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Li C, Wu Y, Yin X, Gong Z, Xing H, Miao J, Wang S, Liu J, Na R, Li QX. Modular synthesis of the pheromone (2S,7S)-2,7-nonanediyl dibutyrate and its racemate and their field efficacy to control orange wheat blossom midge, Sitodiplosis mosellana (Géhin) (Diptera: Cecidomyiidae). PEST MANAGEMENT SCIENCE 2023; 79:97-104. [PMID: 36087296 DOI: 10.1002/ps.7177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/16/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sudden outbreaks of the orange wheat blossom midge, Sitodiplosis mosellana (Géhin) cause huge wheat yield losses. Use of sex pheromones is more efficient than laborious egg counting to monitor these hidden-concealed insects. Quick synthesis of the sex pheromones is therefore required to meet the sudden outbreak needs. RESULTS A synthetic approach of stereospecific and racemic S. mosellana pheromones was presented. This method afforded the stereospecific and racemic S. mosellana pheromones in three steps and high enantioselectivity (> 98% ee for (2S,7S)-2,7-nonanediyl dibutyrate) in less than 1 day with 74% and 73% overall yields, respectively, whereas most conventional methods require longer synthesis time with less than 40% yield. The synthesis routes could quickly and economically afford the pheromones, starting from synthon (S)-but-3-yn-2-ol (1a) or but-3-yn-2-ol (1b), through the same three-step processes of coupling, reduction, and esterification. The Y-tube olfactometer results showed significant attractiveness of the synthetic stereospecific and racemic sex pheromones to S. mosellana males relative to the blank control (P < 0.001). Field trials also demonstrated significant attractiveness of the synthetic stereospecific and racemic sex pheromones relative to the blank control (P < 0.001). CONCLUSION This modular approach is conducive to the deployment of field traps and timely responses to S. mosellana outbreaks and can be a time-saving and cost-effective tool to manage S. mosellana. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Changkai Li
- Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuqing Wu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinming Yin
- Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zhongjun Gong
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hongxia Xing
- Seed Control Station of Agriculture and Rural Bureau, Handan, China
| | - Jin Miao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shuzhi Wang
- Institute of Plant Protection, Luoyang Academy of Agriculture and Forestry Sciences, Luoyang, China
| | - Jia Liu
- Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Risong Na
- Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
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Arif MAR, Waheed MQ, Lohwasser U, Shokat S, Alqudah AM, Volkmar C, Börner A. Genetic Insight Into the Insect Resistance in Bread Wheat Exploiting the Untapped Natural Diversity. Front Genet 2022; 13:828905. [PMID: 35222543 PMCID: PMC8874221 DOI: 10.3389/fgene.2022.828905] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change is an undeniable threat to sustainable wheat production in the future as an increased temperature will significantly increase grain loss due to the increased number of generations per season of multivoltine species that are detrimental to plants. Among insects, orange wheat blossom midge (OWBM), yellow wheat blossom midge (YWBM), saddle gall midge (SGM), thrips, and frit fly (FF) are important wheat pests in the European environments, which can be managed by the development of resistant cultivars. This involves the identification, confirmation, and incorporation of insect resistance sources into new high-yielding cultivars. We used two diverse and unrelated wheat [winter wheat (WW) and spring wheat (SW)] panels to associate single-nucleotide polymorphism (SNP) markers with the mentioned pests using the tools of association mapping. All in all, a total of 645 and 123 significant associations were detected in WW and SW, respectively, which were confined to 246 quantitative trait loci. Many candidate genes were identified using the BLAST analysis of the sequences of associated SNPs. Some of them are involved in controlling the physical structures of plants such as stomatal immunity and closure, cuticular wax in leaf blade, whereas others are involved in the production of certain enzymes in response to biotic and abiotic stresses. To our knowledge, this is the first detailed investigation that deals with YWBM, SGM, thrips, and FF resistance genetics using the natural variation in wheat. The reported germplasm is also readily available to breeders across the world that can make rational decisions to breed for the pest resilience of their interest by including the resistant genotypes being reported.
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Affiliation(s)
- Mian Abdur Rehman Arif
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
- *Correspondence: Mian Abdur Rehman Arif, ; Andreas Börner,
| | - Muhammad Qandeel Waheed
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Ulrike Lohwasser
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Sajid Shokat
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Ahmad M. Alqudah
- Department of Agroecology, Aarhus University at Flakkebjerg, Slagelse, Denmark
| | - Christa Volkmar
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- *Correspondence: Mian Abdur Rehman Arif, ; Andreas Börner,
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Muslu T, Akpinar BA, Biyiklioglu-Kaya S, Yuce M, Budak H. Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes. Int J Mol Sci 2021; 22:ijms222212349. [PMID: 34830231 PMCID: PMC8623949 DOI: 10.3390/ijms222212349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly (Cephus cinctus Norton) and orange wheat blossom midge (Sitodiplosis mosellana) are two of the most economically and agronomically harmful insect pests which cause yield loss in cereals, especially in wheat in North America. There is no effective strategy for suppressing this pest damage yet, and only the plants with intrinsic tolerance mechanisms such as solid stem phenotypes for WSS and antixenosis and/or antibiosis mechanisms for OWBM can limit damage. A major QTL and a causal gene for WSS resistance were previously identified in wheat, and 3 major QTLs and a causal gene for OWBM resistance. Here, we present a comparative analysis of coding and non-coding features of these loci of wheat across important cereal crops, barley, rye, oat, and rice. This research paves the way for our cloning and editing of additional WSS and OWBM tolerance gene(s), proteins, and metabolites.
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Affiliation(s)
- Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | | | - Sezgi Biyiklioglu-Kaya
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | - Meral Yuce
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey;
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA;
- Correspondence:
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Thambugala D, Pozniak CJ, Kumar S, Burt AJ, Wise IL, Smith MAH, Fox SL, Costamagna AC, McCartney CA. Genetic analysis of oviposition deterrence to orange wheat blossom midge in spring wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:647-660. [PMID: 33200319 DOI: 10.1007/s00122-020-03720-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
A major QTL for oviposition deterrence to orange wheat blossom midge was detected on chromosome 1A in the Canadian breeding line BW278 that was inherited from the Chinese variety Sumai-3. Orange wheat blossom midge (OWBM, Sitodiplosis mosellana Géhin, Diptera: Cecidomyiidae) is an important insect pest of wheat (Triticum aestivum L.) that reduces both grain yield and quality. Oviposition deterrence results in a reduction of eggs deposited on spikes relative to that observed on a wheat line preferred by OWBM. Quantification of oviposition deterrence is labor-intensive, so wheat breeders require efficient DNA markers for the selection of this trait. The objective of this study was to identify quantitative trait loci (QTL) for oviposition deterrence in a doubled haploid (DH) population developed from the spring wheat cross Superb/BW278. The DH population and check varieties were evaluated for OWBM kernel damage from five field nurseries over three growing seasons. QTL analysis identified major effect loci on chromosomes 1A (QSm.mrc-1A) and 5A (QSm.mrc-5A). Reduced kernel damage was contributed by BW278 at QSm.mrc-1A and Superb at QSm.mrc-5A. QSm.mrc-1A mapped to the approximate location of the oviposition deterrence QTL previously found in the American variety Reeder. However, haplotype analysis revealed that BW278 inherited this oviposition deterrence allele from the Chinese spring wheat variety Sumai-3. QSm.mrc-5A mapped to the location of awn inhibitor gene B1, suggesting that awns hinder OWBM oviposition. Single-nucleotide polymorphisms (SNPs) were identified for predicting the presence or absence of QSm.mrc-1A based upon haplotype. Functional annotation of candidate genes in 1A QTL intervals revealed eleven potential candidate genes, including a gene involved in terpenoid biosynthesis. SNPs for QSm.mrc-1A and fully awned spikes provide a basis for the selection of oviposition deterrence to OWBM.
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Affiliation(s)
- Dinushika Thambugala
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Andrew J Burt
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Ian L Wise
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
- Department of Entomology, University of Manitoba, Winnipeg, MB, Canada
| | - Marjorie A H Smith
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Stephen L Fox
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
- DL Seeds Inc., Winnipeg, MB, Canada
| | | | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada.
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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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: 374] [Impact Index Per Article: 93.5] [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.
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Zhang L, Geng M, Zhang Z, Zhang Y, Yan G, Wen S, Liu G, Wang R. Molecular mapping of major QTL conferring resistance to orange wheat blossom midge (Sitodiplosis mosellana) in Chinese wheat varieties with selective populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:491-502. [PMID: 31773176 DOI: 10.1007/s00122-019-03480-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
Two novel midge resistance QTL were mapped to a 4.9-Mb interval on chromosome arm 4AL based on the genetic maps constructed with SNP markers. Orange wheat blossom midge (OWBM) is a devastating insect pest affecting wheat production. In order to detect OWBM resistance genes and quantitative trait loci (QTL) for wheat breeding, two recombinant inbred line (RIL) populations were established and used for molecular mapping. A total of seven QTL were detected on chromosomes 2D, 4A, 4D and 7D, respectively, of which positive alleles were all from the resistant parents except for the QTL on 7D. Two stable QTL (QSm.hbau-4A.2-1 and QSm.hbau-4A.2-2) were detected in both populations with the LOD scores ranging from 5.58 to 29.22 under all three environments, and they explained a combined phenotypic variation of 24.4-44.8%. These two novel QTL were mapped to a 4.9-Mb physical interval. The single-nucleotide polymorphism (SNP) markers AX-109543456, AX-108942696 and AX-110928325 were closely linked to the QTL and could be used for marker-assisted selection (MAS) for OWBM resistance in wheat breeding programs.
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Affiliation(s)
- Lijing Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Miaomiao Geng
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Zhe Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Yue Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Guijun Yan
- School of Agriculture and Environment, Faculty of Science, and the Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia
| | - Shumin Wen
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China
| | - Guiru Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China.
| | - Ruihui Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, People's Republic of China.
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Hao Z, Geng M, Hao Y, Zhang Y, Zhang L, Wen S, Wang R, Liu G. Screening for differential expression of genes for resistance to Sitodiplosis mosellana in bread wheat via BSR-seq analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3201-3221. [PMID: 31501915 DOI: 10.1007/s00122-019-03419-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Five putative candidate genes for OWBM resistance in Chinese winter wheat 'Jimai 24' were identified via BSR-seq and differential expression analyses. Orange wheat blossom midge (OWBM), Sitodiplosis mosellana, is one of the most serious threats to wheat production worldwide. Conventional gene mapping methods to identify genes require significant amounts of financial support and time. Here, bulked segregant RNA-seq (BSR-seq) was applied to profile candidate genes and develop associated markers for OWBM resistance. Previously, we identified a major QTL (QSm.hebau-4A) for OWBM resistance on the long arm of chromosome 4A. In this study, we aimed at screening differentially expressed resistance genes associated with this QTL. Twelve differentially expressed genes (DEGs) were obtained based on BSR-seq and differential expression analyses. Among them, four were confirmed to be associated with OWBM resistance via quantitative reverse transcription PCR, using an additional set of wheat samples subjected to OWBM invasion. One SPI-like gene and one Malectin-like gene were revealed by gene annotation, respectively. Sequencing results confirmed that the four DEGs and the SPI gene had SNP polymorphisms between wheat parents. All these five resistance-related genes for OWBM were located in the same genomic region with QSm.hebau-4A. Furthermore, six new markers developed based on sequences of the five genes were also mapped in the same genomic region using genetic population. These five genes may be the candidate genes for OWBM resistance in Chinese wheat 'Jimai 24' and should be the targets for further positional isolation.
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Affiliation(s)
- Zhiming Hao
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China
| | - Miaomiao Geng
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China
| | - Yanran Hao
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China
| | - Yue Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China
| | - Lijing Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China
| | - Shumin Wen
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China
| | - Ruihui Wang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China.
| | - Guiru Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071000, People's Republic of China.
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Yang N, McDonald MC, Solomon PS, Milgate AW. Genetic mapping of Stb19, a new resistance gene to Zymoseptoria tritici in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2765-2773. [PMID: 30238255 DOI: 10.1007/s00122-018-3189-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/10/2018] [Indexed: 05/26/2023]
Abstract
A new and dominant R gene Stb19 is identified from a soft wheat cultivar 'Lorikeet' and was mapped on the distal region of chromosome 1DS. Two tightly linked KASP markers were also discovered and validated for molecular-assisted breeding programs. A new R gene, designated as Stb19, provides resistance to Zymoseptoria tritici in wheat. This new dominant gene resides on the short arm of chromosome 1D, exhibiting complete resistance to three Z. tritici isolates, WAI332, WAI251, and WAI161, at the seedling stage. A genetic linkage map, based on an F2:3 population of 'Lorikeet' and 'Summit,' found the Stb19 gene at a 9.3 cM region on 1DS, closely linked with two Kompetitive Allele-Specific PCR markers, snp_4909967 and snp_1218021. Further, the two markers were tested and validated in another F2:3 population and 266 different wheat accessions, which gave over 95% accuracy of resistance/susceptibility prediction. Combined with the physical location of the identified SNPs and the previous evidence of gene order on chromosome 1DS (centromere-Sr45-Sr33-Lr21-telomere), Stb19 is proposed to be located between Sr33 and Lr21. Thus, the newly discovered Stb19 along with the KASP markers represents an increase in genetic resources available for wheat breeding resistance to Z. tritici.
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Affiliation(s)
- Nannan Yang
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia
| | - Megan C McDonald
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Peter S Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Andrew W Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia.
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Li P, Quan X, Jia G, Xiao J, Cloutier S, You FM. RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants. BMC Genomics 2016; 17:852. [PMID: 27806688 PMCID: PMC5093994 DOI: 10.1186/s12864-016-3197-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/25/2016] [Indexed: 11/10/2022] Open
Abstract
Background Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential R-genes that contain specific conserved domains and motifs. Thus, RGAs can be predicted based on their conserved structural features using bioinformatics tools. Computer programs have been developed for the identification of individual domains and motifs from the protein sequences of RGAs but none offer a systematic assessment of the different types of RGAs. A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes. Results An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets. Conclusions RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3197-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Xiande Quan
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Gaofeng Jia
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.,University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.,National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
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