34
|
Sharma A, Srivastava P, Mavi GS, Kaur S, Kaur J, Bala R, Singh TP, Sohu VS, Chhuneja P, Bains NS, Singh GP. Resurrection of Wheat Cultivar PBW343 Using Marker-Assisted Gene Pyramiding for Rust Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:570408. [PMID: 33643338 PMCID: PMC7905314 DOI: 10.3389/fpls.2021.570408] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 01/07/2021] [Indexed: 05/29/2023]
Abstract
Wheat variety PBW343, released in India in 1995, became the most widely grown cultivar in the country by the year 2000 owing to its wide adaptability and yield potential. It initially succumbed to leaf rust, and resistance genes Lr24 and Lr28 were transferred to PBW343. After an unbroken reign of about 10 years, the virulence against gene Yr27 made PBW343 susceptible to stripe rust. Owing to its wide adaptability and yield potential, PBW343 became the prime target for marker-assisted introgression of stripe rust resistance genes. The leaf rust-resistant versions formed the base for pyramiding stripe rust resistance genes Yr5, Yr10, Yr15, Yr17, and Yr70, in different introgression programs. Advanced breeding lines with different gene combinations, PBW665, PBW683, PBW698, and PBW703 were tested in national trials but could not be released as varieties. The genes from alien segments, Aegilops ventricosa (Lr37/Yr17/Sr38) and Aegilops umbellulata (Lr76/Yr70), were later pyramided in PBW343. Modified marker-assisted backcross breeding was performed, and 81.57% of the genetic background was recovered in one of the selected derivative lines, PBW723. This line was evaluated in coordinated national trials and was released for cultivation under timely sown irrigated conditions in the North Western Plain Zone of India. PBW723 yields an average of 58.0 qtl/ha in Punjab with high potential yields. The genes incorporated are susceptible to stripe rust individually, but PBW723 with both genes showed enhanced resistance. Three years post-release, PBW723 occupies approximately 8-9% of the cultivated area in the Punjab state. A regular inflow of diverse resistant genes, their rapid mobilization to most productive backgrounds, and keeping a close eye on pathogen evolution is essential to protect the overall progress for productivity and resistance in wheat breeding, thus helping breeders to keep pace with pathogen evolution.
Collapse
Affiliation(s)
- Achla Sharma
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Puja Srivastava
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - G. S. Mavi
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Jaspal Kaur
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Ritu Bala
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - V. S. Sohu
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Navtej S. Bains
- Department of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana, India
| | - G. P. Singh
- Indian Institute of Wheat & Barley Research, Karnal, India
| |
Collapse
|
35
|
Gao L, Koo DH, Juliana P, Rife T, Singh D, Lemes da Silva C, Lux T, Dorn KM, Clinesmith M, Silva P, Wang X, Spannagl M, Monat C, Friebe B, Steuernagel B, Muehlbauer GJ, Walkowiak S, Pozniak C, Singh R, Stein N, Mascher M, Fritz A, Poland J. The Aegilops ventricosa 2N vS segment in bread wheat: cytology, genomics and breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:529-542. [PMID: 33184704 PMCID: PMC7843486 DOI: 10.1007/s00122-020-03712-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/17/2020] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, 'Jagger' and 'CDC Stanley,' and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.
Collapse
Affiliation(s)
- Liangliang Gao
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Dal-Hoe Koo
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Philomin Juliana
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237, Texcoco, CP, Mexico
| | - Trevor Rife
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Daljit Singh
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | | | - Thomas Lux
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Kevin M Dorn
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
- United States Department of Agriculture Agricultural Research Service, 1701 Centre Avenue, Fort Collins, CO, 80526, USA
| | - Marshall Clinesmith
- Department of Agronomy, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Paula Silva
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
- Programa de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Ruta 50, km 11.5, 70006, Colonia, Uruguay
| | - Xu Wang
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Cecile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
| | - Bernd Friebe
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Burkhard Steuernagel
- John Innes Centre, Computational and Systems Biology, Norwich Research Park, Norwich, NR47UH, UK
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, Saint Paul, MN, 55108, USA
| | - Sean Walkowiak
- Crop Development Centre, University of Saskatchewan, Agriculture Building, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB, Canada
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Agriculture Building, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Ravi Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237, Texcoco, CP, Mexico
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, 37073, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Allan Fritz
- Department of Agronomy, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Jesse Poland
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS, 66506, USA.
| |
Collapse
|
36
|
Mills KB, Salgado JD, Cruz CD, Valent B, Madden LV, Paul PA. Comparing the Temporal Development of Wheat Spike Blast Epidemics in a Region of Bolivia Where the Disease Is Endemic. PLANT DISEASE 2021; 105:96-107. [PMID: 33197378 DOI: 10.1094/pdis-04-20-0876-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Epidemics of wheat blast, caused the Triticum pathotype of Magnaporthe oryzae, were studied in the Santa Cruz del la Sierra region of Bolivia to quantify and compare the temporal dynamics of the disease under different growing conditions. Six plots of a susceptible wheat cultivar were planted at Cuatro Cañadas (CC), Okinawa 1 (OK1), and Okinawa 2 (OK2) in 2015. Spike blast incidence (INC) and severity (SEV) and leaf blast severity (LEAF) were quantified in each plot at regular intervals on a 10 × 10 grid (n = 100 clusters of spikes), beginning at head emergence (Feekes growth stage 10.5), for a total of nine assessments at CC, six at OK1, and six at OK2. Spike blast increased over time for 20 to 30 days before approaching a mean INC of 100% and a mean SEV of 60 to 75%. The logistic model was the most appropriate for describing the temporal dynamics of spike blast. The highest absolute rates of disease increase occurred earliest at OK1 and latest at OK2, and in all cases it coincided with major rain events. Estimated y0 values (initial blast intensity) were significantly (P < 0.05) higher at OK1 than at CC or OK2, whereas rL values (the logistic rate parameter) were significantly higher at OK2 than at CC or OK1. It took about 10 fewer days for SEV to reach 10, 15, or 20% at OK1 compared with OK2 and CC. Based on survival analyses, the survivor functions for time to 10, 15 and 20% SEV (ts) were significantly different between OK1 and the other locations, with the probabilities of SEV reaching the thresholds being highest at OK1. LEAF at 21 days after Feekes 10.5 had a significant effect on ts at OK1. For every 5% increase in LEAF, the chance of SEV reaching the thresholds by day 21 increased by 30 to 55%.
Collapse
Affiliation(s)
- Karasi B Mills
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - Jorge D Salgado
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - Christian D Cruz
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Laurence V Madden
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| | - Pierce A Paul
- Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691
| |
Collapse
|
37
|
Inoue Y, Vy TTP, Tani D, Tosa Y. Suppression of wheat blast resistance by an effector of Pyricularia oryzae is counteracted by a host specificity resistance gene in wheat. THE NEW PHYTOLOGIST 2021; 229:488-500. [PMID: 32852846 DOI: 10.1111/nph.16894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Wheat blast caused by the Triticum pathotype of Pyricularia oryzae poses a serious threat to wheat production in South America and Asia and is now becoming a pandemic disease. Here, we show that Rmg8, a promising wheat gene for resistance breeding, is suppressed by PWT4, an effector gene of P. oryzae, and in turn that the suppression is counteracted by Rwt4, a wheat gene recognizing PWT4. When PWT4 was introduced into a wheat blast isolate carrying AVR-Rmg8 (an avirulence gene corresponding to Rmg8), PWT4 suppressed wheat resistance conferred by Rmg8. PWT4 did not alter the expression of AVR-Rmg8, but higher expression of PWT4 led to more efficient suppression. This suppression was observed in rwt4 carriers, but not in Rwt4 carriers, indicating that it is counteracted by Rwt4. PWT4 was assumed to have been horizontally transferred from a weed-associated cryptic species, P. pennisetigena, to an Avena isolate of P. oryzae in Brazil. This implies a potential risk of the acquisition of PWT4 by the wheat blast fungus and the 'breakdown' of Rmg8. We suggest that Rmg8 should be introduced together with Rwt4 into a wheat cultivar when it is used for resistance breeding.
Collapse
Affiliation(s)
- Yoshihiro Inoue
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Trinh Thi Phuoug Vy
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Daichi Tani
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan
| |
Collapse
|
38
|
Multiple wheat genomes reveal global variation in modern breeding. Nature 2020; 588:277-283. [PMID: 33239791 PMCID: PMC7759465 DOI: 10.1038/s41586-020-2961-x] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022]
Abstract
Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars. Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.
Collapse
|
39
|
Ayalew H, Sorrells ME, Carver BF, Baenziger PS, Ma XF. Selection signatures across seven decades of hard winter wheat breeding in the Great Plains of the United States. THE PLANT GENOME 2020; 13:e20032. [PMID: 33217215 DOI: 10.1002/tpg2.20032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/15/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Classical plant breeding has been instrumental in changing the genetic makeup of crop plants for better ecological adaptation and improved quality. This paper provides insights of the genomic changes effected in hard winter wheat (Triticum aestivum L.) through decades of breeding and selection in the Great Plains of the United States. Population structure and differentiation analyses were conducted on 185 wheat cultivars released from 1943 to 2013. Cultivars were grouped into four distinct clusters using discriminant analysis of principal components (DAPC). One of the clusters was unique in that 15 out of the 18 individuals were recent releases (2000-2010), while 12 of the 18 shared the cultivar 'Jagger' in their genetic background. Jagger carries a 2NS/2AS translocation segment from Aegilops ventricosa, an important segment for resistance to several foliar diseases. Using the outlier approach, Wright's population fixation index (Fst) identified 450 loci that were directionally selected. The largest signature of selection was found on chromosome 2A. Genetic diversity was high while the inbreeding coefficient was low, indicating extensive hybridization and germplasm exchange among breeding programs within the region. Foliar disease pressure and selection for resistance helped shape the microevolution of wheat in the southern Great Plains. The results showed that high genetic diversity remains in hard winter wheat cultivars adapted to the Great Plains of the USA, and modern plant breeding did not cause any sizable reduction in genetic diversity of the crop in this region.
Collapse
Affiliation(s)
| | - Mark E Sorrells
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Brett F Carver
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Xue-Feng Ma
- Noble Research Institute, Ardmore, OK, 73401, USA
| |
Collapse
|
40
|
Horo JT, Asuke S, Vy TTP, Tosa Y. Effectiveness of the Wheat Blast Resistance Gene Rmg8 in Bangladesh Suggested by Distribution of an AVR-Rmg8 Allele in the Pyricularia oryzae Population. PHYTOPATHOLOGY 2020; 110:1802-1807. [PMID: 32960712 DOI: 10.1094/phyto-03-20-0073-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Wheat blast caused by the Triticum pathotype of Pyricularia oryzae was first reported in 1985 in Brazil and recently spread to Bangladesh. We tested whether Rmg8 and RmgGR119, recently identified resistance genes, were effective against Bangladeshi isolates of the pathogen. Common wheat accessions carrying Rmg8 alone (IL191) or both Rmg8 and RmgGR119 (GR119) were inoculated with Brazilian isolates (Br48, Br5, and Br116.5) and Bangladeshi isolates (T-108 and T-109). Br48, T-108, and T-109 carried the eI type of AVR-Rmg8 (the avirulence gene corresponding to Rmg8) while Br5 and Br116.5 carried its variants, eII and eII' types, respectively. Detached primary leaves of IL191 and GR119 were resistant to all isolates at 25°C. At a higher temperature (28°C), their resistance was still effective against the eI carriers but was reduced to a low level against the eII/eII' carriers. A survey of databases and sequence analyses revealed that all Bangladeshi isolates carried the eI type which induced a higher level of resistance than the eII/eII' types. The resistance of IL191 (Rmg8/-) to the eI carriers was maintained even at the heading stage and at the higher temperature. In addition, GR119 (Rmg8/RmgGR119) displayed higher levels of resistance than IL191 at this stage. These results suggest that Rmg8 combined with RmgGR119 will be useful in breeding for resistance against wheat blast in Bangladesh.
Collapse
Affiliation(s)
- Jemal Tola Horo
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Trinh Thi Phuong Vy
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| |
Collapse
|
41
|
Juliana P, He X, Kabir MR, Roy KK, Anwar MB, Marza F, Poland J, Shrestha S, Singh RP, Singh PK. Genome-wide association mapping for wheat blast resistance in CIMMYT's international screening nurseries evaluated in Bolivia and Bangladesh. Sci Rep 2020; 10:15972. [PMID: 33009436 PMCID: PMC7532450 DOI: 10.1038/s41598-020-72735-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022] Open
Abstract
Wheat blast caused by the fungus Magnaporthe oryzae pathotype Triticum (MoT) is an emerging threat to wheat production. To identify genomic regions associated with blast resistance against MoT isolates in Bolivia and Bangladesh, we performed a large genome-wide association mapping study using 8607 observations on 1106 lines from the International Maize and Wheat Improvement Centre’s International Bread Wheat Screening Nurseries (IBWSNs) and Semi-Arid Wheat Screening Nurseries (SAWSNs). We identified 36 significant markers on chromosomes 2AS, 3BL, 4AL and 7BL with consistent effects across panels or site-years, including 20 markers that were significant in all the 49 datasets and tagged the 2NS translocation from Aegilops ventricosa. The mean blast index of lines with and without the 2NS translocation was 2.7 ± 4.5 and 53.3 ± 15.9, respectively, that substantiates its strong effect on blast resistance. Furthermore, we fingerprinted a large panel of 4143 lines for the 2NS translocation that provided excellent insights into its frequency over years and indicated its presence in 94.1 and 93.7% of lines in the 2019 IBWSN and SAWSN, respectively. Overall, this study reinforces the effectiveness of the 2NS translocation for blast resistance and emphasizes the urgent need to identify novel non-2NS sources of blast resistance.
Collapse
Affiliation(s)
- Philomin Juliana
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Muhammad R Kabir
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur, Bangladesh
| | - Krishna K Roy
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur, Bangladesh
| | - Md Babul Anwar
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur, Bangladesh
| | - Felix Marza
- Instituto Nacional de Innovación Agropecuaria y Forestal (INIAF), La Paz, Bolivia
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| |
Collapse
|
42
|
He X, Kabir MR, Roy KK, Anwar MB, Xu K, Marza F, Odilbekov F, Chawade A, Duveiller E, Huttner E, Singh PK. QTL mapping for field resistance to wheat blast in the Caninde#1/Alondra population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2673-2683. [PMID: 32488302 PMCID: PMC7419448 DOI: 10.1007/s00122-020-03624-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/23/2020] [Indexed: 05/26/2023]
Abstract
Wheat blast resistance in Caninde#1 is controlled by a major QTL on 2NS/2AS translocation and multiple minor QTL in an additive mode. Wheat blast (WB) is a devastating disease in South America, and it recently also emerged in Bangladesh. Host resistance to WB has relied heavily on the 2NS/2AS translocation, but the responsible QTL has not been mapped and its phenotypic effects in different environments have not been reported. In the current study, a recombinant inbred line population with 298 progenies was generated, with the female and male parents being Caninde#1 (with 2NS) and Alondra (without 2NS), respectively. Phenotyping was carried out in two locations in Bolivia, namely Quirusillas and Okinawa, and one location in Bangladesh, Jashore, with two sowing dates in each of the two cropping seasons in each location, during the years 2017-2019. Genotyping was performed with the DArTseq® technology along with five previously reported STS markers in the 2NS region. QTL mapping identified a major and consistent QTL on 2NS/2AS region, explaining between 22.4 and 50.1% of the phenotypic variation in different environments. Additional QTL were detected on chromosomes 1AS, 2BL, 3AL, 4BS, 4DL and 7BS, all additive to the 2NS QTL and showing phenotypic effects less than 10%. Two codominant STS markers, WGGB156 and WGGB159, were linked proximally to the 2NS/2AS QTL with a genetic distance of 0.9 cM, being potentially useful in marker-assisted selection.
Collapse
Affiliation(s)
- Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Muhammad Rezaul Kabir
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur, Bangladesh
| | - Krishna K Roy
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur, Bangladesh
| | - Md Babul Anwar
- Bangladesh Wheat and Maize Research Institute (BWMRI), Nashipur, Dinajpur, Bangladesh
| | - Kaijie Xu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Felix Marza
- Instituto Nacional de Innovación Agropecuaria y Forestal (INIAF), La Paz, Bolivia
| | - Firuz Odilbekov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053, Alnarp, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053, Alnarp, Sweden
| | - Etienne Duveiller
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Eric Huttner
- Australian Centre for International Agricultural Research, 38 Thynne St, Bruce, ACT, 2617, Australia
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| |
Collapse
|
43
|
Goddard R, Steed A, Chinoy C, Ferreira JR, Scheeren PL, Maciel JLN, Caierão E, Torres GAM, Consoli L, Santana FM, Fernandes JMC, Simmonds J, Uauy C, Cockram J, Nicholson P. Dissecting the genetic basis of wheat blast resistance in the Brazilian wheat cultivar BR 18-Terena. BMC PLANT BIOLOGY 2020; 20:398. [PMID: 32854622 PMCID: PMC7451118 DOI: 10.1186/s12870-020-02592-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/12/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Wheat blast, caused by Magnaporthe oryzae Triticum (MoT) pathotype, is a global threat to wheat (Triticum aestivum L.) production. Few blast resistance (R) genes have been identified to date, therefore assessing potential sources of resistance in wheat is important. The Brazilian wheat cultivar BR 18-Terena is considered one of the best sources of resistance to blast and has been widely used in Brazilian breeding programmes, however the underlying genetics of this resistance are unknown. RESULTS BR 18-Terena was used as the common parent in the development of two recombinant inbred line (RIL) F6 populations with the Brazilian cultivars Anahuac 75 and BRS 179. Populations were phenotyped for resistance at the seedling and heading stage using the sequenced MoT isolate BR32, with transgressive segregation being observed. Genetic maps containing 1779 and 1318 markers, were produced for the Anahuac 75 × BR 18-Terena and BR 18-Terena × BRS 179 populations, respectively. Five quantitative trait loci (QTL) associated with seedling resistance, on chromosomes 2B, 4B (2 QTL), 5A and 6A, were identified, as were four QTL associated with heading stage resistance (1A, 2B, 4A and 5A). Seedling and heading stage QTL did not co-locate, despite a significant positive correlation between these traits, indicating that resistance at these developmental stages is likely to be controlled by different genes. BR 18-Terena provided the resistant allele for six QTL, at both developmental stages, with the largest phenotypic effect conferred by a QTL being 24.8% suggesting that BR 18-Terena possesses quantitative resistance. Haplotype analysis of 100 Brazilian wheat cultivars indicates that 11.0% of cultivars already possess a BR 18-Terena-like haplotype for more than one of the identified heading stage QTL. CONCLUSIONS This study suggests that BR 18-Terena possesses quantitative resistance to wheat blast, with nine QTL associated with resistance at either the seedling or heading stage being detected. Wheat blast resistance is also largely tissue-specific. Identification of durable quantitative resistances which can be combined with race-specific R gene-mediated resistance is critical to effectively control wheat blast. Collectively, this work facilitates marker-assisted selection to develop new varieties for cultivation in regions at risk from this emerging disease.
Collapse
Affiliation(s)
- Rachel Goddard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK.
| | - Andrew Steed
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Catherine Chinoy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | | | | | | | | | | | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| |
Collapse
|
44
|
Fernández-Campos M, Góngora-Canul C, Das S, Kabir MR, Valent B, Cruz CD. Epidemiological Criteria to Support Breeding Tactics Against the Emerging, High-Consequence Wheat Blast Disease. PLANT DISEASE 2020; 104:2252-2261. [PMID: 32584156 DOI: 10.1094/pdis-12-19-2672-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Plant disease epidemiology can make a significant contribution for cultivar selection by elucidating the principles of an epidemic under different levels of resistance. For emerging diseases as wheat blast (WB), epidemiological parameters can provide support for better selection of genetic resources. Field experiments were conducted at two locations in Bolivia in 2018-2019 to characterize the temporal dynamics of the disease on 10 cultivars with different levels of reaction to WB. Logistic models best (R2 = 0.70-0.96) fit the disease progress curve in all cultivars followed by Gompertz (R2 = 0.64-0.94), providing additional evidence of a polycyclic disease. Total area under disease progress curve (tAUDPC), final disease severity (Ymax), and logistic apparent infection rates (rL*) were shown to be appropriate epidemiological parameters for describing resistance and cultivar selection. Cultivars that showed a high spike AUDPC (sAUDPC) showed a high leaf AUDPC (lAUDPC). tAUPDC, Ymax, and rL* were positively correlated among them (P < 0.01) and all were negatively correlated with grain weight (P < 0.01). Based on the epidemiological parameters used, cultivars that showed resistance to WB were Urubó, San Pablo, and AN-120, which were previously reported to have effective resistance against the disease under field conditions. The information generated could help breeding programs to make technical decisions about relevant epidemiological parameters to consider prior to cultivar release.
Collapse
Affiliation(s)
- M Fernández-Campos
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| | - C Góngora-Canul
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| | - S Das
- Uttar Banga Krishi Viswavidyalaya, Pundibari, Coochbehar, West Bengal 736165, India
| | - M R Kabir
- Bangladesh Wheat and Maize Research Institute, Nishapur, Dinajpur, Bangladesh
| | - B Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - C D Cruz
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| |
Collapse
|
45
|
Gongora-Canul C, Salgado JD, Singh D, Cruz AP, Cotrozzi L, Couture J, Rivadeneira MG, Cruppe G, Valent B, Todd T, Poland J, Cruz CD. Temporal Dynamics of Wheat Blast Epidemics and Disease Measurements Using Multispectral Imagery. PHYTOPATHOLOGY 2020; 110:393-405. [PMID: 31532351 DOI: 10.1094/phyto-08-19-0297-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wheat blast is a devastating disease caused by the Triticum pathotype of Magnaporthe oryzae. M. oryzae Triticum is capable of infecting leaves and spikes of wheat. Although symptoms of wheat spike blast (WSB) are quite distinct in the field, symptoms on leaves (WLB) are rarely reported because they are usually inconspicuos. Two field experiments were conducted in Bolivia to characterize the change in WLB and WSB intensity over time and determine whether multispectral imagery can be used to accurately assess WSB. Disease progress curves (DPCs) were plotted from WLB and WSB data, and regression models were fitted to describe the nature of WSB epidemics. WLB incidence and severity changed over time; however, the mean WLB severity was inconspicuous before wheat began spike emergence. Overall, both Gompertz and logistic models helped to describe WSB intensity DPCs fitting classic sigmoidal shape curves. Lin's concordance correlation coefficients were estimated to measure agreement between visual estimates and digital measurements of WSB intensity and to estimate accuracy and precision. Our findings suggest that the change of wheat blast intensity in a susceptible host population over time does not follow a pattern of a monocyclic epidemic. We have also demonstrated that WSB severity can be quantified using a digital approach based on nongreen pixels. Quantification was precise (0.96 < r> 0.83) and accurate (0.92 < ρ > 0.69) at moderately low to high visual WSB severity levels. Additional sensor-based methods must be explored to determine their potential for detection of WLB and WSB at earlier stages.
Collapse
Affiliation(s)
- C Gongora-Canul
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| | - J D Salgado
- Department of Plant Pathology, The Ohio State University, Wooster, OH 44691, U.S.A
| | - D Singh
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - A P Cruz
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| | - L Cotrozzi
- Department of Agriculture, Food and Environment, University of Pisa, Italy
| | - J Couture
- Departments of Entomology and Forestry and Natural Resources and Center for Plant Biology, Purdue University, 901 W. State St., West Lafayette, IN 47907, U.S.A
| | - M G Rivadeneira
- Centro de Investigación Agrícola Tropical, Estación Experimental Agrícola de Saavedra-EEAS, Santa Cruz, Bolivia
| | - G Cruppe
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - B Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - T Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - J Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - C D Cruz
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| |
Collapse
|
46
|
Cruppe G, Cruz CD, Peterson G, Pedley K, Asif M, Fritz A, Calderon L, Lemes da Silva C, Todd T, Kuhnem P, Singh PK, Singh RP, Braun HJ, Barma NCD, Valent B. Novel Sources of Wheat Head Blast Resistance in Modern Breeding Lines and Wheat Wild Relatives. PLANT DISEASE 2020; 104:35-43. [PMID: 31660799 DOI: 10.1094/pdis-05-19-0985-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Wheat head blast (WHB), caused by the fungus Magnaporthe oryzae pathotype triticum, is a devastating disease affecting South America and South Asia. Despite 30 years of intensive effort, the 2NVS translocation from Aegilops ventricosa contains the only useful source of resistance to WHB effective against M. oryzae triticum isolates. The objective of this study was to identify non-2NVS sources of resistance to WHB among elite cultivars, breeding lines, landraces, and wild-relative accessions. Over 780 accessions were evaluated under field and greenhouse conditions in Bolivia, greenhouse conditions in Brazil, and at two biosafety level-3 laboratories in the United States. The M. oryzae triticum isolates B-71 (2012), 008 (2015), and 16MoT001 (2016) were used for controlled experiments, while isolate 008 was used for field experiments. Resistant and susceptible checks were included in all experiments. Under field conditions, susceptible spreaders were inoculated at the tillering stage to guarantee sufficient inoculum. Disease incidence and severity were evaluated as the average rating for each 1-m-row plot. Under controlled conditions, heads were inoculated after full emergence and individually rated for percentage of diseased spikelets. The diagnostic marker Ventriup-LN2 was used to test for the presence of the 2NVS translocation. Four non-2NVS spring wheat International Maize and Wheat Improvement Center breeding lines (CM22, CM49, CM52, and CM61) and four wheat wild-relatives (A. tauschii TA10142, TA1624, TA1667, and TA10140) were identified as resistant (<5% of severity) or moderately resistant (5 to <25% severity) to WHB. Experiments conducted at the seedling stage showed little correlation with disease severity at the head stage. M. oryzae triticum isolate 16MoT001 was significantly more aggressive against 2NVS-based varieties. The low frequency of WHB resistance and the increase in aggressiveness of newer M. oryzae triticum isolates highlight the threat that the disease poses to wheat production worldwide and the urgent need to identify and characterize new resistance genes that can be used in breeding for durably resistant varieties.
Collapse
Affiliation(s)
- Giovana Cruppe
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Christian D Cruz
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Gary Peterson
- United States Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MD 21702, U.S.A
| | - Kerry Pedley
- United States Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, MD 21702, U.S.A
| | - Mohammad Asif
- Heartland Plant Innovations, Manhattan, KS 66506, U.S.A
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Lidia Calderon
- Asociacion de Productores de Oleaginosas y Trigo, Santa Cruz de la Sierra, Bolivia
| | | | - Tim Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Paulo Kuhnem
- Biotrigo Genetica, Passo Fundo, Rio Grande do Sul 99052, Brazil
| | - Pawan K Singh
- International Maize and Wheat Improvement Center, El Batan, Texcoco 56237, Mexico
| | - Ravi P Singh
- International Maize and Wheat Improvement Center, El Batan, Texcoco 56237, Mexico
| | - Hans-Joachim Braun
- International Maize and Wheat Improvement Center, El Batan, Texcoco 56237, Mexico
| | - Naresh C D Barma
- Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| |
Collapse
|
47
|
Aucique-Pérez CE, Resende RS, Neto LBC, Dornelas F, DaMatta FM, Rodrigues FÁ. Picolinic acid spray stimulates the antioxidative metabolism and minimizes impairments on photosynthesis on wheat leaves infected by Pyricularia oryzae. PHYSIOLOGIA PLANTARUM 2019; 167:628-644. [PMID: 30628091 DOI: 10.1111/ppl.12917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/26/2018] [Indexed: 05/26/2023]
Abstract
Fungal pathogens produce toxins that are important for their pathogenesis and/or aggressiveness towards their hosts. Picolinic acid (PA), a non-host selective toxin, causes lesions on rice leaves resembling those originated from Pyricularia oryzae infection. Considering that non-host selective toxins can be useful for plant diseases control, this study investigated whether the foliar spray with PA on wheat (Triticum aestivum L.) plants, in a non-phytotoxic concentration, could increase their resistance to blast, stimulate the anti-oxidative metabolism, and minimize alterations in photosynthesis. The PA spray at concentrations greater than 0.1 mg ml-1 caused foliar lesions, compromised the photosynthesis and was linked with greater accumulation of hydrogen peroxide (H2 O2 ) and superoxide anion radical (O2 •- ). Fungal mycelial growth, conidia production and germination decreased by PA at 0.3 mg ml-1 . Blast severity was significantly reduced by 59 and 23%, respectively, at 72 and 96 h after inoculation for plants sprayed with PA (0.1 mg ml-1 ) at 24 h before fungal inoculation compared to non-sprayed plants. Reduction on blast symptoms was linked with increases on ascorbate peroxidase (EC 1.11.1.11), catalase (EC 1.11.1.6), glutathione peroxidase (EC 1.11.1.9), glutathione reductase (EC 1.8.1.7), glutathione-S-transferase (EC 2.5.1.18), peroxidase (EC 1.11.1.7), and superoxide dismutase (EC 1.15.1.1) activities, lower H2 O2 and O2 •- accumulation, reduced malondialdehyde production as well as less impairments to the photosynthetic apparatus. A more efficient antioxidative metabolism that rapidly scavenges the reactive oxygen species generated during P. oryzae infection, without dramatically decreasing the photosynthetic performance, was a remarkable effect obtained with PA spray.
Collapse
Affiliation(s)
- Carlos Eduardo Aucique-Pérez
- Department of Plant Pathology, Laboratory of Host-Pathogen Interaction, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900, Brazil
- Department of Plant Biology, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900, Brazil
| | - Renata Sousa Resende
- Department of Plant Pathology, Laboratory of Host-Pathogen Interaction, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900, Brazil
| | - Lara Beatriz Cruz Neto
- Department of Plant Pathology, Laboratory of Host-Pathogen Interaction, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900, Brazil
| | - Fernanda Dornelas
- Department of Plant Pathology, Laboratory of Host-Pathogen Interaction, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900, Brazil
| | - Fábio Murilo DaMatta
- Department of Plant Biology, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900, Brazil
| | - Fabrício Ávila Rodrigues
- Department of Plant Pathology, Laboratory of Host-Pathogen Interaction, Universidade Federal de Viçosa (UFV), Viçosa, 36570-900, Brazil
| |
Collapse
|
48
|
Zhang P, Li X, Gebrewahid TW, Liu H, Xia X, He Z, Li Z, Liu D. QTL Mapping of Adult-Plant Resistance to Leaf and Stripe Rust in Wheat Cross SW 8588/Thatcher using the Wheat 55K SNP Array. PLANT DISEASE 2019; 103:3041-3049. [PMID: 31613193 DOI: 10.1094/pdis-02-19-0380-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Wheat leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) cause large production losses in many regions of the world. The objective of this study was to identify quantitative trait loci (QTL) for resistance to leaf rust and stripe rust in a recombinant inbred line population derived from a cross between wheat cultivars SW 8588 and Thatcher. The population and parents were genotyped with the Wheat 55K SNP Array and SSR markers and phenotyped for leaf rust severity at Zhoukou in Henan Province and Baoding in Hebei Province. Stripe rust responses were also evaluated at Chengdu in Sichuan Province, and at Baoding. Seven and six QTL were detected for resistance to leaf rust and stripe rust, respectively. Four QTL on chromosomes 1BL, 2AS, 5AL, and 7BL conferred resistance to both rusts. The QTL on 1BL and 2AS were identified as Lr46/Yr29 and Lr37/Yr17, respectively. QLr.hebau-2DS from Thatcher, identified as Lr22b that was previously thought to be ineffective in China, contributed a large effect for leaf rust resistance. QLr.hebau-5AL/QYr.hebau-5AL, QLr.hebau-3BL, QLr.hebau-6DS, QYr.hebau-4BS, and QYr.hebau-6DS are likely to be new QTL, but require further validation. Kompetitive allele-specific PCR (KASP) markers for QLr.hebau-2DS and QLr.hebau-5AL/QYr.hebau-5AL were successfully developed and validated in a diverse wheat panel from Sichuan Province, indicating their usefulness under different genetic backgrounds. These QTL and their closely linked SNP and SSR markers will be useful for fine mapping, candidate gene discovery, and marker-assisted selection in breeding for durable resistance to both leaf and stripe rusts.
Collapse
Affiliation(s)
- Peipei Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xing Li
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Takele-Weldu Gebrewahid
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
- College of Agriculture, Aksum University, Shire-Indaslassie, Tigray 314, Ethiopia
| | - Hexing Liu
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing 100081, China
| | - Zaifeng Li
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Daqun Liu
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei 071001, China
| |
Collapse
|
49
|
Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics. Nat Genet 2019; 51:1530-1539. [DOI: 10.1038/s41588-019-0496-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/13/2019] [Indexed: 01/11/2023]
|
50
|
Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genet 2019; 15:e1008272. [PMID: 31513573 PMCID: PMC6741851 DOI: 10.1371/journal.pgen.1008272] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 11/28/2022] Open
Abstract
Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome. The emerging blast disease on wheat is proving even harder to control than the ancient, still-problematic rice blast disease. Potential wheat resistance identified using strains isolated soon after disease emergence are no longer effective in controlling recent aggressive field isolates from wheat in South America and South Asia. We construct a high-quality assembly of an aggressive, recently-isolated wheat blast fungal strain and the first assembled mini-chromosome genome sequence of wheat and rice blast pathogens. We report that recent wheat pathogens can contain one or two highly-variable dispensable mini-chromosomes, each with an amalgamation of fungal effector genes and other sequences that are duplicated or absent from indispensable core chromosome ends. Well-studied effectors found on different core chromosomes in rice pathogens appear side-by-side in wheat pathogen mini-chromosomes. The rice pathogen often overcomes deployed resistance genes by deleting triggering effector genes. We propose that the fast-evolving effector-rich compartment of the wheat blast fungus is a combination of core chromosome ends and mobile mini-chromosomes that are easily lost from individual strains. Localization of effectors on mini-chromosomes would therefore accelerate pathogen adaptation in the field.
Collapse
Affiliation(s)
- Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- * E-mail: (BV); (SL)
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- * E-mail: (BV); (SL)
| |
Collapse
|