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Jia J, Zhao G, Li D, Wang K, Kong C, Deng P, Yan X, Zhang X, Lu Z, Xu S, Jiao Y, Chong K, Liu X, Cui D, Li G, Zhang Y, Du C, Wu L, Li T, Yan D, Zhan K, Chen F, Wang Z, Zhang L, Kong X, Ru Z, Wang D, Gao L. Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement. MOLECULAR PLANT 2023; 16:1893-1910. [PMID: 37897037 DOI: 10.1016/j.molp.2023.10.015] [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: 08/14/2022] [Revised: 07/12/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.
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Affiliation(s)
- Jizeng Jia
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Wang
- Xi'An Shansheng Biosciences Co., Ltd., Xi'an 710000, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pingchuan Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 612100, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyong Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shujuan Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Chong
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dangqun Cui
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Guangwei Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chunguang Du
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Liang Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan 562000, China
| | - Tianbao Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Yan
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kehui Zhan
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Feng Chen
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Zhiyong Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Daowen Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Lifeng Gao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Zhang X, Wang H, Sun H, Li Y, Feng Y, Jiao C, Li M, Song X, Wang T, Wang Z, Yuan C, Sun L, Lu R, Zhang W, Xiao J, Wang X. A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement. MOLECULAR PLANT 2023; 16:432-451. [PMID: 36587241 DOI: 10.1016/j.molp.2022.12.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Dasypyrum villosum is one of the most valuable gene resources in wheat improvement, especially for disease resistance. The mining of favorable genes from D. villosum is frustrated by the lack of a whole genome sequence. In this study, we generated a doubled-haploid line, 91C43DH, using microspore culture and obtained a 4.05-GB high-quality, chromosome-scale genome assembly for D. villosum. The assembly contains39 727 high-confidence genes, and 85.31% of the sequences are repetitive. Two reciprocal translocation events were detected, and 7VS-4VL is a unique translocation in D. villosum. The prolamin seed storage protein-coding genes were found to be duplicated; in particular, the genes encoding low-molecular-weight glutenin at the Glu-V3 locus were significantly expanded. RNA sequencing (RNA-seq) analysis indicated that, after Blumeria graminearum f.sp tritici (Bgt) inoculation, there were more upregulated genes involved in the pattern-triggered immunity and effector-triggered immunity defense pathways in D. villosum than in Triticum urartu. MNase hypersensitive sequencing (MH-seq) identified two Bgt-inducible MH sites (MHSs), one in the promoter and one in the 3' terminal region of the powdery mildew resistance (Pm) gene NLR1-V. Each site had two subpeaks and they were termed MHS1 (MHS1.1/1.2) and MHS2 (MHS2.1/2.2). Bgt-inducible MHS2.2 was uniquely present in D. villosum, and MHS1.1 was more inducible in D. villosum than in wheat, suggesting that MHSs may be critical for regulation of NLR1-V expression and plant defense. In summary, this study provides a valuable genome resource for functional genomics studies and wheat-D. villosum introgression breeding. The identified regulatory mechanisms may also be exploited to develop new strategies for enhancing Pm resistance by optimizing gene expression in wheat.
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Affiliation(s)
- Xu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Yingbo Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yilong Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Chengzhi Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Mengli Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Xinying Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Tong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Li Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Ruiju Lu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
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Lafiandra D, Shewry PR. Wheat Glutenin polymers 2, the role of wheat glutenin subunits in polymer formation and dough quality. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Semagn K, Iqbal M, Chen H, Perez-Lara E, Bemister DH, Xiang R, Zou J, Asif M, Kamran A, N'Diaye A, Randhawa H, Beres BL, Pozniak C, Spaner D. Physical mapping of QTL associated with agronomic and end-use quality traits in spring wheat under conventional and organic management systems. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3699-3719. [PMID: 34333664 DOI: 10.1007/s00122-021-03923-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Using phenotypic data of four biparental spring wheat populations evaluated at multiple environments under two management systems, we discovered 152 QTL and 22 QTL hotspots, of which two QTL accounted for up to 37% and 58% of the phenotypic variance, consistently detected in all environments, and fell within genomic regions harboring known genes. Identification of the physical positions of quantitative trait loci (QTL) would be highly useful for developing functional markers and comparing QTL results across multiple independent studies. The objectives of the present study were to map and characterize QTL associated with nine agronomic and end-use quality traits (tillering ability, plant height, lodging, grain yield, grain protein content, thousand kernel weight, test weight, sedimentation volume, and falling number) in hard red spring wheat recombinant inbred lines (RILs) using the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map. We evaluated a total of 698 RILs from four populations derived from crosses involving seven parents at 3-8 conventionally (high N) and organically (low N) managed field environments. Using the phenotypic data combined across all environments per management, and the physical map between 1058 and 6526 markers per population, we identified 152 QTL associated with the nine traits, of which 29 had moderate and 2 with major effects. Forty-nine of the 152 QTL mapped across 22 QTL hotspot regions with each region coincident to 2-6 traits. Some of the QTL hotspots were physically located close to known genes. QSv.dms-1A and QPht.dms-4B.1 individually explained up to 37% and 58% of the variation in sedimentation volume and plant height, respectively, and had very large LOD scores that varied from 19.0 to 35.7 and from 16.7 to 55.9, respectively. We consistently detected both QTL in the combined and all individual environments, laying solid ground for further characterization and possibly for cloning.
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Affiliation(s)
- Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Hua Chen
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, 59 Qinglong Road, Mianyang, 621010, Sichuan, China
| | - Enid Perez-Lara
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Darcy H Bemister
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Rongrong Xiang
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Jun Zou
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Muhammad Asif
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Agronomy, 2004 Throckmorton Plant Science Center, Kansas State University, Manhattan, KS, 66506, USA
- Heartland Plant Innovations, Kansas Wheat Innovation Center, 1990 Kimball Avenue, Manhattan, KS, 66502, USA
| | - Atif Kamran
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Department of Botany, Seed Centre, The University of Punjab, New Campus, Lahore, 54590, Pakistan
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Harpinder Randhawa
- Agriculture, and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Brian L Beres
- Agriculture, and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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Cho K, Jang YR, Lim SH, Altenbach SB, Gu YQ, Simon-Buss A, Lee JY. Proteomic Determination of Low-Molecular-Weight Glutenin Subunit Composition in Aroona Near-Isogenic Lines and Standard Wheat Cultivars. Int J Mol Sci 2021; 22:ijms22147709. [PMID: 34299329 PMCID: PMC8306524 DOI: 10.3390/ijms22147709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The low-molecular weight glutenin subunit (LMW-GS) composition of wheat (Triticum aestivum) flour has important effects on end-use quality. However, assessing the contributions of each LMW-GS to flour quality remains challenging because of the complex LMW-GS composition and allelic variation among wheat cultivars. Therefore, accurate and reliable determination of LMW-GS alleles in germplasm remains an important challenge for wheat breeding. In this study, we used an optimized reversed-phase HPLC method and proteomics approach comprising 2-D gels coupled with liquid chromatography–tandem mass spectrometry (MS/MS) to discriminate individual LMW-GSs corresponding to alleles encoded by the Glu-A3, Glu-B3, and Glu-D3 loci in the ‘Aroona’ cultivar and 12 ‘Aroona’ near-isogenic lines (ARILs), which contain unique LMW-GS alleles in the same genetic background. The LMW-GS separation patterns for ‘Aroona’ and ARILs on chromatograms and 2-D gels were consistent with those from a set of 10 standard wheat cultivars for Glu-3. Furthermore, 12 previously uncharacterized spots in ‘Aroona’ and ARILs were excised from 2-D gels, digested with chymotrypsin, and subjected to MS/MS. We identified their gene haplotypes and created a 2-D gel map of LMW-GS alleles in the germplasm for breeding and screening for desirable LMW-GS alleles for wheat quality improvement.
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Affiliation(s)
- Kyoungwon Cho
- Department of Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - You-Ran Jang
- National Institute of Agricultural Science, RDA, Jeonju 54874, Korea;
| | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Korea;
| | - Susan B. Altenbach
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (S.B.A.); (Y.Q.G.); (A.S.-B.)
| | - Yong Q. Gu
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (S.B.A.); (Y.Q.G.); (A.S.-B.)
| | - Annamaria Simon-Buss
- USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; (S.B.A.); (Y.Q.G.); (A.S.-B.)
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Jong-Yeol Lee
- National Institute of Agricultural Science, RDA, Jeonju 54874, Korea;
- Correspondence: ; Tel.: +82-62-238-4616
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Proteome and transcriptome analyses of wheat near isogenic lines identifies key proteins and genes of wheat bread quality. Sci Rep 2021; 11:9978. [PMID: 33976249 PMCID: PMC8113351 DOI: 10.1038/s41598-021-89140-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/21/2021] [Indexed: 11/08/2022] Open
Abstract
The regulation of wheat protein quality is a highly complex biological process involving multiple metabolic pathways. To reveal new insights into the regulatory pathways of wheat glutenin synthesis, we used the grain-filling period wheat grains of the near-isogenic lines NIL-723 and NIL-1010, which have large differences in quality, to perform a combined transcriptome and proteome analysis. Compared with NIL-1010, NIL-723 had 1287 transcripts and 355 proteins with significantly different abundances. Certain key significantly enriched pathway were identified, and wheat quality was associated with alanine, aspartate and glutamate metabolism, nitrogen metabolism and alpha-linolenic acid metabolism. Differentially expressed proteins (DEPs) or Differentially expressed genes (DEGs) in amino acid synthesis pathways were upregulated primarily in the glycine (Gly), methionine (Met), threonine (Thr), glutamic acid (Glu), proline (proC), cysteine (Cys), and arginine (Arg) synthesis and downregulated in the tryptophan (trpE), leucine (leuC), citrulline (argE), and ornithine (argE) synthesis. Furthermore, to elucidate changes in glutenin in the grain synthesis pathway, we plotted a regulatory pathway map and found that DEGs and DEPs in ribosomes (RPL5) and the ER (HSPA5, HYOU1, PDIA3, PDIA1, Sec24, and Sec31) may play key roles in regulating glutenin synthesis. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the transcriptome and proteomic results.
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Gao Y, An K, Guo W, Chen Y, Zhang R, Zhang X, Chang S, Rossi V, Jin F, Cao X, Xin M, Peng H, Hu Z, Guo W, Du J, Ni Z, Sun Q, Yao Y. The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality. THE PLANT CELL 2021; 33:603-622. [PMID: 33955492 PMCID: PMC8136912 DOI: 10.1093/plcell/koaa040] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/16/2020] [Indexed: 05/03/2023]
Abstract
In wheat (Triticum aestivum L.), breeding efforts have focused intensively on improving grain yield and quality. For quality, the content and composition of seed storage proteins (SSPs) determine the elasticity of wheat dough and flour processing quality. Moreover, starch levels in seeds are associated with yield. However, little is known about the mechanisms that coordinate SSP and starch accumulation in wheat. In this study, we explored the role of the endosperm-specific NAC transcription factor TaNAC019 in coordinating SSP and starch accumulation. TaNAC019 binds to the promoters of TaGlu-1 loci, encoding high molecular weight glutenin (HMW-GS), and of starch metabolism genes. Triple knock-out mutants of all three TaNAC019 homoeologs exhibited reduced transcript levels for all SSP types and genes involved in starch metabolism, leading to lower gluten and starch contents, and in flour processing quality parameters. TaNAC019 directly activated the expression of HMW-GS genes by binding to a specific motif in their promoters and interacting with the TaGlu-1 regulator TaGAMyb. TaNAC019 also indirectly regulated the expression of TaSPA, an ortholog of maize Opaque2 that activates SSP accumulation. Therefore, TaNAC019 regulation of starch- and SSP-related genes has key roles in wheat grain quality. Finally, we identified an elite allele (TaNAC019-BI) associated with flour processing quality, providing a candidate gene for breeding wheat with improved quality.
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Affiliation(s)
- Yujiao Gao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kexin An
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weiwei Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Ruijie Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xue Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Siyuan Chang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Vincenzo Rossi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, I-24126 Bergamo, Italy
| | - Fangming Jin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xinyou Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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8
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Hu X, Dai S, Yan Y, Liu Y, Zhang J, Lu Z, Wei Y, Zheng Y, Cong H, Yan Z. The genetic diversity of group-1 homoeologs and characterization of novel LMW-GS genes from Chinese Xinjiang winter wheat landraces (Triticum aestivum L.). J Appl Genet 2020; 61:379-389. [PMID: 32548810 DOI: 10.1007/s13353-020-00564-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 11/26/2022]
Abstract
Group-1 homoelog genes in wheat genomes encode storage proteins and are the major determinants of wheat product properties. Consequently, understanding the genetic diversity of group-1 homoelogs and genes encoding storage proteins, especially the low-molecular-weight glutenins (LMW-GSs), within wheat landrace genomes is necessary to further improve the quality of modern wheat crops. The genetic diversity of group-1 homoelogs in 75 Xinjiang winter wheat landraces was evaluated by Diversity Arrays Technology (DArT) markers. These data were used to select 15 landraces for additional LMW-GS gene isolation. The genetic similarity coefficients among landraces were highly similar regardless if considering the diversity markers on 1A, 1B, and 1D chromosomes individually or using all of the markers together. These similarities were evinced by the generation of four similar cluster dendrograms that comprised 11-15 landrace groups, regardless of the dataset used to generate the dendrograms. A total of 105 LMW-GS sequences corresponding to 79 unique genes were identified overall by using primers designed to target Glu-A3 and Glu-B3 loci, and 54 mature proteins were predicted from the unique LMW-GS genes. Nine novel chimeric LMW-GS genes were also identified, of which, one was recombinant for -i/-m, one for -s/-m, and seven for -m/-m parent genes, respectively. Phylogenetic analysis separated all of the LMW-GSs into three clades that were supported by moderate bootstrap values (> 70%). The clades corresponded to LMW-GS genes primarily harboring different N-terminals. These results provide useful information for better understanding the evolutionary genetics of the important Glu-3 locus of wheat, and they also provide new novel gene targets that can potentially be exploited to improve wheat quality.
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Affiliation(s)
- Xinkun Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Shoufen Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yongliang Yan
- Institute of Crop Germplasm Resource, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China.
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Jinbo Zhang
- Institute of Crop Germplasm Resource, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China
| | - Zifeng Lu
- Institute of Crop Germplasm Resource, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Hua Cong
- Institute of Crop Germplasm Resource, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, People's Republic of China
| | - Zehong Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.
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9
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Low-molecular-weight glutenin subunit LMW-N13 improves dough quality of transgenic wheat. Food Chem 2020; 327:127048. [PMID: 32454285 DOI: 10.1016/j.foodchem.2020.127048] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/26/2020] [Accepted: 05/11/2020] [Indexed: 11/21/2022]
Abstract
In our previous study, a novel LMW-GS designated as LMW-N13 with a unique molecular structure was identified from Aegilops uniaristata. LMW-N13 has been characterized as the largest LMW-GS, so far, and possesses an extra cysteine residue compared with typical LMW-GS. In order to analyze the contribution of LMW-N13 to dough quality, in this work, three transgenic wheat lines overexpressing LMW-N13 were generated. Compared with non-transformation (NT) lines, transgenic (TG) lines demonstrated superior dough properties. These superior dough properties were accompanied by the higher contents of glutenin macropolymer (GMP) and total protein. The microstructure of the dough was further investigated by scanning electron microscopy; starch granules in NT lines were smaller than those in transgenic lines. The protein matrix in NT lines was relatively loose and discontinuous. Conversely, the protein matrix in transgenic lines was more continuous and tight. The application of LMW-N13 in wheat breeding is also discussed.
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10
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Wang D, Li F, Cao S, Zhang K. Genomic and functional genomics analyses of gluten proteins and prospect for simultaneous improvement of end-use and health-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1521-1539. [PMID: 32020238 PMCID: PMC7214497 DOI: 10.1007/s00122-020-03557-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/24/2020] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE Recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins, which are important determinants of wheat grain quality traits. The new insights obtained and the availability of precise, versatile and high-throughput genome editing technologies will accelerate simultaneous improvement of wheat end-use and health-related traits. Being a major staple food crop in the world, wheat provides an indispensable source of dietary energy and nutrients to the human population. As worldwide population grows and living standards rise in both developed and developing countries, the demand for wheat with high quality attributes increases globally. However, efficient breeding of high-quality wheat depends on critically the knowledge on gluten proteins, which mainly include several families of prolamin proteins specifically accumulated in the endospermic tissues of grains. Although gluten proteins have been studied for many decades, efficient manipulation of these proteins for simultaneous enhancement of end-use and health-related traits has been difficult because of high complexities in their expression, function and genetic variation. However, recent genomic and functional genomics analyses have substantially improved the understanding on gluten proteins. Therefore, the main objective of this review is to summarize the genomic and functional genomics information obtained in the last 10 years on gluten protein chromosome loci and genes and the cis- and trans-factors regulating their expression in the grains, as well as the efforts in elucidating the involvement of gluten proteins in several wheat sensitivities affecting genetically susceptible human individuals. The new insights gathered, plus the availability of precise, versatile and high-throughput genome editing technologies, promise to speed up the concurrent improvement of wheat end-use and health-related traits and the development of high-quality cultivars for different consumption needs.
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Affiliation(s)
- Daowen Wang
- College of Agronomy, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, 15 Longzi Lake College Park, Zhengzhou, 450046, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, 1 West Beichen Road, Beijing, 100101, China.
| | - Feng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, 1 West Beichen Road, Beijing, 100101, China
| | - Shuanghe Cao
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Kunpu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Science, 1 West Beichen Road, Beijing, 100101, China.
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11
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Physicochemical properties of starch in relation to rheological properties of wheat dough (Triticum aestivum L.). Food Chem 2019; 297:125000. [DOI: 10.1016/j.foodchem.2019.125000] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/30/2019] [Accepted: 06/11/2019] [Indexed: 11/24/2022]
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12
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Overexpressing wheat low-molecular-weight glutenin subunits in rice ( Oryza sativa L. japonica cv. Koami) seeds. 3 Biotech 2019; 9:49. [PMID: 30729073 DOI: 10.1007/s13205-019-1579-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 01/17/2019] [Indexed: 10/27/2022] Open
Abstract
Genes encoding wheat low-molecular-weight glutenin subunits (LMW-GSs) that confer dough strength and extensibility were previously identified from Korean wheat cultivars. To improve low viscoelasticity of rice (Oryza sativa L.) dough caused by the lack of seed storage proteins comparable to wheat gluten, two genes, LMW03 and LMW28, encoding LMW-GSs are cloned from Korean wheat cultivar Jokyoung. The LMW genes are inserted into binary vectors under the control of the rice endosperm-specific Glu-B1 promoter. Transgenic rice plants expressing LMW03 or LMW28 in their seeds are generated using Agrobacterium-mediated transformation. The expression of recombinant wheat LMW-GS in the transgenic rice seeds was confirmed by SDS-PAGE and immunoblot analysis. Their accumulation in the endosperm and aleurone layers of rice seeds was observed through in situ immuno-hybridization.
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13
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Montagner Souza T, de Miranda MZ, Mateus Prando A, Tilley M, Payton ME, Rayas-Duarte P. Gluten viscoelasticity: Rapid method for classification of soft-like wheat genotypes. Cereal Chem 2019. [DOI: 10.1002/cche.10128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Thiago Montagner Souza
- Robert M. Kerr Food & Agricultural Products Center; Oklahoma State University; Stillwater Oklahoma
| | | | | | | | - Mark E. Payton
- Department of Statistics; Oklahoma State University; Stillwater Oklahoma
| | - Patricia Rayas-Duarte
- Robert M. Kerr Food & Agricultural Products Center, Department of Biochemistry and Molecular Biology; Oklahoma State University; Stillwater Oklahoma
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14
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Shen L, Luo G, Song Y, Song S, Li Y, Yang W, Li X, Sun J, Liu D, Zhang A. Low molecular weight glutenin subunit gene composition at Glu-D3 loci of Aegilops tauschii and common wheat and a further view of wheat evolution. THEORETICAL AND APPLIED GENETICS 2018; 131:2745-2763. [PMID: 30225644 DOI: 10.1007/s00122-018-3188-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023]
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15
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Huang L, He Y, Jin Y, Wang F, He J, Feng L, Liu D, Wu B. Characterization of novel LMW glutenin subunit genes at the Glu-M3 locus from Aegilops comosa. 3 Biotech 2018; 8:379. [PMID: 30148029 DOI: 10.1007/s13205-018-1407-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 08/14/2018] [Indexed: 10/28/2022] Open
Abstract
We report the characterization of seven novel low-molecular-weight glutenin subunit (LMW-GS) genes from Aegilops comosa (2n = 2x = 14, MM). We found that all seven LMW-GS genes possessed the same primary structure shared by other known LMW-GSs. Three genes (comosa-M1, comosa-M2, and comosa-M3) encode LMW-m-type subunits, two (comosa-I1 and comosa-I2) encode LWM-i-type subunits, and two (comosa-L1 and comosa-L2) encode LWM-l-type subunits. The comosa-M1 possessed seven cysteine residues, which resulted from a single-nucleotide polymorphism (SNP) of the G-A transition in the fifth position of the N-terminal sequence. Two l-type subunits, comosa-L1 and comosa-L2, contained nine cysteine residues with an extra cysteine residue located in the signal peptide and repetitive domain. In addition, a long insertion of 13 residues (LGQQPQ8/LVQQPQ8) was present in the end of the C-terminal II. Phylogenetic analysis implied that the comosa-L2 may be the intermediate type during the evolution of LMW-l and LMW-i-type genes. Our results demonstrated that the novel LMW-GSs, such as comosa-M1, comosa-L1, and comosa-L2, may have positive effects on dough properties.
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16
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Ruiz M, Bernal G, Giraldo P. An update of low molecular weight glutenin subunits in durum wheat relevant to breeding for quality. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2018.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Li D, Jin H, Zhang K, Wang Z, Wang F, Zhao Y, Huo N, Liu X, Gu YQ, Wang D, Dong L. Analysis of the Gli-D2 locus identifies a genetic target for simultaneously improving the breadmaking and health-related traits of common wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:414-426. [PMID: 29752764 DOI: 10.1111/tpj.13956] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 05/22/2023]
Abstract
Gliadins are a major component of wheat seed proteins. However, the complex homoeologous Gli-2 loci (Gli-A2, -B2 and -D2) that encode the α-gliadins in commercial wheat are still poorly understood. Here we analyzed the Gli-D2 locus of Xiaoyan 81 (Xy81), a winter wheat cultivar. A total of 421.091 kb of the Gli-D2 sequence was assembled from sequencing multiple bacterial artificial clones, and 10 α-gliadin genes were annotated. Comparative genomic analysis showed that Xy81 carried only eight of the α-gliadin genes of the D genome donor Aegilops tauschii, with two of them each experiencing a tandem duplication. A mutant line lacking Gli-D2 (DLGliD2) consistently exhibited better breadmaking quality and dough functionalities than its progenitor Xy81, but without penalties in other agronomic traits. It also had an elevated lysine content in the grains. Transcriptome analysis verified the lack of Gli-D2 α-gliadin gene expression in DLGliD2. Furthermore, the transcript and protein levels of protein disulfide isomerase were both upregulated in DLGliD2 grains. Consistent with this finding, DLGliD2 had increased disulfide content in the flour. Our work sheds light on the structure and function of Gli-D2 in commercial wheat, and suggests that the removal of Gli-D2 and the gliadins specified by it is likely to be useful for simultaneously enhancing the end-use and health-related traits of common wheat. Because gliadins and homologous proteins are widely present in grass species, the strategy and information reported here may be broadly useful for improving the quality traits of diverse cereal crops.
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Affiliation(s)
- Da Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huaibing Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunpu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Agronomy and State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhaojun Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Faming Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yue Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA
| | - Xin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California, 94710, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- College of Agronomy and State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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18
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Wang D, Zhang K, Dong L, Dong Z, Li Y, Hussain A, Zhai H. Molecular genetic and genomic analysis of wheat milling and end-use traits in China: Progress and perspectives. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2017.10.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Huo N, Zhang S, Zhu T, Dong L, Wang Y, Mohr T, Hu T, Liu Z, Dvorak J, Luo MC, Wang D, Lee JY, Altenbach S, Gu YQ. Gene Duplication and Evolution Dynamics in the Homeologous Regions Harboring Multiple Prolamin and Resistance Gene Families in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:673. [PMID: 29875781 PMCID: PMC5974169 DOI: 10.3389/fpls.2018.00673] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/03/2018] [Indexed: 05/19/2023]
Abstract
Improving end-use quality and disease resistance are important goals in wheat breeding. The genetic loci controlling these traits are highly complex, consisting of large families of prolamin and resistance genes with members present in all three homeologous A, B, and D genomes in hexaploid bread wheat. Here, orthologous regions harboring both prolamin and resistance gene loci were reconstructed and compared to understand gene duplication and evolution in different wheat genomes. Comparison of the two orthologous D regions from the hexaploid wheat Chinese Spring and the diploid progenitor Aegilops tauschii revealed their considerable difference due to the presence of five large structural variations with sizes ranging from 100 kb to 2 Mb. As a result, 44% of the Ae. tauschii and 71% of the Chinese Spring sequences in the analyzed regions, including 79 genes, are not shared. Gene rearrangement events, including differential gene duplication and deletion in the A, B, and D regions, have resulted in considerable erosion of gene collinearity in the analyzed regions, suggesting rapid evolution of prolamin and resistance gene families after the separation of the three wheat genomes. We hypothesize that this fast evolution is attributed to the co-evolution of the two gene families dispersed within a high recombination region. The identification of a full set of prolamin genes facilitated transcriptome profiling and revealed that the A genome contributes the least to prolamin expression because of its smaller number of expressed intact genes and their low expression levels, while the B and D genomes contribute similarly.
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Affiliation(s)
- Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Shengli Zhang
- Hena Institute of Science and Technology, Xinxiang, China
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Toni Mohr
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Tiezhu Hu
- Hena Institute of Science and Technology, Xinxiang, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jong-Yeol Lee
- National Institute of Agricultural Science, Rural Development Administration, Jeonju, South Korea
| | - Susan Altenbach
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
- *Correspondence: Susan Altenbach, Yong Q. Gu,
| | - Yong Q. Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
- *Correspondence: Susan Altenbach, Yong Q. Gu,
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20
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Beom HR, Kim JS, Jang YR, Lim SH, Kim CK, Lee CK, Lee JY. Proteomic analysis of low-molecular-weight glutenin subunits and relationship with their genes in a common wheat variety. 3 Biotech 2018; 8:56. [PMID: 29354367 DOI: 10.1007/s13205-017-1081-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/28/2017] [Indexed: 11/30/2022] Open
Abstract
Although many studies on low-molecular-weight glutenin subunit (LMW-GS) function have been reported, a comprehensive comparison between specific genes and their protein product is still lacking. This study aimed to link the 43 genes isolated from the Korean wheat variety "Jokyoung" in the authors' previous study to their protein products. Proteins were separated using two-dimensional gel electrophoresis (2-DGE) and identified by tandem mass spectrometry (MS/MS) at the gene haplotype level. Using MS/MS analysis of 17 protein spots, two spots were identified in the Glu-A3 locus and the corresponding haplotype was GluA3-13(Glu-A3c). Six spots were identified in the Glu-B3 locus and the corresponding haplotypes were GluB3-33 and GluB3-43 (Glu-B3h). Eight spots were identified in the Glu-D3 locus and the corresponding haplotypes were GluD3-11, GluD3-21, GluD3-31, GluD3-5, and GluD3-6 (Glu-D3a), and one spot was contaminated with gamma gliadin. Phylogenetic analysis and alignment of nucleotide and amino acid sequences assigned 35 of the 43 genes to seven haplotypes: GluA3-13, GluB3-43, GluD3-11, GluD3-21, GluD3-31, GluD3-42, and GluD3-5. Taken together, except for GluB3-33 and GluD3-6, which were not isolated, linking of each gene to the corresponding protein products at the gene haplotype level was accomplished using proteomic tools and phylogenetic analysis.
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Affiliation(s)
- Hye-Rang Beom
- National Institute of Agricultural Science, RDA, Jeonju, 54874 Republic of Korea
| | - Jin Sun Kim
- National Institute of Agricultural Science, RDA, Jeonju, 54874 Republic of Korea
| | - You-Ran Jang
- National Institute of Agricultural Science, RDA, Jeonju, 54874 Republic of Korea
| | - Sun-Hyung Lim
- National Institute of Agricultural Science, RDA, Jeonju, 54874 Republic of Korea
| | - Chang-Kug Kim
- National Institute of Agricultural Science, RDA, Jeonju, 54874 Republic of Korea
| | - Choung Keun Lee
- National Institute of Agricultural Science, RDA, Jeonju, 54874 Republic of Korea
| | - Jong-Yeol Lee
- National Institute of Agricultural Science, RDA, Jeonju, 54874 Republic of Korea
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Huo N, Dong L, Zhang S, Wang Y, Zhu T, Mohr T, Altenbach S, Liu Z, Dvorak J, Anderson OD, Luo MC, Wang D, Gu YQ. New insights into structural organization and gene duplication in a 1.75-Mb genomic region harboring the α-gliadin gene family in Aegilops tauschii, the source of wheat D genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:571-583. [PMID: 28857322 DOI: 10.1111/tpj.13675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Among the wheat prolamins important for its end-use traits, α-gliadins are the most abundant, and are also a major cause of food-related allergies and intolerances. Previous studies of various wheat species estimated that between 25 and 150 α-gliadin genes reside in the Gli-2 locus regions. To better understand the evolution of this complex gene family, the DNA sequence of a 1.75-Mb genomic region spanning the Gli-2 locus was analyzed in the diploid grass, Aegilops tauschii, the ancestral source of D genome in hexaploid bread wheat. Comparison with orthologous regions from rice, sorghum, and Brachypodium revealed rapid and dynamic changes only occurring to the Ae. tauschii Gli-2 region, including insertions of high numbers of non-syntenic genes and a high rate of tandem gene duplications, the latter of which have given rise to 12 copies of α-gliadin genes clustered within a 550-kb region. Among them, five copies have undergone pseudogenization by various mutation events. Insights into the evolutionary relationship of the duplicated α-gliadin genes were obtained from their genomic organization, transcription patterns, transposable element insertions and phylogenetic analyses. An ancestral glutamate-like receptor (GLR) gene encoding putative amino acid sensor in all four grass species has duplicated only in Ae. tauschii and generated three more copies that are interspersed with the α-gliadin genes. Phylogenetic inference and different gene expression patterns support functional divergence of the Ae. tauschii GLR copies after duplication. Our results suggest that the duplicates of α-gliadin and GLR genes have likely taken different evolutionary paths; conservation for the former and neofunctionalization for the latter.
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Affiliation(s)
- Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shengli Zhang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Toni Mohr
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Susan Altenbach
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Olin D Anderson
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
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22
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Sajjad M, Ma X, Habibullah Khan S, Shoaib M, Song Y, Yang W, Zhang A, Liu D. TaFlo2-A1, an ortholog of rice Flo2, is associated with thousand grain weight in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:164. [PMID: 29037166 PMCID: PMC5644068 DOI: 10.1186/s12870-017-1114-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND The Flo2 gene is a member of a conserved gene family in plants. This gene has been found to be related to thousand grain weight (TGW) in rice. Its orthologs in hexaploid wheat were cloned, and the haplotype variation in TaFlo2-A1 was tested for association with TGW. RESULTS The cloned sequences of TaFlo2-A1, TaFlo2-B1 and TaFlo2-D1 contained 23, 23 and 24 exons, respectively. The deduced proteins of TaFlo2-A1 (1734 aa), TaFlo2-B1 (1698 aa) and TaFlo2-D1 (1682 aa) were highly similar (>94%) and exhibited >77% similarity with the rice FLO2 protein. Like the rice FLO2 protein, four tetratricopeptide repeat (TPR) motifs were observed in the deduced TaFLO2 protein. An 8-bp InDel (-10 to -17 bp) in the promoter region and five SNPs in first intron of TaFlo2-A1 together formed two haplotypes, TaFlo2-A1a and TaFlo2-A1b, in bread wheat. TaFlo2 was located on homeologous group 2 chromosomes. TaFlo2-A1 was inferred to be located on deletion bin '2AL1-0.85-1.00'. The TaFlo2-A1 haplotypes were characterized in the Chinese Micro Core Collection (MCC) and Pakistani wheat collection using the molecular marker TaFlo2-Indel8. TaFlo2-A1 was found to be associated with TGW but not with grain number per spike (GpS) in both the MCC and Pakistani wheat collections. The frequency of TaFlo2-A1b (positive haplotype) was low in commercial wheat cultivars; thus this haplotype can be selected to improve grain weight without negatively affecting GpS. The expression level of TaFlo2-A1 in developing grains at 5 DAF (days after flowering) was positively correlated with TGW in cultivars carrying the positive haplotype. CONCLUSION This study will likely lead to additional investigations to understand the regulatory mechanism of the Flo2 gene in hexaploid wheat. Furthermore, the newly developed molecular marker 'TaFlo2-InDel8' could be incorporated into the kit of wheat breeders for use in marker-assisted selection.
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Affiliation(s)
- Muhammad Sajjad
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,Department of Environmental Sciences, COMSATS Institute of Information Technology, Vehari, 61100, Pakistan
| | - Xiaoling Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sultan Habibullah Khan
- U.S.-Pakistan Center for Advanced Studies in Agriculture and Food Security (US-PCAS-AFS), University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Muhammad Shoaib
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhong Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China. .,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China.
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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23
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Ibba MI, Kiszonas AM, Morris CF. Influence of Low-Molecular-Weight Glutenin Subunit Haplotypes on Dough Rheology in Elite Common Wheat Varieties. Cereal Chem 2017. [DOI: 10.1094/cchem-07-17-0137-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Maria I. Ibba
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, U.S.A
| | | | - Craig F. Morris
- USDA-ARS Western Wheat Quality Laboratory, Pullman, WA, U.S.A
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24
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Wang Z, Li Y, Yang Y, Liu X, Qin H, Dong Z, Zheng S, Zhang K, Wang D. New insight into the function of wheat glutenin proteins as investigated with two series of genetic mutants. Sci Rep 2017; 7:3428. [PMID: 28611351 PMCID: PMC5469833 DOI: 10.1038/s41598-017-03393-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/27/2017] [Indexed: 11/21/2022] Open
Abstract
Among the three major food crops (rice, wheat and maize), wheat is unique in accumulating gluten proteins in its grains. Of these proteins, the high and low molecular weight glutenin subunits (HMW-GSs and LMW-GSs) form glutenin macropolymers that are vital for the diverse end-uses of wheat grains. In this work, we developed a new series of deletion mutants lacking one or two of the three Glu-1 loci (Glu-A1, -B1 and -D1) specifying HMW-GSs. Comparative analysis of single and double deletion mutants reinforced the suggestion that Glu-D1 (encoding the HMW-GSs 1Dx2 and 1Dy12) has the largest effects on the parameters related to gluten and dough functionalities and breadmaking quality. Consistent with this suggestion, the deletion mutants lacking Glu-D1 or its combination with Glu-A1 or Glu-B1 generally exhibited strong decreases in functional glutenin macropolymers (FGMPs) and in the incorporation of HMW-GSs and LMW-GSs into FGMPs. Further examination of two knockout mutants missing 1Dx2 or 1Dy12 showed that 1Dx2 was clearly more effective than 1Dy12 in promoting FGMPs by enabling the incorporation of more HMW-GSs and LMW-GSs into FGMPs. The new insight obtained and the mutants developed by us may aid further research on the control of wheat end-use quality by glutenin proteins.
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Affiliation(s)
- Zhaojun Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiwen Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yushuang Yang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenying Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuhai Zheng
- Zhaoxian Institute of Agricultural Sciences, Zhaoxian, 051530, China
| | - Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Collaborative Innovation Center for Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.
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25
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Ibba MI, Kiszonas AM, Morris CF. Evidence of intralocus recombination at the Glu-3 loci in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:891-902. [PMID: 28289804 DOI: 10.1007/s00122-017-2858-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/17/2017] [Indexed: 06/06/2023]
Abstract
Recombination at the Glu-3 loci was identified, and strong genetic linkage was observed only between the amplicons representing i-type and s-type genes located, respectively, at the Glu-A3 and Glu-B3 loci. The low-molecular weight glutenin subunits (LMW-GSs) are one of the major components of wheat seed storage proteins and play a critical role in the determination of wheat end-use quality. The genes encoding this class of proteins are located at the orthologous Glu-3 loci (Glu-A3, Glu-B3, and Glu-D3). Due to the complexity of these chromosomal regions and the high sequence similarity between different LMW-GS genes, their organization and recombination characteristics are still incompletely understood. This study examined intralocus recombination at the Glu-3 loci in two recombinant inbred line (RIL) and one doubled haploid (DH) population, all segregating for the Glu-A3, Glu-B3, and Glu-D3 loci. The analysis was conducted using a gene marker system that consists of the amplification of the complete set of the LMW-GS genes and their visualization by capillary electrophoresis. Recombinant marker haplotypes were detected in all three populations with different recombination rates depending on the locus and the population. No recombination was observed between the amplicons representing i-type and s-type LMW-GS genes located, respectively, at the Glu-A3 and Glu-B3 loci, indicating tight linkage between these genes. Results of this study contribute to better understanding the genetic linkage and recombination between different LMW-GS genes, the structure of the Glu-3 loci, and the development of more specific molecular markers that better represent the genetic diversity of these loci. In this way, a more precise analysis of the contribution of various LMW-GSs to end-use quality of wheat may be achieved.
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Affiliation(s)
- Maria I Ibba
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | | | - Craig F Morris
- USDA-ARS Western Wheat Quality Laboratory, Pullman, WA, USA.
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26
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Teng W, Zhao YY, Zhao XQ, He X, Ma WY, Deng Y, Chen XP, Tong YP. Genome-wide Identification, Characterization, and Expression Analysis of PHT1 Phosphate Transporters in Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:543. [PMID: 28443126 PMCID: PMC5386973 DOI: 10.3389/fpls.2017.00543] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
The PHT1 family of phosphate (Pi) transporters mediates phosphorus (P) uptake and re-mobilization in plants. A genome-wide sequence analysis of PHT1 genes in wheat (Triticum aestivum) was conducted, and their expression locations and responses to P availability were further investigated. We cloned 21 TaPHT1 genes from the homologous alleles at TaPHT1.1 to 1.10 through screening a BAC library and amplifying genomic sequences. The TaPHT1 transporters were clustered into five branches in the phylogenetic tree of PHT1 proteins, and the TaPHT1 genes from a given branch shared high similarities in sequences, expression locations, and responses to P availability. The seven tested PHT1 genes all showed Pi-transport activity in yeast (Saccharomyces cerevisiae) cells grown under both low Pi and high Pi conditions. The expression of TaPHT1.1/1.9, 1.2, and 1.10 were root specific. The expression of these TaPHT1 genes at flowering positively correlated with P uptake after stem elongation across three P application rates and two wheat varieties in a field experiment. Therefore, modification of PHT1 expression may improve P use efficiency in a broad regime of P availability.
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Affiliation(s)
- Wan Teng
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yan-Yan Zhao
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Xue-Qiang Zhao
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Xue He
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Wen-Ying Ma
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Yan Deng
- Institute of Tropical Agriculture and Forestry, Hainan UniversityHaikou, China
| | - Xin-Ping Chen
- Research Center of Resource, Environment and Food Security, China Agricultural UniversityBeijing, China
| | - Yi-Ping Tong
- The State Key Laboratory for Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
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27
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Cuesta S, Alvarez JB, Guzmán C. Identification and molecular characterization of novel LMW-m and -s glutenin genes, and a chimeric -m/-i glutenin gene in 1A chromosome of three diploid Triticum species. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2017.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Ibba MI, Kiszonas AM, Guzmán C, Morris CF. Definition of the low molecular weight glutenin subunit gene family members in a set of standard bread wheat (Triticum aestivum L.) varieties. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2017.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Yu K, Liu D, Wu W, Yang W, Sun J, Li X, Zhan K, Cui D, Ling H, Liu C, Zhang A. Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring. THEORETICAL AND APPLIED GENETICS 2016; 130:53-70. [PMID: 27659843 DOI: 10.1007/s00122-016-2791-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/12/2016] [Indexed: 11/26/2022]
Abstract
KEY MESSAGE An integrated genetic map was constructed for einkorn wheat A genome and provided valuable information for QTL mapping and genome sequence anchoring. Wheat is one of the most widely grown food grain crops in the world. The construction of a genetic map is a key step to organize biologically or agronomically important traits along the chromosomes. In the present study, an integrated linkage map of einkorn wheat was developed using 109 recombinant inbred lines (RILs) derived from an inter sub-specific cross, KT1-1 (T. monococcum ssp. boeoticum) × KT3-5 (T. monococcum ssp. monococcum). The map contains 926 molecular markers assigned to seven linkage groups, and covers 1,377 cM with an average marker interval of 1.5 cM. A quantitative trait locus (QTL) analysis of five agronomic traits identified 16 stable QTL on all seven chromosomes, except 6A. The total phenotypic variance explained by these stable QTL using multiple regressions varied across environments from 8.8 to 87.1 % for days to heading, 24.4-63.0 % for spike length, 48.2-79.6 % for spikelet number per spike, 13.1-48.1 % for plant architecture, and 12.2-26.5 % for plant height, revealing that much of the RIL phenotypic variation had been genetically dissected. Co-localizations of closely linked QTL for different traits were frequently observed, especially on 3A and 7A. The QTL on 3A, 5A and 7A were closely associated with Eps-A m 3, Vrn1 and Vrn3 loci, respectively. Furthermore, this genetic map facilitated the anchoring of 237 T. urartu scaffolds onto seven chromosomes with a physical length of 26.15 Mb. This map and the QTL data provide valuable genetic information to dissect important agronomic and developmental traits in diploid wheat and contribute to the genetic ordering of the genome assembly.
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Affiliation(s)
- Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, People's Republic of China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Wenying Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Kehui Zhan
- Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Dangqun Cui
- Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Chunming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, People's Republic of China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, Henan, 450002, People's Republic of China.
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30
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Dong L, Huo N, Wang Y, Deal K, Wang D, Hu T, Dvorak J, Anderson OD, Luo MC, Gu YQ. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:495-506. [PMID: 27228577 DOI: 10.1111/tpj.13214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi-gene families, the DNA sequence of a 2.8-Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance-like gene families, was analyzed in the diploid grass Aegilops tauschii, the D-genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non-syntenic genes and only 13 ancestral genes are shared among these grass species. These non-syntenic genes, including prolamin and resistance-like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non-syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin-related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance-like genes and subsequent differential expansion of each R gene family. The high frequency of non-syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8-Mb region with nine-fold higher than the genome-wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.
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Affiliation(s)
- Lingli Dong
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Karin Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tiezhu Hu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Olin D Anderson
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA.
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31
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Peng Y, Yu Z, Islam S, Zhang Y, Wang X, Lei Z, Yu K, Sun D, Ma W. Allelic variation of LMW-GS composition in Chinese wheat landraces of the Yangtze-River region detected by MALDI-TOF-MS. BREEDING SCIENCE 2016; 66:646-652. [PMID: 27795690 PMCID: PMC5010313 DOI: 10.1270/jsbbs.16050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Low molecular weight glutenin subunits are important components of wheat storage proteins, which play an important role in determining end-use quality of common wheat. A newly established matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) procedure was used to analyze 478 landraces of bread wheat collected from the Yangtze-River region in China. Results indicated that 17 alleles at three loci: Glu-A3, Glu-B3 and Glu-D3 were identified, resulting in 87 different allele combinations. Of the 17 alleles detected at all the Glu-3 loci, five belonged to Glu-A3, seven to Glu-B3 and five to Glu-D3 locus. MALDI-TOF-MS indicated Glu-A3a/c was present in 72.8%, Glu-A3b in 8.4%, Glu-A3d in 8.4%, Glu-A3f in 5.2% and Glu-A3e in 3.6% lines. Seven types of alleles were identified at the Glu-B3 locus: Glu-B3d/i (25.5%), Glu-B3b (21.3%), Glu-B3c (16.9%), Glu-B3h (13.8%), Glu-B3f (8.4%), Glu-B3a (8.2%), and Glu-B3g (5.2%). Five types of Glu-D3 alleles were detected: Glu-D3a (58.4%), Glu-D3c (22.6%), Glu-D3d (15.5%), Glu-D3b (3.3%) and Glu-D3f (0.2%). Four new alleles that showed abnormal MALDI-TOF spectrum patterns were identified at the Glu-A3 and Glu-B3 loci. A detailed study is needed to further characterize these alleles and their potential usage for wheat improvement.
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Affiliation(s)
- Yanchun Peng
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan 430070,
China
- State Agriculture Biotechnology Centre, Murdoch Unievrsity,
WA 6150,
Australia
- Australian Export Grain Innovation Centre,
Perth, WA 6150,
Australia
| | - Zitong Yu
- State Agriculture Biotechnology Centre, Murdoch Unievrsity,
WA 6150,
Australia
- Australian Export Grain Innovation Centre,
Perth, WA 6150,
Australia
| | - Shahidul Islam
- State Agriculture Biotechnology Centre, Murdoch Unievrsity,
WA 6150,
Australia
- Australian Export Grain Innovation Centre,
Perth, WA 6150,
Australia
| | - Yujuan Zhang
- State Agriculture Biotechnology Centre, Murdoch Unievrsity,
WA 6150,
Australia
- Australian Export Grain Innovation Centre,
Perth, WA 6150,
Australia
| | - Xiaolong Wang
- State Agriculture Biotechnology Centre, Murdoch Unievrsity,
WA 6150,
Australia
- Australian Export Grain Innovation Centre,
Perth, WA 6150,
Australia
| | - Zhensheng Lei
- Wheat Research Institute, Henan Academy of Agricultural Sciences,
Zhengzhou 450002,
China
| | - Kan Yu
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan 430070,
China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan 430070,
China
- Hubei Collaborative Innovation Center for Grain Industry,
Jingzhou 434025,
China
| | - Wujun Ma
- State Agriculture Biotechnology Centre, Murdoch Unievrsity,
WA 6150,
Australia
- Australian Export Grain Innovation Centre,
Perth, WA 6150,
Australia
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Zhang J, Li B, Yang Y, Mu P, Qian W, Dong L, Zhang K, Liu X, Qin H, Ling H, Wang D. A novel allele of L-galactono-1,4-lactone dehydrogenase is associated with enhanced drought tolerance through affecting stomatal aperture in common wheat. Sci Rep 2016; 6:30177. [PMID: 27443220 PMCID: PMC4957090 DOI: 10.1038/srep30177] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/28/2016] [Indexed: 12/18/2022] Open
Abstract
In higher plants, L-galactono-1,4-lactone dehydrogenase (GLDH) plays important roles in ascorbic acid (AsA) biosynthesis and assembly of respiration complex I. Here we report three homoeologous genes (TaGLDH-A1, -B1 and -D1) encoding common wheat GLDH isozymes and a unique allelic variant (TaGLDH-A1b) associated with enhanced drought tolerance. TaGLDH-A1, -B1 and -D1 were located on chromosomes 5A, 5B and 5D, respectively, and their transcripts were found in multiple organs. The three homoeologs each conferred increased GLDH activity when ectopically expressed in tobacco. Decreasing TaGLDH expression in wheat significantly reduced GLDH activity and AsA content. TaGLDH-A1b differed from wild type allele TaGLDH-A1a by an in-frame deletion of three nucleotides. TaGLDH-A1b was biochemically less active than TaGLDH-A1a, and the total GLDH activity levels were generally lower in the cultivars carrying TaGLDH-A1b relative to those with TaGLDH-A1a. Interestingly, TaGLDH-A1b cultivars showed stronger water deficiency tolerance than TaGLDH-A1a cultivars, and TaGLDH-A1b co-segregated with decreased leaf water loss in a F2 population. Finally, TaGLDH-A1b cultivars generally exhibited smaller leaf stomatal aperture than TaGLDH-A1a varieties in control or water deficiency environments. Our work provides new information on GLDH genes and function in higher plants. TaGLDH-A1b is likely useful for further studying and improving wheat tolerance to drought stress.
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Affiliation(s)
- Juncheng Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanping Yang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyuan Mu
- Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Shihezi 832000, China
| | - Weiqiang Qian
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingli Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongqing Ling
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,The Collaborative Innovation Center for Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
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Low molecular weight glutenin subunit gene Glu-B3h confers superior dough strength and breadmaking quality in wheat (Triticum aestivum L.). Sci Rep 2016; 6:27182. [PMID: 27273251 PMCID: PMC4895167 DOI: 10.1038/srep27182] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/13/2016] [Indexed: 11/09/2022] Open
Abstract
Low molecular weight glutenin subunit is one of the important quality elements in wheat (Triticum aestivum L.). Although considerable allelic variation has been identified, the functional properties of individual alleles at Glu-3 loci are less studied. In this work, we performed the first comprehensive study on the molecular characteristics and functional properties of the Glu-B3h gene using the wheat cultivar CB037B and its Glu-B3 deletion line CB037C. The results showed that the Glu-B3h deletion had no significant effects on plant morphological or yield traits, but resulted in a clear reduction in protein body number and size and main quality parameters, including inferior mixing property, dough strength, loaf volume, and score. Molecular characterization showed that the Glu-B3h gene consists of 1179 bp, and its encoded B-subunit has a longer repetitive domain and an increased number of α-helices, as well as higher expression, which could contribute to superior flour quality. The SNP-based allele-specific PCR markers designed for the Glu-B3h gene were developed and validated with bread wheat holding various alleles at Glu-B3 locus, which could effectively distinguish the Glu-B3h gene from others at the Glu-B3 locus, and have potential applications for wheat quality improvement through marker-assisted selection.
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Comprehensive identification of LMW-GS genes and their protein products in a common wheat variety. Funct Integr Genomics 2016; 16:269-79. [PMID: 26882917 DOI: 10.1007/s10142-016-0482-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 01/24/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
Although it is well known that low-molecular-weight glutenin subunits (LMW-GS) from wheat affect bread and noodle processing quality, the function of specific LMW-GS proteins remains unclear. It is important to find the genes that correspond to individual LMW-GS proteins in order to understand the functions of specific proteins. The objective of this study was to link LMW-GS genes and haplotypes characterized using well known Glu-A3, Glu-B3, and Glu-D3 gene-specific primers to their protein products in a single wheat variety. A total of 36 LMW-GS genes and pseudogenes were amplified from the Korean cultivar Keumkang. These include 11 Glu-3 gene haplotypes, two from the Glu-A3 locus, two from the Glu-B3 locus, and seven from the Glu-D3 locus. To establish relationships between gene haplotypes and their protein products, a glutenin protein fraction was separated by two-dimensional gel electrophoresis (2-DGE) and 17 protein spots were analyzed by N-terminal amino acid sequencing and tandem mass spectrometry (MS/MS). LMW-GS proteins were identified that corresponded to all Glu-3 gene haplotypes except the pseudogenes. This is the first report of the comprehensive characterization of LMW-GS genes and their corresponding proteins in a single wheat cultivar. Our approach will be useful to understand the contributions of individual LMW-GS to the end-use quality of flour.
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35
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Dong L, Liu H, Zhang J, Yang S, Kong G, Chu JSC, Chen N, Wang D. Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research. BMC Genomics 2015; 16:1039. [PMID: 26645802 PMCID: PMC4673716 DOI: 10.1186/s12864-015-2257-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/30/2015] [Indexed: 11/25/2022] Open
Abstract
Background The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging single-molecule real-time (SMRT) sequencing technology PacBio RSII, and assessed the resultant data for improving common wheat genome annotation and grain transcriptome research. Results We obtained 197,709 full-length non-chimeric (FLNC) reads, 74.6 % of which were estimated to carry complete open reading frame. A total of 91,881 high-quality FLNC reads were identified and mapped to 16,188 chromosomal loci, corresponding to 13,162 known genes and 3026 new genes not annotated previously. Although some FLNC reads could not be unambiguously mapped to the current draft genome sequence, many of them are likely useful for studying highly similar homoeologous or paralogous loci or for improving chromosomal contig assembly in further research. The 91,881 high-quality FLNC reads represented 22,768 unique transcripts, 9591 of which were newly discovered. We found 180 transcripts each spanning two or three previously annotated adjacent loci, suggesting that they should be merged to form correct gene models. Finally, our data facilitated the identification of 6030 genes differentially regulated during caryopsis development, and full-length transcripts for 72 transcribed gluten gene members that are important for the end-use quality control of common wheat. Conclusions Our work demonstrated the value of PacBio transcript sequencing for improving common wheat genome annotation through uncovering the loci and full-length transcripts not discovered previously. The resource obtained may aid further structural genomics and grain transcriptome studies of common wheat. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2257-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lingli Dong
- The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hongfang Liu
- Frasergen, Wuhan East Lake High-tech Zone, Wuhan, 430075, China.
| | - Juncheng Zhang
- The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Shuangjuan Yang
- The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Guanyi Kong
- Frasergen, Wuhan East Lake High-tech Zone, Wuhan, 430075, China.
| | - Jeffrey S C Chu
- Frasergen, Wuhan East Lake High-tech Zone, Wuhan, 430075, China. .,School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Nansheng Chen
- School of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430075, China. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Daowen Wang
- The State Key Laboratory of Plant cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,The Collaborative Innovation Center for Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.
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Towards the understanding of end-use quality in intermediate wheatgrass (Thinopyrum intermedium): High-molecular-weight glutenin subunits, protein polymerization, and mixing characteristics. J Cereal Sci 2015. [DOI: 10.1016/j.jcs.2015.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cuesta S, Guzmán C, Alvarez JB. Molecular characterization of novel LMW-i glutenin subunit genes from Triticum urartu Thum. ex Gandil. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2155-65. [PMID: 26152575 DOI: 10.1007/s00122-015-2574-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 06/23/2015] [Indexed: 05/07/2023]
Abstract
A high level of genetic diversity was found in LMW-i genes from Triticum urartu, resulting in detection of 11 novel alleles. The variability detected could affect gluten quality. Low-molecular weight glutenin subunits are important in determining the viscoelastic properties of wheat dough. Triticum urartu Thum. ex Gandil., which is related to the A genome of polyploid wheat, has been shown as a good source of variation for these subunits. The present study evaluated the variability of LMW-i genes in this species. High polymorphism was found in the sequences analysed and resulted in the detection of 11 novel alleles, classified into two sets (Group-I and -II) showing unique SNPs and InDels. Both groups were associated with Glu-A3-1 genes from common wheat. In general, deduced proteins from Group-II genes possessed a higher proportion of glutamine and proline, which has been previously suggested to be related with good quality. Moreover, there were other changes compared to common wheat. This novel variation could affect dough quality. Additional epitopes for celiac disease were also detected, suggesting that these subunits could be highly reactive. The results showed that T. urartu could be an important source of genetic variability for LMW-i genes that could enlarge the genetic pool of modern wheat.
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Affiliation(s)
- Susana Cuesta
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Universidad de Córdoba, Campus de Rabanales, CeiA3, 14071, Córdoba, Spain
| | - Carlos Guzmán
- Wheat Chemistry and Quality Laboratory, Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Juan B Alvarez
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Universidad de Córdoba, Campus de Rabanales, CeiA3, 14071, Córdoba, Spain.
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Genetic analysis of chromosomal loci affecting the content of insoluble glutenin in common wheat. J Genet Genomics 2015; 42:495-505. [PMID: 26408094 DOI: 10.1016/j.jgg.2015.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/10/2015] [Accepted: 04/27/2015] [Indexed: 11/21/2022]
Abstract
In common wheat, insoluble glutenin (IG) is an important fraction of flour glutenin macropolymers, and insoluble glutenin content (IGC) is positively associated with key end-use quality parameters. Here, we present a genetic analysis of the chromosomal loci affecting IGC with the data collected from 90 common wheat varieties cultivated in four environments. Statistical analysis showed that IGC was controlled mainly genetically and influenced by the environment. Among the major genetic components known to affect end-use quality, 1BL/1RS translocation had a significantly negative effect on IGC across all four environments. As to the different alleles of Glu-A1, -B1 and -D1 loci, Glu-A1a, Glu-B1b and Glu-D1d exhibited relatively strong positive effects on IGC in all environments. To identify new loci affecting IGC, association mapping with 1355 DArT markers was conducted. A total of 133 markers were found associated with IGC in two or more environments (P < 0.05), ten of which consistently affected IGC in all four environments. The phenotypic variance explained by the ten markers varied from 4.66% to 8.03%, and their elite alleles performed significantly better than the inferior counterparts in enhancing IGC. Among the ten markers, wPt-3743 and wPt-733835 reflected the action of Glu-D1, and wPt-664972 probably indicated the effect of Glu-A1. The other seven markers, forming three clusters on 2AL, 3BL or 7BL chromosome arms, represented newly identified genetic determinants of IGC. Our work provided novel insights into the genetic control of IGC, which may facilitate wheat end-use quality improvement through molecular breeding in the future.
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39
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Zhang Y, Luo G, Liu D, Wang D, Yang W, Sun J, Zhang A, Zhan K. Genome-, Transcriptome- and Proteome-Wide Analyses of the Gliadin Gene Families in Triticum urartu. PLoS One 2015; 10:e0131559. [PMID: 26132381 PMCID: PMC4489009 DOI: 10.1371/journal.pone.0131559] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/03/2015] [Indexed: 12/30/2022] Open
Abstract
Gliadins are the major components of storage proteins in wheat grains, and they play an essential role in the dough extensibility and nutritional quality of flour. Because of the large number of the gliadin family members, the high level of sequence identity, and the lack of abundant genomic data for Triticum species, identifying the full complement of gliadin family genes in hexaploid wheat remains challenging. Triticum urartu is a wild diploid wheat species and considered the A-genome donor of polyploid wheat species. The accession PI428198 (G1812) was chosen to determine the complete composition of the gliadin gene families in the wheat A-genome using the available draft genome. Using a PCR-based cloning strategy for genomic DNA and mRNA as well as a bioinformatics analysis of genomic sequence data, 28 gliadin genes were characterized. Of these genes, 23 were α-gliadin genes, three were γ-gliadin genes and two were ω-gliadin genes. An RNA sequencing (RNA-Seq) survey of the dynamic expression patterns of gliadin genes revealed that their synthesis in immature grains began prior to 10 days post-anthesis (DPA), peaked at 15 DPA and gradually decreased at 20 DPA. The accumulation of proteins encoded by 16 of the expressed gliadin genes was further verified and quantified using proteomic methods. The phylogenetic analysis demonstrated that the homologs of these α-gliadin genes were present in tetraploid and hexaploid wheat, which was consistent with T. urartu being the A-genome progenitor species. This study presents a systematic investigation of the gliadin gene families in T. urartu that spans the genome, transcriptome and proteome, and it provides new information to better understand the molecular structure, expression profiles and evolution of the gliadin genes in T. urartu and common wheat.
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Affiliation(s)
- Yanlin Zhang
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, Zhengzhou, China
| | - Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Aimin Zhang
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- * E-mail: (KZ); (AZ)
| | - Kehui Zhan
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, Zhengzhou, China
- * E-mail: (KZ); (AZ)
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Luo G, Zhang X, Zhang Y, Yang W, Li Y, Sun J, Zhan K, Zhang A, Liu D. Composition, variation, expression and evolution of low-molecular-weight glutenin subunit genes in Triticum urartu. BMC PLANT BIOLOGY 2015; 15:68. [PMID: 25849991 PMCID: PMC4364320 DOI: 10.1186/s12870-014-0322-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/06/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Wheat (AABBDD, 2n = 6x = 42) is a major dietary component for many populations across the world. Bread-making quality of wheat is mainly determined by glutenin subunits, but it remains challenging to elucidate the composition and variation of low-molecular-weight glutenin subunits (LMW-GS) genes, the major components for glutenin subunits in hexaploid wheat. This problem, however, can be greatly simplified by characterizing the LMW-GS genes in Triticum urartu, the A-genome donor of hexaploid wheat. In the present study, we exploited the high-throughput molecular marker system, gene cloning, proteomic methods and molecular evolutionary genetic analysis to reveal the composition, variation, expression and evolution of LMW-GS genes in a T. urartu population from the Fertile Crescent region. RESULTS Eight LMW-GS genes, including four m-type, one s-type and three i-type, were characterized in the T. urartu population. Six or seven genes, the highest number at the Glu-A3 locus, were detected in each accession. Three i-type genes, each containing more than six allelic variants, were tightly linked because of their co-segregation in every accession. Only 2-3 allelic variants were detected for each m- and s-type gene. The m-type gene, TuA3-385, for which homologs were previously characterized only at Glu-D3 locus in common wheat and Aegilops tauschii, was detected at Glu-A3 locus in T. urartu. TuA3-460 was the first s-type gene identified at Glu-A3 locus. Proteomic analysis showed 1-4 genes, mainly i-type, expressed in individual accessions. About 62% accessions had three active i-type genes, rather than one or two in common wheat. Southeastern Turkey might be the center of origin and diversity for T. urartu due to its abundance of LMW-GS genes/genotypes. Phylogenetic reconstruction demonstrated that the characterized T. urartu might be the direct donor of the Glu-A3 locus in common wheat varieties. CONCLUSIONS Compared with the Glu-A3 locus in common wheat, a large number of highly diverse LMW-GS genes and active genes were characterized in T. urartu, demonstrating that this progenitor might provide valuable genetic resources for LMW-GS genes to improve the quality of common wheat. The phylogenetic analysis provided molecular evidence and confirmed that T. urartu was the A-genome donor of hexaploid wheat.
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Affiliation(s)
- Guangbin Luo
- />State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District Beijing, 100101 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaofei Zhang
- />State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District Beijing, 100101 China
- />Present address: Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Buford Circle, St. Paul, MN 55108 USA
| | - Yanlin Zhang
- />College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Wenlong Yang
- />State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District Beijing, 100101 China
| | - Yiwen Li
- />State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District Beijing, 100101 China
| | - Jiazhu Sun
- />State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District Beijing, 100101 China
| | - Kehui Zhan
- />College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Aimin Zhang
- />State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District Beijing, 100101 China
- />College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002 China
| | - Dongcheng Liu
- />State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District Beijing, 100101 China
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Zhen S, Han C, Ma C, Gu A, Zhang M, Shen X, Li X, Yan Y. Deletion of the low-molecular-weight glutenin subunit allele Glu-A3a of wheat (Triticum aestivum L.) significantly reduces dough strength and breadmaking quality. BMC PLANT BIOLOGY 2014; 14:367. [PMID: 25524150 PMCID: PMC4275963 DOI: 10.1186/s12870-014-0367-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/05/2014] [Indexed: 05/12/2023]
Abstract
BACKGROUND Low-molecular-weight glutenin subunits (LMW-GS), encoded by Glu-3 complex loci in hexaploid wheat, play important roles in the processing quality of wheat flour. To date, the molecular characteristics and effects on dough quality of individual Glu-3 alleles and their encoding proteins have been poorly studied. We used a Glu-A3 deletion line of the Chinese Spring (CS-n) wheat variety to conduct the first comprehensive study on the molecular characteristics and functional properties of the LMW-GS allele Glu-A3a. RESULTS The Glu-A3a allele at the Glu-A3 locus in CS and its deletion in CS-n were identified and characterized by proteome and molecular marker methods. The deletion of Glu-A3a had no significant influence on plant morphological and yield traits, but significantly reduced the dough strength and breadmaking quality compared to CS. The complete sequence of the Glu-A3a allele was cloned and characterized, which was found to encode a B-subunit with longer repetitive domains and an increased number of α-helices. The Glu-A3a-encoded B-subunit showed a higher expression level and accumulation rate during grain development. These characteristics of the Glu-A3a allele could contribute to achieving superior gluten quality and demonstrate its potential application to wheat quality improvement. Furthermore, an allele-specific polymerase chain reaction (AS-PCR) marker for the Glu-A3a allele was developed and validated using different bread wheat cultivars, including near-isogenic lines (NILs) and recombinant inbred lines (RILs), which could be used as an effective molecular marker for gluten quality improvement through marker-assisted selection. CONCLUSIONS This work demonstrated that the LMW-GS allele Glu-A3a encodes a specific LMW-i type B-subunit that significantly affects wheat dough strength and breadmaking quality. The Glu-A3a-encoded B-subunit has a long repetitive domain and more α-helix structures as well as a higher expression level and accumulation rate during grain development, which could facilitate the formation of wheat with a stronger dough structure and superior breadmaking quality.
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Affiliation(s)
- Shoumin Zhen
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Caixia Han
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Chaoying Ma
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Aiqin Gu
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Ming Zhang
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xixi Shen
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiaohui Li
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yueming Yan
- Laboratory of Molecular Genetics and Proteomics, College of Life Science, Capital Normal University, 100048 Beijing, China
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Rasheed A, Xia X, Yan Y, Appels R, Mahmood T, He Z. Wheat seed storage proteins: Advances in molecular genetics, diversity and breeding applications. J Cereal Sci 2014. [DOI: 10.1016/j.jcs.2014.01.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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44
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Zhang X, DeHaan LR, Higgins L, Markowski TW, Wyse DL, Anderson JA. New insights into high-molecular-weight glutenin subunits and sub-genomes of the perennial crop Thinopyrum intermedium (Triticeae). J Cereal Sci 2014. [DOI: 10.1016/j.jcs.2014.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Plessis A, Ravel C, Bordes J, Balfourier F, Martre P. Association study of wheat grain protein composition reveals that gliadin and glutenin composition are trans-regulated by different chromosome regions. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3627-44. [PMID: 23881399 PMCID: PMC3745720 DOI: 10.1093/jxb/ert188] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wheat grain storage protein (GSP) content and composition are the main determinants of the end-use value of bread wheat (Triticum aestivum L.) grain. The accumulation of glutenins and gliadins, the two main classes of GSP in wheat, is believed to be mainly controlled at the transcriptional level through a network of transcription factors. This regulation network could lead to stable cross-environment allometric scaling relationships between the quantity of GSP classes/subunits and the total quantity of nitrogen per grain. This work conducted a genetic mapping study of GSP content and composition and allometric scaling parameters of grain N allocation using a bread wheat worldwide core collection grown in three environments. The core collection was genotyped with 873 markers for genome-wide association and 167 single nucleotide polymorphism markers in 51 candidate genes for candidate association. The candidate genes included 35 transcription factors (TFs) expressed in grain. This work identified 74 loci associated with 38 variables, of which 19 were candidate genes or were tightly linked with candidate genes. Besides structural GSP genes, several loci putatively trans-regulating GSP accumulation were identified. Seven candidate TFs, including four wheat orthologues of barley TFs that control hordein gene expression, were associated or in strong linkage disequilibrium with markers associated with the composition or quantity of glutenin or gliadin, or allometric grain N allocation parameters, confirming the importance of the transcriptional control of GSP accumulation. Genome-wide association results suggest that the genes regulating glutenin and gliadin compositions are mostly distinct from each other and operate differently.
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Affiliation(s)
- Anne Plessis
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Catherine Ravel
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- * These authors contributed equally to this manuscript
| | - Jacques Bordes
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - François Balfourier
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
| | - Pierre Martre
- INRA, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, F-63100 Clermont-Ferrand, France
- Blaise Pascal University, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, F-63170 Aubière, France
- To whom correspondence should be addressed. E-mail:
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Effect of Glu-B3 allelic variation on sodium dodecyl sulfate sedimentation volume in common wheat (Triticum aestivum L.). ScientificWorldJournal 2013; 2013:848549. [PMID: 23861659 PMCID: PMC3703908 DOI: 10.1155/2013/848549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/03/2013] [Indexed: 11/18/2022] Open
Abstract
Sodium dodecyl sulfate (SDS) sedimentation volume has long been used to characterize wheat flours and meals with the aim of predicting processing and end-product qualities. In order to survey the influence of low-molecular-weight glutenin subunits (LMW-GSs) at Glu-B3 locus on wheat SDS sedimentation volume, a total of 283 wheat (Triticum aestivum L.) varieties including landraces and improved and introduced cultivars were analyzed using 10 allele-specific PCR markers at the Glu-B3 locus. The highest allele frequency observed in the tested varieties was Glu-B3i with 21.9% in all varieties, 21.1% in landraces, 25.5% in improved cultivars, and 12% in introduced cultivars. Glu-B3 locus represented 8.6% of the variance in wheat SDS sedimentation volume, and Glu-B3b, Glu-B3g, and Glu-B3h significantly heightened the SDS sedimentation volume, but Glu-B3a, Glu-B3c, and Glu-B3j significantly lowered the SDS sedimentation volume. For the bread-making quality, the most desirable alleles Glu-B3b and Glu-B3g become more and more popular and the least desirable alleles Glu-B3a and Glu-B3c got less and less in modern improved cultivars, suggesting that wheat grain quality in China has been significantly improved through breeding effort.
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Zhang X, Liu D, Zhang J, Jiang W, Luo G, Yang W, Sun J, Tong Y, Cui D, Zhang A. Novel insights into the composition, variation, organization, and expression of the low-molecular-weight glutenin subunit gene family in common wheat. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2027-40. [PMID: 23536608 PMCID: PMC3638834 DOI: 10.1093/jxb/ert070] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Low-molecular-weight glutenin subunits (LMW-GS), encoded by a complex multigene family, play an important role in the processing quality of wheat flour. Although members of this gene family have been identified in several wheat varieties, the allelic variation and composition of LMW-GS genes in common wheat are not well understood. In the present study, using the LMW-GS gene molecular marker system and the full-length gene cloning method, a comprehensive molecular analysis of LMW-GS genes was conducted in a representative population, the micro-core collections (MCC) of Chinese wheat germplasm. Generally, >15 LMW-GS genes were identified from individual MCC accessions, of which 4-6 were located at the Glu-A3 locus, 3-5 at the Glu-B3 locus, and eight at the Glu-D3 locus. LMW-GS genes at the Glu-A3 locus showed the highest allelic diversity, followed by the Glu-B3 genes, while the Glu-D3 genes were extremely conserved among MCC accessions. Expression and sequence analysis showed that 9-13 active LMW-GS genes were present in each accession. Sequence identity analysis showed that all i-type genes present at the Glu-A3 locus formed a single group, the s-type genes located at Glu-B3 and Glu-D3 loci comprised a unique group, while high-diversity m-type genes were classified into four groups and detected in all Glu-3 loci. These results contribute to the functional analysis of LMW-GS genes and facilitate improvement of bread-making quality by wheat molecular breeding programmes.
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Affiliation(s)
- Xiaofei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jianghua Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
- Department of Agronomy/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, China
| | - Wei Jiang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Dangqun Cui
- Department of Agronomy/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, 63 Nongye Road, Zhengzhou 450002, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing 100101, China
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Zhang X, Jin H, Zhang Y, Liu D, Li G, Xia X, He Z, Zhang A. Composition and functional analysis of low-molecular-weight glutenin alleles with Aroona near-isogenic lines of bread wheat. BMC PLANT BIOLOGY 2012; 12:243. [PMID: 23259617 PMCID: PMC3562532 DOI: 10.1186/1471-2229-12-243] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 12/17/2012] [Indexed: 05/05/2023]
Abstract
BACKGROUND Low-molecular-weight glutenin subunits (LMW-GS) strongly influence the bread-making quality of bread wheat. These proteins are encoded by a multi-gene family located at the Glu-A3, Glu-B3 and Glu-D3 loci on the short arms of homoeologous group 1 chromosomes, and show high allelic variation. To characterize the genetic and protein compositions of LMW-GS alleles, we investigated 16 Aroona near-isogenic lines (NILs) using SDS-PAGE, 2D-PAGE and the LMW-GS gene marker system. Moreover, the composition of glutenin macro-polymers, dough properties and pan bread quality parameters were determined for functional analysis of LMW-GS alleles in the NILs. RESULTS Using the LMW-GS gene marker system, 14-20 LMW-GS genes were identified in individual NILs. At the Glu-A3 locus, two m-type and 2-4 i-type genes were identified and their allelic variants showed high polymorphisms in length and nucleotide sequences. The Glu-A3d allele possessed three active genes, the highest number among Glu-A3 alleles. At the Glu-B3 locus, 2-3 m-type and 1-3 s-type genes were identified from individual NILs. Based on the different compositions of s-type genes, Glu-B3 alleles were divided into two groups, one containing Glu-B3a, B3b, B3f and B3g, and the other comprising Glu-B3c, B3d, B3h and B3i. Eight conserved genes were identified among Glu-D3 alleles, except for Glu-D3f. The protein products of the unique active genes in each NIL were detected using protein electrophoresis. Among Glu-3 alleles, the Glu-A3e genotype without i-type LMW-GS performed worst in almost all quality properties. Glu-B3b, B3g and B3i showed better quality parameters than the other Glu-B3 alleles, whereas the Glu-B3c allele containing s-type genes with low expression levels had an inferior effect on bread-making quality. Due to the conserved genes at Glu-D3 locus, Glu-D3 alleles showed no significant differences in effects on all quality parameters. CONCLUSIONS This work provided new insights into the composition and function of 18 LMW-GS alleles in bread wheat. The variation of i-type genes mainly contributed to the high diversity of Glu-A3 alleles, and the differences among Glu-B3 alleles were mainly derived from the high polymorphism of s-type genes. Among LMW-GS alleles, Glu-A3e and Glu-B3c represented inferior alleles for bread-making quality, whereas Glu-A3d, Glu-B3b, Glu-B3g and Glu-B3i were correlated with superior bread-making quality. Glu-D3 alleles played minor roles in determining quality variation in bread wheat. Thus, LMW-GS alleles not only affect dough extensibility but greatly contribute to the dough resistance, glutenin macro-polymers and bread quality.
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Affiliation(s)
- Xiaofei Zhang
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Beijing, 100101, China
| | - Hui Jin
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yan Zhang
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Beijing, 100101, China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Beijing, 100101, China
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Cloning of a conserved receptor-like protein kinase gene and its use as a functional marker for homoeologous group-2 chromosomes of the triticeae species. PLoS One 2012; 7:e49718. [PMID: 23272050 PMCID: PMC3521742 DOI: 10.1371/journal.pone.0049718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 10/12/2012] [Indexed: 11/26/2022] Open
Abstract
Receptor-like kinases (RLKs) play broad biological roles in plants. We report on a conserved receptor-like protein kinase (RPK) gene from wheat and other Triticeae species. The TaRPK1 was isolated from the Triticum aestivum cv. Prins - Triticum timopheevii introgression line IGVI-465 carrying the powdery mildew resistance gene Pm6. The TaRPK1 was mapped to homoeologous chromosomes 2A (TaRPK1-2A), 2D (TaRPK1-2D) and the Pm6-carrier chromosome 2G (TaRPK1-2G) of IGVI-465. Under the tested conditions, only the TaRPK1-2G allele was actively transcribed, producing two distinct transcripts via alternative splicing. The predicted 424-amino acid protein of TaRPK1-2G contained a signal peptide, a transmembrane domain and an intracellular serine/threonine kinase domain, but lacked a typical extracellular domain. The expression of TaRPK1-2G gene was up-regulated upon the infection by Blumeria graminis f.sp. tritici (Bgt) and treatment with methyl jasmonate (MeJA), but down-regulated in response to treatments of SA and ABA. Over-expression of TaRPK1-2G in the powdery mildew susceptible wheat variety Prins by a transient expression assay showed that it slightly reduced the haustorium index of the infected Bgt. These data indicated that TaRPK1-2G participated in the defense response to Bgt infection and in the JA signaling pathway. Phylogenetic analysis indicated that TaRPK1-2G was highly conserved among plant species, and the amino acid sequence similarity of TaRPK1-2G among grass species was more than 86%. Based on its conservation, the RPK gene-based STS primers were designed, and used to amplify the RPK orthologs from the homoeologous group-2 chromosomes of all the tested Triticeae species, such as chromosome 2G of T. timopheevii, 2R of Secale cereale, 2H of Hordeum vulgare, 2S of Aegilops speltoides, 2Sl of Ae. longissima, 2Mg of Ae. geniculata, 2Sp and 2Up of Ae. peregrina. The developed STS markers serve as conserved functional markers for the identification of homoeologous group-2 chromosomes of the Triticeae species.
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Wang S, Wang K, Chen G, Lv D, Han X, Yu Z, Li X, Ye X, Hsam SLK, Ma W, Appels R, Yan Y. Molecular characterization of LMW-GS genes in Brachypodium distachyon L. reveals highly conserved Glu-3 loci in Triticum and related species. BMC PLANT BIOLOGY 2012; 12:221. [PMID: 23171363 PMCID: PMC3547698 DOI: 10.1186/1471-2229-12-221] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/30/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND Brachypodium distachyon L. is a newly emerging model plant system for temperate cereal crop species. However, its grain protein compositions are still not clear. In the current study, we carried out a detailed proteomics and molecular genetics study on grain glutenin proteins in B. distachyon. RESULTS SDS-PAGE and RP-HPLC analysis of grain proteins showed that Brachypodium has few gliadins and high molecular weight glutenin subunits. In contrast the electrophoretic patterns for the albumin, globulin and low molecular weight glutenin subunit (LMW-GS) fractions of the grain protein were similar to those in wheat. In particular, the LMW-C type subunits in Brachypodium were more abundant than the equivalent proteins in common wheat. Southern blotting analysis confirmed that Brachypodium has 4-5 copies of LMW-GS genes. A total of 18 LMW-GS genes were cloned from Brachypodium by allele specific PCR. LMW-GS and 4 deduced amino acid sequences were further confirmed by using Western-blotting and MALDI-TOF-MS. Phylogenetic analysis indicated that Brachypodium was closer to Ae. markgrafii and Ae. umbellulata than to T. aestivum. CONCLUSIONS Brachypodium possessed a highly conserved Glu-3 locus that is closely related to Triticum and related species. The presence of LMW-GS in B. distachyon grains indicates that B. distachyon may be used as a model system for studying wheat quality attributes.
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Affiliation(s)
- Shunli Wang
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, 100081, Beijing, China
| | - Guanxing Chen
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Dongwen Lv
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xiaofeng Han
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Zitong Yu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xiaohui Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, 100081, Beijing, China
| | - SLK Hsam
- Division of Plant Breeding and Applied Genetics, Technical University of Munich, D-85350, Freising-Weihenstephan, Germany
| | - Wujun Ma
- State Agriculture Biotechnology Centre, Murdoch University; Western Australian Department of Agriculture and Food, Perth, WA, 6150, Australia
| | - Rudi Appels
- State Agriculture Biotechnology Centre, Murdoch University; Western Australian Department of Agriculture and Food, Perth, WA, 6150, Australia
| | - Yueming Yan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, 100048, Beijing, China
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