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Safdar LB, Dugina K, Saeidan A, Yoshicawa GV, Caporaso N, Gapare B, Umer MJ, Bhosale RA, Searle IR, Foulkes MJ, Boden SA, Fisk ID. Reviving grain quality in wheat through non-destructive phenotyping techniques like hyperspectral imaging. Food Energy Secur 2023; 12:e498. [PMID: 38440412 PMCID: PMC10909436 DOI: 10.1002/fes3.498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 03/06/2024] Open
Abstract
A long-term goal of breeders and researchers is to develop crop varieties that can resist environmental stressors and produce high yields. However, prioritising yield often compromises improvement of other key traits, including grain quality, which is tedious and time-consuming to measure because of the frequent involvement of destructive phenotyping methods. Recently, non-destructive methods such as hyperspectral imaging (HSI) have gained attention in the food industry for studying wheat grain quality. HSI can quantify variations in individual grains, helping to differentiate high-quality grains from those of low quality. In this review, we discuss the reduction of wheat genetic diversity underlying grain quality traits due to modern breeding, key traits for grain quality, traditional methods for studying grain quality and the application of HSI to study grain quality traits in wheat and its scope in breeding. Our critical review of literature on wheat domestication, grain quality traits and innovative technology introduces approaches that could help improve grain quality in wheat.
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Affiliation(s)
- Luqman B. Safdar
- International Flavour Research Centre, Division of Food, Nutrition and DieteticsUniversity of NottinghamLoughboroughUK
- International Flavour Research Centre (Adelaide), School of Agriculture, Food and Wine and Waite Research InstituteUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamLoughboroughUK
- Plant Research Centre, School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Kateryna Dugina
- International Flavour Research Centre, Division of Food, Nutrition and DieteticsUniversity of NottinghamLoughboroughUK
| | - Ali Saeidan
- International Flavour Research Centre, Division of Food, Nutrition and DieteticsUniversity of NottinghamLoughboroughUK
| | - Guilherme V. Yoshicawa
- Plant Research Centre, School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
| | | | - Brighton Gapare
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamLoughboroughUK
| | - M. Jawad Umer
- Cotton Research InstituteChinese Academy of Agricultural SciencesAnyangChina
| | - Rahul A. Bhosale
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamLoughboroughUK
| | - Iain R. Searle
- School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - M. John Foulkes
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamLoughboroughUK
| | - Scott A. Boden
- Plant Research Centre, School of Agriculture, Food and WineUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Ian D. Fisk
- International Flavour Research Centre, Division of Food, Nutrition and DieteticsUniversity of NottinghamLoughboroughUK
- International Flavour Research Centre (Adelaide), School of Agriculture, Food and Wine and Waite Research InstituteUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
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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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Hu J, Xiao G, Jiang P, Zhao Y, Zhang G, Ma X, Yao J, Xue L, Su P, Bao Y. QTL detection for bread wheat processing quality in a nested association mapping population of semi-wild and domesticated wheat varieties. BMC PLANT BIOLOGY 2022; 22:129. [PMID: 35313801 PMCID: PMC8935700 DOI: 10.1186/s12870-022-03523-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Wheat processing quality is an important factor in evaluating overall wheat quality, and dough characteristics are important when assessing the processing quality of wheat. As a notable germplasm resource, semi-wild wheat has a key role in the study of wheat processing quality. RESULTS In this study, four dough rheological characteristics were collected in four environments using a nested association mapping (NAM) population consisting of semi-wild and domesticated wheat varieties to identify quantitative trait loci (QTL) for wheat processing quality. A total of 49 QTL for wheat processing quality were detected, explaining 0.36-10.82% of the phenotypic variation. These QTL were located on all wheat chromosomes except for 2D, 3A, 3D, 6B, 6D and 7D. Compared to previous studies, 29 QTL were newly identified. Four novel QTL, QMlPH-1B.4, QMlPH-3B.4, QWdEm-1B.2 and QWdEm-3B.2, were stably identified in three or more environments, among which QMlPH-3B.4 was a major QTL. Moreover, eight important genetic regions for wheat processing quality were identified on chromosomes 1B, 3B and 4D, which showed pleiotropy for dough characteristics. In addition, out of 49 QTL, 15 favorable alleles came from three semi-wild parents, suggesting that the QTL alleles provided by the semi-wild parent were not utilized in domesticated varieties. CONCLUSIONS The results show that semi-wild wheat varieties can enrich the existing wheat gene pool and provide broader variation resources for wheat genetic research.
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Affiliation(s)
- Junmei Hu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 The People’s Republic of China
| | - Guilian Xiao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 The People’s Republic of China
| | - Peng Jiang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 The People’s Republic of China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 The People’s Republic of China
| | - Guangxu Zhang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, 222000 The People’s Republic of China
| | - Xin Ma
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 The People’s Republic of China
| | - Jie Yao
- Yantai Academy of Agricultural Sciences in Shandong Province, Yantai, 265500 The People’s Republic of China
| | - Lixia Xue
- Agricultural Technology Station, Sunwu Sub-district Office, Huimin County, Shandong Province 251700 Binzhou, The People’s Republic of China
| | - Peisen Su
- College of Agriculture, Liaocheng University, Liaocheng, 252059 The People’s Republic of China
| | - Yinguang Bao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 The People’s Republic of China
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Genome-wide identification, characteristics and expression of the prolamin genes in Thinopyrum elongatum. BMC Genomics 2021; 22:864. [PMID: 34852761 PMCID: PMC8638145 DOI: 10.1186/s12864-021-08088-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022] Open
Abstract
Background Prolamins, unique to Gramineae (grasses), play a key role in the human diet. Thinopyrum elongatum (syn. Agropyron elongatum or Lophopyrum elongatum), a grass of the Triticeae family with a diploid E genome (2n = 2x = 14), is genetically well-characterized, but little is known about its prolamin genes and the relationships with homologous loci in the Triticeae species. Results In this study, a total of 19 α-gliadin, 9 γ-gliadin, 19 ω-gliadin, 2 high-molecular-weight glutenin subunit (HMW-GS), and 5 low-molecular-weight glutenin subunit (LMW-GS) genes were identified in the Th. elongatum genome. Micro-synteny and phylogenetic analysis revealed dynamic changes of prolamin gene regions and genetic affinities among Th. elongatum, Triticum aestivum, T. urartu and Aegilops tauschii. The Th. elongatum genome, like the B subgenome of T. aestivum, only contained celiac disease epitope DQ8-glia-α1/DQ8.5-glia-α1, which provided a theoretical basis for the low gluten toxicity wheat breeding. The transcriptome data of Th. elongatum exhibited differential expression in quantity and pattern in the same subfamily or different subfamilies. Dough rheological properties of T. aestivum-Th. elongatum disomic substitution (DS) line 1E(1D) showed higher peak height values than that of their parents, and DS6E(6D) exhibited fewer α-gliadins, which indicates the potential usage for wheat quality breeding. Conclusions Overall, this study provided a comprehensive overview of the prolamin gene family in Th. elongatum, and suggested a promising use of this species in the generation of improved wheat breeds intended for the human diet. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08088-x.
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Metakovsky E, Melnik V, Pascual L, Wrigley CW. Some intra-varietal non-uniformities in Triticum aestivum can be explained as repeated spontaneous mutations at the Gli loci. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Metakovsky E, Pascual L, Vaccino P, Melnik V, Rodriguez-Quijano M, Popovych Y, Chebotar S, Rogers WJ. Heteroalleles in Common Wheat: Multiple Differences between Allelic Variants of the Gli-B1 Locus. Int J Mol Sci 2021; 22:ijms22041832. [PMID: 33673225 PMCID: PMC7917834 DOI: 10.3390/ijms22041832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/30/2021] [Accepted: 02/07/2021] [Indexed: 11/21/2022] Open
Abstract
The Gli-B1-encoded γ-gliadins and non-coding γ-gliadin DNA sequences for 15 different alleles of common wheat have been compared using seven tests: electrophoretic mobility (EM) and molecular weight (MW) of the encoded major γ-gliadin, restriction fragment length polymorphism patterns (RFLPs) (three different markers), Gli-B1-γ-gliadin-pseudogene known SNP markers (Single nucleotide polymorphisms) and sequencing the pseudogene GAG56B. It was discovered that encoded γ-gliadins, with contrasting EM, had similar MWs. However, seven allelic variants (designated from I to VII) differed among them in the other six tests: I (alleles Gli-B1i, k, m, o), II (Gli-B1n, q, s), III (Gli-B1b), IV (Gli-B1e, f, g), V (Gli-B1h), VI (Gli-B1d) and VII (Gli-B1a). Allele Gli-B1c (variant VIII) was identical to the alleles from group IV in four of the tests. Some tests might show a fine difference between alleles belonging to the same variant. Our results attest in favor of the independent origin of at least seven variants at the Gli-B1 locus that might originate from deeply diverged genotypes of the donor(s) of the B genome in hexaploid wheat and therefore might be called “heteroallelic”. The donor’s particularities at the Gli-B1 locus might be conserved since that time and decisively contribute to the current high genetic diversity of common wheat.
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Affiliation(s)
- Eugene Metakovsky
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (E.M.); (M.R.-Q.)
| | - Laura Pascual
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (E.M.); (M.R.-Q.)
- Correspondence:
| | - Patrizia Vaccino
- Consiglio per la Recerca in Agricultura e l’Analisi dell’Economia Agraria, Research Centre for Cereal and Industrial Crops, 13100 Vercelli, Italy;
| | - Viktor Melnik
- Vavilov Institute of General Genetics RAS, 117971 Moscow, Russia;
| | - Marta Rodriguez-Quijano
- Department of Biotechnology-Plant Biology, School of Agricultural, Food and Biosystems Engineering, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (E.M.); (M.R.-Q.)
| | - Yulia Popovych
- Department of Genetics and Molecular Biology, National I.I. Mechnikov University, 65058 Odessa, Ukraine; (Y.P.); (S.C.)
| | - Sabina Chebotar
- Department of Genetics and Molecular Biology, National I.I. Mechnikov University, 65058 Odessa, Ukraine; (Y.P.); (S.C.)
| | - William John Rogers
- Departamento de Biología Aplicada, CIISAS, CIC-BIOLAB, CONICET-INBIOTEC, CRESCA, Facultad de Agronomía, Universidad Nacional del Centro de la Provincia Buenos Aires, 7300 Azul, Provincia de Buenos Aires, Argentina;
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Markgren J, Hedenqvist M, Rasheed F, Skepö M, Johansson E. Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations. Biomolecules 2020; 10:E1095. [PMID: 32717949 PMCID: PMC7465137 DOI: 10.3390/biom10081095] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022] Open
Abstract
Gluten protein crosslinking is a predetermined process where specific intra- and intermolecular disulfide bonds differ depending on the protein and cysteine motif. In this article, all-atom Monte Carlo simulations were used to understand the formation of disulfide bonds in gliadins and low molecular weight glutenin subunits (LMW-GS). The two intrinsically disordered proteins appeared to contain mostly turns and loops and showed "self-avoiding walk" behavior in water. Cysteine residues involved in intramolecular disulfide bonds were located next to hydrophobic peptide sections in the primary sequence. Hydrophobicity of neighboring peptide sections, synthesis chronology, and amino acid chain flexibility were identified as important factors in securing the specificity of intramolecular disulfide bonds formed directly after synthesis. The two LMW-GS cysteine residues that form intermolecular disulfide bonds were positioned next to peptide sections of lower hydrophobicity, and these cysteine residues are more exposed to the cytosolic conditions, which influence the crosslinking behavior. In addition, coarse-grained Monte Carlo simulations revealed that the protein folding is independent of ionic strength. The potential molecular behavior associated with disulfide bonds, as reported here, increases the biological understanding of seed storage protein function and provides opportunities to tailor their functional properties for different applications.
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Affiliation(s)
- Joel Markgren
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, SE-230 53 Alnarp, Sweden;
| | - Mikael Hedenqvist
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden; (M.H.); (F.R.)
| | - Faiza Rasheed
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden; (M.H.); (F.R.)
| | - Marie Skepö
- Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden;
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, SE-230 53 Alnarp, Sweden;
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Effect of high-nitrogen fertilizer on gliadin and glutenin subproteomes during kernel development in wheat (Triticum aestivum L.). ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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9
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Metakovsky E, Melnik V, Pascual L, Wrigley C. Gliadin genotypes worldwide for spring wheats (Triticum aestivum L.) 1. Genetic diversity and grain-quality gliadin alleles during the 20th century. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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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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Juhász A, Belova T, Florides CG, Maulis C, Fischer I, Gell G, Birinyi Z, Ong J, Keeble-Gagnère G, Maharajan A, Ma W, Gibson P, Jia J, Lang D, Mayer KFX, Spannagl M, Tye-Din JA, Appels R, Olsen OA. Genome mapping of seed-borne allergens and immunoresponsive proteins in wheat. SCIENCE ADVANCES 2018; 4:eaar8602. [PMID: 30128352 PMCID: PMC6097586 DOI: 10.1126/sciadv.aar8602] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 07/11/2018] [Indexed: 05/24/2023]
Abstract
Wheat is an important staple grain for humankind globally because of its end-use quality and nutritional properties and its adaptability to diverse climates. For a small proportion of the population, specific wheat proteins can trigger adverse immune responses and clinical manifestations such as celiac disease, wheat allergy, baker's asthma, and wheat-dependent exercise-induced anaphylaxis (WDEIA). Establishing the content and distribution of the immunostimulatory regions in wheat has been hampered by the complexity of the wheat genome and the lack of complete genome sequence information. We provide novel insights into the wheat grain proteins based on a comprehensive analysis and annotation of the wheat prolamin Pfam clan grain proteins and other non-prolamin allergens implicated in these disorders using the new International Wheat Genome Sequencing Consortium bread wheat reference genome sequence, RefSeq v1.0. Celiac disease and WDEIA genes are primarily expressed in the starchy endosperm and show wide variation in protein- and transcript-level expression in response to temperature stress. Nonspecific lipid transfer proteins and α-amylase trypsin inhibitor gene families, implicated in baker's asthma, are primarily expressed in the aleurone layer and transfer cells of grains and are more sensitive to cold temperature. The study establishes a new reference map for immunostimulatory wheat proteins and provides a fresh basis for selecting wheat lines and developing diagnostics for products with more favorable consumer attributes.
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Affiliation(s)
- Angéla Juhász
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | | | - Chris G. Florides
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Csaba Maulis
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Iris Fischer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Gyöngyvér Gell
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Zsófia Birinyi
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Jamie Ong
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Gabriel Keeble-Gagnère
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia
| | | | - Wujun Ma
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Peter Gibson
- Department of Medicine Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Daniel Lang
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Klaus F. X. Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Technical University of Munich, School of Life Sciences, Campus Weihenstephan, Freising, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | | | - Jason A. Tye-Din
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Rudi Appels
- State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
- Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, VIC 3083, Australia
- School of BioSciences, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
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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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13
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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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Jouanin A, Gilissen LJWJ, Boyd LA, Cockram J, Leigh FJ, Wallington EJ, van den Broeck HC, van der Meer IM, Schaart JG, Visser RGF, Smulders MJM. Food processing and breeding strategies for coeliac-safe and healthy wheat products. Food Res Int 2017; 110:11-21. [PMID: 30029701 DOI: 10.1016/j.foodres.2017.04.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 01/01/2023]
Abstract
A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients. The first approach is based on food processing strategies, which aim to remove gliadins or all gluten from edible products. We find that several of the candidate food processing techniques to produce low gluten-immunogenic products from wheat already exist. The second approach focuses on wheat breeding strategies to remove immunogenic epitopes from the gluten proteins, while maintaining their food-processing properties. A combination of breeding strategies, including mutation breeding and possibly genome editing, will be necessary to produce coeliac-safe wheat. Individuals suffering from CD and people genetically susceptible who may develop CD after prolonged gluten consumption would benefit from reduced CD-immunogenic wheat. Although the production of healthy and less CD-toxic wheat varieties and food products will be challenging, increasing global demand may require these issues to be addressed in the near future by food processing and cereal breeding companies.
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Affiliation(s)
- Aurélie Jouanin
- Wageningen University & Research, Wageningen, The Netherlands; NIAB, Cambridge CB3 0LE, UK
| | | | | | | | | | | | | | | | - Jan G Schaart
- Wageningen University & Research, Wageningen, The Netherlands
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15
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Lee JY, Kang CS, Beom HR, Jang YR, Altenbach SB, Lim SH, Kim YM, Park CS. Characterization of a wheat mutant missing low-molecular-weight glutenin subunits encoded by the B-genome. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2016.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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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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17
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Subburaj S, Luo N, Lu X, Li X, Cao H, Hu Y, Li J, Yan Y. Molecular characterization and evolutionary origins of farinin genes in Brachypodium distachyon L. J Appl Genet 2015; 57:287-303. [PMID: 26519166 DOI: 10.1007/s13353-015-0316-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 08/29/2015] [Accepted: 09/01/2015] [Indexed: 10/22/2022]
Abstract
Farinins are one of the oldest members of the gluten family in wheat and Aegilops species, and they influence dough properties. Here, we performed the first detailed molecular genetic study on farinin genes in Brachypodium distachyon L., the model species for Triticum aestivum. A total of 51 b-type farinin genes were cloned and characterized, including 27 functional and 24 non-functional pseudogenes from 14 different B. distachyon accessions. All genes were highly similar to those previously reported from wheat and Aegilops species. The identification of deduced amino acid sequences showed that b-type farinins across Triticeae genomes could be classified as b1-, b2-, b3-, and b4-type farinins; however, B. distachyon had only b3- and b4-type farinins. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) revealed that farinin genes are transcribed into mRNA in B. distachyon at much lower levels than in Triticeae, despite the presence of cis-acting elements in promoter regions. Phylogenetic analysis suggested that Brachypodium farinins may have closer relationships with common wheat and further confirmed four different types of b-type farinins in Triticeae and Brachypodium genomes, corresponding to b1, b2, b3 (group 1), and b4 (group 2). A putative evolutionary origin model of farinin genes in Brachypodium, Triticum, and the related species suggests that all b-type farinins diverged from their common ancestor ~3.2 million years ago (MYA). The b3 and b4 types could be considered older in the farinin family. The results explain the loss of b1- and b2-type farinin alleles in Brachypodium.
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Affiliation(s)
| | - Nana Luo
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaobing Lu
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Hui Cao
- College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yingkao Hu
- College of Life Science, Capital Normal University, Beijing, 100048, China.
| | - Jiarui Li
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, 100048, China. .,Hubei Collaborative Innovation Center for Grain Industry (HCICGI), 434025, Jingzhou, China.
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18
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Li GR, Lang T, Yang EN, Liu C, Yang ZJ. Characterization and phylogenetic analysis of α-gliadin gene sequences reveals significant genomic divergence in Triticeae species. J Genet 2015; 93:725-31. [PMID: 25572231 DOI: 10.1007/s12041-014-0441-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although the unique properties of wheat α-gliadin gene family are well characterized, little is known about the evolution and genomic divergence of α-gliadin gene family within the Triticeae. We isolated a total of 203 α-gliadin gene sequences from 11 representative diploid and polyploid Triticeae species, and found 108 sequences putatively functional. Our results indicate that α-gliadin genes may have possibly originated from wild Secale species, where the sequences contain the shortest repetitive domains and display minimum variation. A miniature inverted-repeat transposable element insertion is reported for the first time in α-gliadin gene sequence of Thinopyrum intermedium in this study, indicating that the transposable element might have contributed to the diversification of α-gliadin genes family among Triticeae genomes. The phylogenetic analyses revealed that the α-gliadin gene sequences of Dasypyrum, Australopyrum, Lophopyrum, Eremopyrum and Pseudoroengeria species have amplified several times. A search for four typical toxic epitopes for celiac disease within the Triticeae α-gliadin gene sequences showed that the α-gliadins of wild Secale, Australopyrum and Agropyron genomes lack all four epitopes, while other Triticeae species have accumulated these epitopes, suggesting that the evolution of these toxic epitopes sequences occurred during the course of speciation, domestication or polyploidization of Triticeae.
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Affiliation(s)
- Guang-Rong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, People's Republic of China.
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19
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Novoselskaya-Dragovich AY. Genetics and genomics of wheat: Storage proteins, ecological plasticity, and immunity. RUSS J GENET+ 2015. [DOI: 10.1134/s102279541505004x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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20
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Cao S, Li Z, Gong C, Xu H, Yang R, Hao S, Wang X, Wang D, Zhang X. Identification and characterization of high-molecular-weight glutenin subunits from Agropyron intermedium. PLoS One 2014; 9:e87477. [PMID: 24503781 PMCID: PMC3913593 DOI: 10.1371/journal.pone.0087477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/23/2013] [Indexed: 11/18/2022] Open
Abstract
High-molecular-weight glutenin subunit (HMW-GS) is a primary determinant of processing quality of wheat. Considerable progress has been made in understanding the structure, function and genetic regulation of HMW-GS in wheat and some of its related species, but less is known about their orthologs in Agropyron intermedium, a useful related species for wheat improvement. Here seven HMW-GSs in Ag. intermedium were identified using SDS-PAGE and Western blotting experiments. Subsequently, the seven genes (Glu-1Aix1 ∼ 4 and Glu-1Aiy1 ∼ 3) encoding the seven HMW-GSs were isolated using PCR technique with degenerate primers, and confirmed by bacterial expression and Western blotting. Sequence analysis indicated that the seven Ag. intermedium HMW-GSs shared high similarity in primary structure to those of wheat, but four of the seven subunits were unusually small compared to the representatives of HMW-GS from wheat and two of them possessed extra cysteine residues. The alignment and clustering analysis of deduced amino acid sequences revealed that 1Aix1 and 1Aiy1 subunits had special molecular structure, belonging to the hybrid type compounding between typical x- and y-type subunit. The xy-type subunit 1Aix1 is composed of the N-terminal of x-type and C-terminal of y-type, whereas yx-type subunit 1Aiy1 comprises the N-terminal of y-type and C-terminal of x-type. This result strongly supported the hypothesis of unequal crossover mechanism that might generate the novel coding sequence for the hybrid type of HMW-GSs. In addition to the aforementioned, the other novel characteristics of the seven subunits were also discussed. Finally, phylogenetic analysis based on HMW-GS genes was carried out and provided new insights into the evolutionary biology of Ag. intermedium.
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Affiliation(s)
- Shuanghe Cao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhixin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Caiyan Gong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hong Xu
- College of life sciences, Northwest Sci-Tech University of Agriculture and Forestry, Yangling, Shanxi, China
| | - Ran Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shanting Hao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xianping Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiangqi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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21
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Zhang H, Mao X, Zhang J, Chang X, Jing R. Single-nucleotide polymorphisms and association analysis of drought-resistance gene TaSnRK2.8 in common wheat. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 70:174-81. [PMID: 23774379 DOI: 10.1016/j.plaphy.2013.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/10/2013] [Indexed: 05/21/2023]
Abstract
TaSnRK2.8, an SnRK2 (sucrose non-fermenting1-related protein kinase 2) member of wheat, confers enhanced multi-stress tolerances in carbohydrate metabolism. In the study, two types of genomic sequences of TaSnRK2.8 were detected in common wheat. Sequencing analysis showed that there was a variation-enriched region, designated TaSnRK2.8-A-C, covering the eighth intron, the ninth exon and the 3'-flanking region of TaSnRK2.8-A, and no divergence occurred in TaSnRK2.8-B. Single nucleotide polymorphisms in the TaSnRK2.8-A-C region were investigated in 165 wheat accessions. Three of 751 sequenced nucleotide sites were polymorphic. Nucleotide diversity (π) in the region was 0.00068. Sliding-window analysis demonstrated that the nucleotide diversity was highest in the 3'-flanking sequence. As predicted, the highly frequent SNP was significantly associated with seedling biomass under normal conditions, plant height, flag leaf width and water-soluble carbohydrate content under drought conditions. Analysis of variance of correlated traits between accessions with the A and G genotypes indicated that the A variant was the more favorable allele associated with significantly increased seedling biomass and water-soluble carbohydrates. Based on the SNP, we developed a functional marker of TaSnRK2.8-A-C, that could be utilized in wheat breeding programs aimed at improving seedling biomass and water-soluble carbohydrates, and consequently to enhance stress resistance in wheat.
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Affiliation(s)
- Hongying Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou 450002, China
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22
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Antonyuk MZ, Shpylchyn VV, Ternovska TK. Permanent genetic variability in the introgressive lines and amphidiploids of Triticeae. CYTOL GENET+ 2013. [DOI: 10.3103/s0095452713040026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang K, Zhang X, Zhao Y, Chen F, Xia G. Structure, variation and expression analysis of glutenin gene promoters from Triticum aestivum cultivar Chinese Spring shows the distal region of promoter 1Bx7 is key regulatory sequence. Gene 2013; 527:484-90. [PMID: 23850729 DOI: 10.1016/j.gene.2013.06.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
Abstract
In this study, ten glutenin gene promoters were isolated from model wheat (Triticum aestivum L. cv. Chinese Spring) using a genomic PCR strategy with gene-specific primers. Six belonged to high-molecular-weight glutenin subunit (HMW-GS) gene promoters, and four to low-molecular-weight glutenin subunit (LMW-GS). Sequence lengths varied from 1361 to 2,554 bp. We show that the glutenin gene promoter motifs are conserved in diverse sequences in this study, with HMW-GS and LMW-GS gene promoters characterized by distinct conserved motif combinations. Our findings show that HMW-GS promoters contain more functional motifs in the distal region of the glutenin gene promoter (> -700 bp) compared with LMW-GS. The y-type HMW-GS gene promoters possess unique motifs including RY repeat and as-2 box compared to the x-type. We also identified important motifs in the distal region of HMW-GS gene promoters including the 5'-UTR Py-rich stretch motif and the as-2 box motif. We found that cis-acting elements in the distal region of promoter 1Bx7 enhanced the expression of HMW-GS gene 1Bx7. Taken together, these data support efforts in designing molecular breeding strategies aiming to improve wheat quality. Our results offer insight into the regulatory mechanisms of glutenin gene expression.
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Affiliation(s)
- Kai Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, PR China
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24
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Wang ZN, Banik M, Cloutier S. Divergent evolutionary mechanisms of co-located Tak/Lrk and Glu-D3 loci revealed by comparative analysis of grass genomes. Genome 2013; 56:195-204. [PMID: 23706072 DOI: 10.1139/gen-2012-0172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Seed storage and disease resistance proteins are major traits of wheat. The study of their gene organization and evolution has some implications in breeding. In this study, we characterized the hexaploid wheat D-genome BAC clone TaBAC703A9 that contains a low molecular weight glutenin locus (Glu-D3) and a resistance gene analogue cluster. With a gene density of one gene per 4.8 kb, the cluster contains four resistance gene analogues, namely Tak703-1, Lrr703, Tak703, and Lrk703. This structural cluster unit was conserved across nine grass genomes, but divergent evolutionary mechanisms have been involved in shaping the Tak/Lrk loci in the different species. Gene duplication was the major force for the Tak/Lrk evolution in oats, maize, barley, wheat, sorghum, and Brachypodium, while tandem duplication drove the expansion of this locus in japonica rice. Despite the close proximity of the Glu-D3 and the Tak/Lrk loci in wheat, the evolutionary mechanisms that drove their amplification differ. The Glu-D3 region had a lower gene density, and its amplification was driven by retroelements.
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Affiliation(s)
- Zi-Ning Wang
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg MB R3T 2M9, Canada
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25
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Anderson OD, Huo N, Gu YQ. The gene space in wheat: the complete γ-gliadin gene family from the wheat cultivar Chinese Spring. Funct Integr Genomics 2013; 13:261-73. [PMID: 23564033 DOI: 10.1007/s10142-013-0321-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/14/2013] [Accepted: 03/19/2013] [Indexed: 12/20/2022]
Abstract
The complete set of unique γ-gliadin genes is described for the wheat cultivar Chinese Spring using a combination of expressed sequence tag (EST) and Roche 454 DNA sequences. Assemblies of Chinese Spring ESTs yielded 11 different γ-gliadin gene sequences. Two of the sequences encode identical polypeptides and are assumed to be the result of a recent gene duplication. One gene has a 3' coding mutation that changes the reading frame in the final eight codons. A second assembly of Chinese Spring γ-gliadin sequences was generated using Roche 454 total genomic DNA sequences. The 454 assembly confirmed the same 11 active genes as the EST assembly plus two pseudogenes not represented by ESTs. These 13 γ-gliadin sequences represent the complete unique set of γ-gliadin genes for cv Chinese Spring, although not ruled out are additional genes that are exact duplications of these 13 genes. A comparison with the ESTs of two other hexaploid cultivars (Butte 86 and Recital) finds that the most active genes are present in all three cultivars, with exceptions likely due to too few ESTs for detection in Butte 86 and Recital. A comparison of the numbers of ESTs per gene indicates differential levels of expression within the γ-gliadin gene family. Genome assignments were made for 6 of the 13 Chinese Spring γ-gliadin genes, i.e., one assignment from a match to two γ-gliadin genes found within a tetraploid wheat A genome BAC and four genes that match four distinct γ-gliadin sequences assembled from Roche 454 sequences from Aegilops tauschii, the hexaploid wheat D-genome ancestor.
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Affiliation(s)
- Olin D Anderson
- Genomics and Gene Discovery Research Unit, Western Regional Research Unit, Agricultural Research Service, US Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA.
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26
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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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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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Goryunova SV, Salentijn EMJ, Chikida NN, Kochieva EZ, van der Meer IM, Gilissen LJWJ, Smulders MJM. Expansion of the gamma-gliadin gene family in Aegilops and Triticum. BMC Evol Biol 2012; 12:215. [PMID: 23137212 PMCID: PMC3537741 DOI: 10.1186/1471-2148-12-215] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The gamma-gliadins are considered to be the oldest of the gliadin family of storage proteins in Aegilops/Triticum. However, the expansion of this multigene family has not been studied in an evolutionary perspective. RESULTS We have cloned 59 gamma-gliadin genes from Aegilops and Triticum species (Aegilops caudata L., Aegilops comosa Sm. in Sibth. & Sm., Aegilops mutica Boiss., Aegilops speltoides Tausch, Aegilops tauschii Coss., Aegilops umbellulata Zhuk., Aegilops uniaristata Vis., and Triticum monococcum L.) representing eight different genomes: Am, B/S, C, D, M, N, T and U. Overall, 15% of the sequences contained internal stop codons resulting in pseudogenes, but this percentage was variable among genomes, up to over 50% in Ae. umbellulata. The most common length of the deduced protein, including the signal peptide, was 302 amino acids, but the length varied from 215 to 362 amino acids, both obtained from Ae. speltoides. Most genes encoded proteins with eight cysteines. However, all Aegilops species had genes that encoded a gamma-gliadin protein of 302 amino acids with an additional cysteine. These conserved nine-cysteine gamma-gliadins may perform a specific function, possibly as chain terminators in gluten network formation in protein bodies during endosperm development. A phylogenetic analysis of gamma-gliadins derived from Aegilops and Triticum species and the related genera Lophopyrum, Crithopsis, and Dasypyrum showed six groups of genes. Most Aegilops species contained gamma-gliadin genes from several of these groups, which also included sequences from the genera Lophopyrum, Crithopsis, and Dasypyrum. Hordein and secalin sequences formed separate groups. CONCLUSIONS We present a model for the evolution of the gamma-gliadins from which we deduce that the most recent common ancestor (MRCA) of Aegilops/Triticum-Dasypyrum-Lophopyrum-Crithopsis already had four groups of gamma-gliadin sequences, presumably the result of two rounds of duplication of the locus.
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Affiliation(s)
- Svetlana V Goryunova
- Wageningen UR Plant Breeding, Wageningen UR, P,O, Box 16, Wageningen, NL-6700 AA, The Netherlands
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Aversano R, Ercolano MR, Caruso I, Fasano C, Rosellini D, Carputo D. Molecular tools for exploring polyploid genomes in plants. Int J Mol Sci 2012; 13:10316-10335. [PMID: 22949863 PMCID: PMC3431861 DOI: 10.3390/ijms130810316] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/03/2012] [Accepted: 08/06/2012] [Indexed: 11/16/2022] Open
Abstract
Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.
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Affiliation(s)
- Riccardo Aversano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Maria Raffaella Ercolano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Immacolata Caruso
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Carlo Fasano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
| | - Daniele Rosellini
- Department of Applied Biology, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy; E-Mail:
| | - Domenico Carputo
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy; E-Mails: (R.A.); (M.R.E.); (I.C.); (C.F.)
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Involvement of disperse repetitive sequences in wheat/rye genome adjustment. Int J Mol Sci 2012; 13:8549-8561. [PMID: 22942719 PMCID: PMC3430250 DOI: 10.3390/ijms13078549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 06/25/2012] [Accepted: 07/04/2012] [Indexed: 01/09/2023] Open
Abstract
The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploidization functional implications. We intend to attain a deeper knowledge of dispersed repetitive sequence involvement in parental genome reshuffle in triticale and in wheat-rye addition lines that have the entire wheat genome plus each rye chromosome pair. Through Random Amplified Polymorphic DNA (RAPD) analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. Moreover, the sequential nature of those events was revealed by the increased absence of rye-origin bands in wheat-rye addition lines in comparison with triticale. Remodeled band sequencing revealed that both repetitive and coding genome domains are affected in wheat-rye hybrid genotypes. Additionally, the amplification and sequencing of pSc20H internal segments showed that the disappearance of parental bands may result from restricted sequence alterations and unraveled the involvement of wheat/rye related repetitive sequences in genome adjustment needed for hybrid plant stabilization.
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31
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Salentijn EMJ, Mitea DC, Goryunova SV, van der Meer IM, Padioleau I, Gilissen LJWJ, Koning F, Smulders MJM. Celiac disease T-cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation. BMC Genomics 2012; 13:277. [PMID: 22726570 PMCID: PMC3469346 DOI: 10.1186/1471-2164-13-277] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 05/02/2012] [Indexed: 02/04/2023] Open
Abstract
Background Celiac disease (CD) is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes) that mediate the stimulation of HLA-DQ2/8 restricted T-cells. Next to the thoroughly characterized major T-cell epitopes derived from the α-gliadin fraction of gluten, γ-gliadin peptides are also known to stimulate T-cells of celiac disease patients. To pinpoint CD-toxic γ-gliadins in hexaploid bread wheat, we examined the variation of T-cell epitopes involved in CD in γ-gliadin transcripts of developing bread wheat grains. Results A detailed analysis of the genetic variation present in γ-gliadin transcripts of bread wheat (T. aestivum, allo-hexaploid, carrying the A, B and D genome), together with genomic γ-gliadin sequences from ancestrally related diploid wheat species, enabled the assignment of sequence variants to one of the three genomic γ-gliadin loci, Gli-A1, Gli-B1 or Gli-D1. Almost half of the γ-gliadin transcripts of bread wheat (49%) was assigned to locus Gli-D1. Transcripts from each locus differed in CD epitope content and composition. The Gli-D1 transcripts contained the highest frequency of canonical CD epitope cores (on average 10.1 per transcript) followed by the Gli-A1 transcripts (8.6) and the Gli-B1 transcripts (5.4). The natural variants of the major CD epitope from γ-gliadins, DQ2-γ-I, showed variation in their capacity to induce in vitro proliferation of a DQ2-γ-I specific and HLA-DQ2 restricted T-cell clone. Conclusions Evaluating the CD epitopes derived from γ-gliadins in their natural context of flanking protein variation, genome specificity and transcript frequency is a significant step towards accurate quantification of the CD toxicity of bread wheat. This approach can be used to predict relative levels of CD toxicity of individual wheat cultivars directly from their transcripts (cDNAs).
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Affiliation(s)
- Elma M J Salentijn
- Plant Research International, Wageningen UR, P.O. Box 16, NL-6700 AA, Wageningen, The Netherlands.
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33
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Genome change in wheat observed through the structure and expression of α/β-gliadin genes. Funct Integr Genomics 2012; 12:341-55. [PMID: 22370744 DOI: 10.1007/s10142-012-0269-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 01/08/2023]
Abstract
To better understand genome structure and the expression of α/β-gliadin multigenes in hexaploid wheat, bacterial artificial chromosome (BAC) clones containing α/β-gliadin genes from the three loci, Gli-A2, Gli-B2, and Gli-D2, were screened. Based on their restriction fragment patterns, we selected five BAC clones, namely, two clones for Gli-A2, two clones for Gli-B2, and one clone for Gli-D2, to fully sequence. Approximately 200 kb was sequenced for each locus. In total, twelve α/β-gliadin intact genes and four pseudogenes were found, and retrotransposons or other transposons existed in each BAC clone. Dot-plot analysis revealed the pattern of genome segmental duplication within each BAC. We calculated time since duplication of each set of α/β-gliadin genes and insertion of retrotransposons. Duplication of all adjacent genes within the same BAC clone took place before or after allotetrapolyploidization, but duplication of certain genes occurred before diploid differentiation of wheat species. Retrotransposons were also inserted before and after the segmental duplication events. Furthermore, translocation of α/β-gliadin genes from chromosomes 1 to 6 apparently occurred before the diversification of various wheat genomes. Duplication of genome segments containing α/β-gliadin genes and retrotransposons were brought about through unequal crossing-over or saltatory replication and α/β-gliadin genes per se were duplicated without any recombination events. Out of twelve intact α/β-gliadin genes detected from their sequences, nine were expressed, although their patterns of expression were distinct. Since they have similar cis-elements and promoter structures, the mechanisms underlying their distinct gene expression and possible applications are discussed.
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Fonceka D, Tossim HA, Rivallan R, Vignes H, Faye I, Ndoye O, Moretzsohn MC, Bertioli DJ, Glaszmann JC, Courtois B, Rami JF. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC PLANT BIOLOGY 2012; 12:26. [PMID: 22340522 PMCID: PMC3312858 DOI: 10.1186/1471-2229-12-26] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/17/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication. RESULTS A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication. CONCLUSION In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives.
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Affiliation(s)
- Daniel Fonceka
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | | | - Ronan Rivallan
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Hélène Vignes
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Issa Faye
- ISRA/Ceraas, Route de Khombole, BP 3320, Thiès Escale, Senegal
| | - Ousmane Ndoye
- ISRA/Ceraas, Route de Khombole, BP 3320, Thiès Escale, Senegal
| | - Márcio C Moretzsohn
- Embrapa Recursos Genéticos e Biotecnologia, C.P. 02372, CEP 70.770-900 Brasilia, DF, Brazil
| | - David J Bertioli
- Universidade de Brasília, Campus Universitário, CEP 70.910-900 Brasília, DF, Brazil
| | | | - Brigitte Courtois
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
| | - Jean-François Rami
- Cirad, UMR AGAP, TA A108/3, Avenue Agropolis, Montpellier F-34398, France
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Zhuang Q, Zhang Z, Chen F, Xia G. Comparative and evolutionary analysis of new variants of ω-gliadin genes from three A-genome diploid wheats. J Appl Genet 2011; 53:125-31. [PMID: 22072274 DOI: 10.1007/s13353-011-0075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 10/07/2011] [Accepted: 10/14/2011] [Indexed: 11/25/2022]
Abstract
A genomic polymerase chain reaction (PCR) cloning strategy was applied to isolate ω-gliadin sequences from three A-genome diploid wheats (Triticum monococcum, T. boeoticum and T. urartu). Amplicon lengths varied from 744 and 1,044 bp, and those of the corresponding deduced mature proteins from 248 to 348 residues. The primary structure of the deduced polypeptides comprised a short N- and C-terminal conserved domain, and a long, variable repetitive domain. A phylogenetic analysis recognised several clades: the first consisted of three T. aestivum sequences; the second and the third two T. boeoticum and six T. monococcum sequences; and the rest four T. urartu and three T. aestivum sequences. Among the functional (non-pseudogene) ARQ/E-type ω-gliadin sequences, two were derived from T. boeoticum and three from T. monococcum; one of the latter sequences appeared to be a chimera originating via illegitimate recombination between the other two T. monococcum sequences. None of the 12 intact ω-gliadin sequences contained any cysteine or methionine residues. We discussed the variation and evolution of A-genome ω-gliadin genes.
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Affiliation(s)
- Qianqian Zhuang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, 250100 People's Republic of China
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Wang K, Gao L, Wang S, Zhang Y, Li X, Zhang M, Xie Z, Yan Y, Belgard M, Ma W. Phylogenetic relationship of a new class of LMW-GS genes in the M genome of Aegilops comosa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1411-1425. [PMID: 21301802 DOI: 10.1007/s00122-011-1541-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 01/14/2011] [Indexed: 05/26/2023]
Abstract
A new class of low molecular weight glutenin subunit (LMW-GS) genes was isolated and characterized from Aegilops comosa (2n = 2x = 14, MM). Although their DNA structure displayed high similarity to LMW-i type genes, there are some key differences. The deduced amino acid sequences of their mature proteins showed that the first amino acid residue of each gene was leucine and therefore they were designated as LMW-l type subunits. An extra cysteine residue was present in the signal peptide and the first cysteine residue of mature proteins located at the end of repetitive domain. Additionally, a long insertion of 10-22 residues (LGQQPQ(5-17)) occurred in the end of the C-terminal II. Comparative analysis demonstrated that LMW-l type glutenin genes possessed a great number of single-nucleotide polymorphisms and insertions/deletions. A new classification system was proposed according to the gene structure and phylogenetic analysis. In this new system, LMW-GS is classified into two major classes, LMW-M and LMW-I, with each including two subclasses. The former included LMW-m and LMW-s types while the latter contained LMW-l and LMW-i types. Analysis of their evolutionary origin showed that the LMW-l genes diverged from the group 2 of LMW-m type genes at about 12-14 million years ago (MYA) while LMW-i type evolved from LMW-l type at approximately 8-12 MYA. The LMW-s type was a variant form of group 1 of LMW-m type and their divergence occurred about 4-6 MYA. In addition to homologous recombination, non-homologous illegitimate recombination could be an important molecular mechanism for the origin and evolution of LMW-GS gene family. The secondary structure prediction suggested that the novel LMW-l type subunits, such as AcLMW-L1 and AcLMW-L2, may have positive effects on dough properties.
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Affiliation(s)
- Ke Wang
- College of Life Science, Capital Normal University, 100048, Beijing, China
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Zhou L, Huang B, Meng X, Wang G, Wang F, Xu Z, Song R. The amplification and evolution of orthologous 22-kDa α-prolamin tandemly arrayed genes in coix, sorghum and maize genomes. PLANT MOLECULAR BIOLOGY 2010; 74:631-643. [PMID: 20938800 DOI: 10.1007/s11103-010-9705-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 09/30/2010] [Indexed: 05/30/2023]
Abstract
Tandemly arrayed genes (TAGs) account for about one-third of the duplicated genes in eukaryotic genomes. They provide raw genetic material for biological evolution, and play important roles in genome evolution. The 22-kDa prolamin genes in cereal genomes represent typical TAG organization, and provide the good material to investigate gene amplification of TAGs in closely related grass genomes. Here, we isolated and sequenced the Coix 22-kDa prolamin (coixin) gene cluster (283 kb), and carried out a comparative analysis with orthologous 22-kDa prolamin gene clusters from maize and sorghum. The 22-kDa prolamin gene clusters descended from orthologous ancestor genes, but underwent independent gene amplification paths after the separation of these species, therefore varied dramatically in sequence and organization. Our analysis indicated that the gene amplification model of 22-kDa prolamin gene clusters can be divided into three major stages. In the first stage, rare gene duplications occurred from the ancestor gene copy accidentally. In the second stage, rounds of gene amplification occurred by unequal crossing over to form tandem gene array(s). In the third stage, gene array was further diverged by other genomic activities, such as transposon insertions, segmental rearrangements, etc. Unlike their highly conserved sequences, the amplified 22-kDa prolamin genes diverged rapidly at their expression capacities and expression levels. Such processes had no apparent correlation to age or order of amplified genes within TAG cluster, suggesting a fast evolving nature of TAGs after gene amplification. These results provided insights into the amplification and evolution of TAG families in grasses.
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Affiliation(s)
- Liangliang Zhou
- Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444, Shanghai, People's Republic of China
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Xie Z, Wang C, Wang K, Wang S, Li X, Zhang Z, Ma W, Yan Y. Molecular characterization of the celiac disease epitope domains in α-gliadin genes in Aegilops tauschii and hexaploid wheats (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1239-51. [PMID: 20556595 DOI: 10.1007/s00122-010-1384-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2010] [Accepted: 06/03/2010] [Indexed: 05/24/2023]
Abstract
Nineteen novel full-ORF α-gliadin genes and 32 pseudogenes containing at least one stop codon were cloned and sequenced from three Aegilops tauschii accessions (T15, T43 and T26) and two bread wheat cultivars (Gaocheng 8901 and Zhongyou 9507). Analysis of three typical α-gliadin genes (Gli-At4, Gli-G1 and Gli-Z4) revealed some InDels and a considerable number of SNPs among them. Most of the pseudogenes were resulted from C to T change, leading to the generation of TAG or TAA in-frame stop codon. The putative proteins of both Gli-At3 and Gli-Z7 genes contained an extra cysteine residue in the unique domain II. Analysis of toxic epitodes among 19 deduced α-gliadins demonstrated that 14 of these contained 1-5 T cell stimulatory toxic epitopes while the other 5 did not contain any toxic epitopes. The glutamine residues in two specific ployglutamine domains ranged from 7 to 27, indicating a high variation in length. According to the numbers of 4 T cell stimulatory toxic epitopes and glutamine residues in the two ployglutamine domains among the 19 α-gliadin genes, 2 were assigned to chromosome 6A, 5 to chromosome 6B and 12 to chromosome 6D. These results were consistent with those from wheat cv. Chinese Spring nulli-tetrasomic and phylogenetic analysis. Secondary structure prediction showed that all α-gliadins had high content of β-strands and most of the α-helixes and β-strands were present in two unique domains. Phylogenetic analysis demonstrated that α-gliadin genes had a high homology with γ-gliadin, B-hordein, and LMW-GS genes and they diverged at approximate 39 MYA. Finally, the five α-gliadin genes were successfully expressed in E. coli, and their expression amount reached to the maximum after 4 h induced by IPTG, indicating that the α-gliadin genes can express in a high level under the control of T(7) promoter.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Celiac Disease/genetics
- Celiac Disease/immunology
- Chromosome Mapping
- Cloning, Molecular
- DNA, Plant/genetics
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Escherichia coli
- Genes, Plant/genetics
- Genes, Plant/immunology
- Gliadin/chemistry
- Gliadin/genetics
- Gliadin/immunology
- Humans
- INDEL Mutation
- Open Reading Frames
- Peptides
- Phylogeny
- Polymorphism, Single Nucleotide
- Protein Structure, Secondary
- Pseudogenes
- Sequence Alignment
- Sequence Analysis, DNA
- Triticum/genetics
- Triticum/immunology
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Affiliation(s)
- Zhenze Xie
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, China
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39
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Dong L, Zhang X, Liu D, Fan H, Sun J, Zhang Z, Qin H, Li B, Hao S, Li Z, Wang D, Zhang A, Ling HQ. New insights into the organization, recombination, expression and functional mechanism of low molecular weight glutenin subunit genes in bread wheat. PLoS One 2010; 5:e13548. [PMID: 20975830 PMCID: PMC2958824 DOI: 10.1371/journal.pone.0013548] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/24/2010] [Indexed: 12/03/2022] Open
Abstract
The bread-making quality of wheat is strongly influenced by multiple low molecular weight glutenin subunit (LMW-GS) proteins expressed in the seeds. However, the organization, recombination and expression of LMW-GS genes and their functional mechanism in bread-making are not well understood. Here we report a systematic molecular analysis of LMW-GS genes located at the orthologous Glu-3 loci (Glu-A3, B3 and D3) of bread wheat using complementary approaches (genome wide characterization of gene members, expression profiling, proteomic analysis). Fourteen unique LMW-GS genes were identified for Xiaoyan 54 (with superior bread-making quality). Molecular mapping and recombination analyses revealed that the three Glu-3 loci of Xiaoyan 54 harbored dissimilar numbers of LMW-GS genes and covered different genetic distances. The number of expressed LMW-GS in the seeds was higher in Xiaoyan 54 than in Jing 411 (with relatively poor bread-making quality). This correlated with the finding of higher numbers of active LMW-GS genes at the A3 and D3 loci in Xiaoyan 54. Association analysis using recombinant inbred lines suggested that positive interactions, conferred by genetic combinations of the Glu-3 locus alleles with more numerous active LMW-GS genes, were generally important for the recombinant progenies to attain high Zeleny sedimentation value (ZSV), an important indicator of bread-making quality. A higher number of active LMW-GS genes tended to lead to a more elevated ZSV, although this tendency was influenced by genetic background. This work provides substantial new insights into the genomic organization and expression of LMW-GS genes, and molecular genetic evidence suggesting that these genes contribute quantitatively to bread-making quality in hexaploid wheat. Our analysis also indicates that selection for high numbers of active LMW-GS genes can be used for improvement of bread-making quality in wheat breeding.
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Affiliation(s)
- Lingli Dong
- 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
| | - 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, Beijing, 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, Beijing, China
| | - Huajie Fan
- 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
| | - 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, Beijing, China
| | - Zhongjuan 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, Beijing, China
| | - Huanju Qin
- 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
| | - Bin 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, Beijing, China
| | - Shanting Hao
- 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
| | - Zhensheng 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, Beijing, China
| | - 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
- * E-mail: (HQL); (AZ); (DW)
| | - 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, Beijing, China
- * E-mail: (HQL); (AZ); (DW)
| | - Hong-Qing Ling
- 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
- * E-mail: (HQL); (AZ); (DW)
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40
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Nakamura S, Ohtsubo K. PCR method for the detection and identification of cultivars of rice flours used in yeast leavened breads containing both wheat and rice flours. J Cereal Sci 2010. [DOI: 10.1016/j.jcs.2010.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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Wang L, Li G, Peña RJ, Xia X, He Z. Development of STS markers and establishment of multiplex PCR for Glu-A3 alleles in common wheat (Triticum aestivum L.). J Cereal Sci 2010. [DOI: 10.1016/j.jcs.2010.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Wang ZN, Huang XQ, Cloutier S. Recruitment of closely linked genes for divergent functions: the seed storage protein (Glu-3) and powdery mildew (Pm3) genes in wheat (Triticum aestivum L.). Funct Integr Genomics 2009; 10:241-51. [PMID: 20012664 DOI: 10.1007/s10142-009-0150-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 11/03/2009] [Accepted: 11/09/2009] [Indexed: 11/25/2022]
Abstract
Wheat seed storage protein gene loci (Glu-3) and powdery mildew resistance gene loci (Pm3 and Pm3-like) are closely linked on the short arms of homoeologous group 1 chromosomes. To study the structural organization of the Glu-3/Pm3 loci, three bacterial artificial chromosome clones were sequenced from the A, B, and D genomes of hexaploid wheat. The A and B genome clones contained a Glu-3 adjacent to a Pm3-like gene organized in a conserved Glu-3/SFR159/Pm3-like structure. The D genome clone contained clusters of resistance gene analogs but no Pm3. Its similarity to the A and B genome was limited to the Glu-3/SFR159 region. Comparison of the B genome PM3-like deduced amino acid sequence with known PM3 functional isotypes reinforced the hypothesis of allelic evolution via block exchange by gene conversion/recombination. The advent of glutenin genes and the formation of the Glu-3/SFR159/Pm3 locus occurred after divergence of wheat from rice and Brachypodium. Comparison of the A genome homologous sequences permitted an estimate of time of divergence of approximately 0.3 million years ago. The B genome sequences were not colinear indicating that they could either be paralogs or represent different B genome progenitors. Analysis of the 11 complete retrotransposons indicated a time of divergence ranging from 0.29 to 5.62 million years ago, consistent with their complex nested structure.
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Affiliation(s)
- Zi-Ning Wang
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, MB, Canada, R3T 2M9
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43
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Xu JH, Messing J. Amplification of prolamin storage protein genes in different subfamilies of the Poaceae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1397-412. [PMID: 19727653 DOI: 10.1007/s00122-009-1143-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 08/12/2009] [Indexed: 05/20/2023]
Abstract
Prolamins are seed storage proteins in cereals and represent an important source of essential amino acids for feed and food. Genes encoding these proteins resulted from dispersed and tandem amplification. While previous studies have concentrated on protein sequences from different grass species, we now can add a new perspective to their relationships by asking how their genes are shared by ancestry and copied in different lineages of the same family of species. These differences are derived from alignment of chromosomal regions, where collinearity is used to identify prolamin genes in syntenic positions, also called orthologous gene copies. New or paralogous gene copies are inserted in tandem or new locations of the same genome. More importantly, one can detect the loss of older genes. We analyzed chromosomal intervals containing prolamin genes from rice, sorghum, wheat, barley, and Brachypodium, representing different subfamilies of the Poaceae. The Poaceae commonly known as the grasses includes three major subfamilies, the Ehrhartoideae (rice), Pooideae (wheat, barley, and Brachypodium), and Panicoideae (millets, maize, sorghum, and switchgrass). Based on chromosomal position and sequence divergence, it becomes possible to infer the order of gene amplification events. Furthermore, the loss of older genes in different subfamilies seems to permit a faster pace of divergence of paralogous genes. Change in protein structure affects their physical properties, subcellular location, and amino acid composition. On the other hand, regulatory sequence elements and corresponding transcriptional activators of new gene copies are more conserved than coding sequences, consistent with the tissue-specific expression of these genes.
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Affiliation(s)
- Jian-Hong Xu
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA
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44
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Mann G, Diffey S, Cullis B, Azanza F, Martin D, Kelly A, McIntyre L, Schmidt A, Ma W, Nath Z, Kutty I, Leyne PE, Rampling L, Quail KJ, Morell MK. Genetic control of wheat quality: interactions between chromosomal regions determining protein content and composition, dough rheology, and sponge and dough baking properties. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1519-1537. [PMID: 19283360 DOI: 10.1007/s00122-009-1000-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2008] [Accepted: 02/17/2009] [Indexed: 05/25/2023]
Abstract
While the genetic control of wheat processing characteristics such as dough rheology is well understood, limited information is available concerning the genetic control of baking parameters, particularly sponge and dough (S&D) baking. In this study, a quantitative trait loci (QTL) analysis was performed using a population of doubled haploid lines derived from a cross between Australian cultivars Kukri x Janz grown at sites across different Australian wheat production zones (Queensland in 2001 and 2002 and Southern and Northern New South Wales in 2003) in order to examine the genetic control of protein content, protein expression, dough rheology and sponge and dough baking performance. The study highlighted the inconsistent genetic control of protein content across the test sites, with only two loci (3A and 7A) showing QTL at three of the five sites. Dough rheology QTL were highly consistent across the 5 sites, with major effects associated with the Glu-B1 and Glu-D1 loci. The Glu-D1 5 + 10 allele had consistent effects on S&D properties across sites; however, there was no evidence for a positive effect of the high dough strength Glu-B1-al allele at Glu-B1. A second locus on 5D had positive effects on S&D baking at three of five sites. This study demonstrated that dough rheology measurements were poor predictors of S&D quality. In the absence of robust predictive tests, high heritability values for S&D demonstrate that direct selection is the current best option for achieving genetic gain in this product category.
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Affiliation(s)
- Gulay Mann
- CSIRO Plant Industry and the Food Futures Flagship, GPO BOX 1600, Canberra, ACT, 2601, Australia
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45
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Charles M, Tang H, Belcram H, Paterson A, Gornicki P, Chalhoub B. Sixty million years in evolution of soft grain trait in grasses: emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae. Mol Biol Evol 2009; 26:1651-61. [PMID: 19395588 DOI: 10.1093/molbev/msp076] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Together maize, Sorghum, rice, and wheat grass (Poaceae) species are the most important cereal crops in the world and exhibit different "grain endosperm texture." This trait has been studied extensively in wheat because of its pivotal role in determining quality of products obtained from wheat grain. Grain softness protein-1 and Puroindolines A and B (grain storage proteins), encoded by Ha-like genes: Gsp-1, Pina, and Pinb, of the Hardness (Ha) locus, are the main determinants of the grain softness/hardness trait in wheat. The origin and evolution of grain endosperm texture in grasses was addressed by comparing genomic sequences of the Ha orthologous region of wheat, Brachypodium, rice, and Sorghum. Results show that the Ha-like genes are present in wheat and Brachypodium but are absent from Sorghum bicolor. A truncated remnant of an Ha-like gene is present in rice. Synteny analysis of the genomes of these grass species shows that only one of the paralogous Ha regions, created 70 My by whole-genome duplication, contained Ha-like genes. The comparative genome analysis and evolutionary comparison with genes encoding grain reserve proteins of grasses suggest that an ancestral Ha-like gene emerged, as a new member of the prolamin gene family, in a common ancestor of the Pooideae (Triticeae and Brachypoidieae tribes) and Ehrhartoideae (rice), between 60 and 50 My, after their divergence from Panicoideae (Sorghum). It was subsequently lost in Ehrhartoideae. Recurring duplications, deletions, and/or truncations occurred independently and appear to characterize Ha-like gene evolution in the grass species. The Ha-like genes gained a new function in Triticeae, such as wheat, underlying the soft grain phenotype. Loss of these genes in some wheat species leads, in turn, to hard endosperm seeds.
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Affiliation(s)
- Mathieu Charles
- Unité de Recherches en Génomique Végétale, Institut National de la Recherche Agronomique, Unite Mixte de Recherche 1165-CNRS 8114UEVE), Organization and evolution of Plant Genomes, Evry, France
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46
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Anderson OD, Gu YQ, Kong X, Lazo GR, Wu J. The wheat omega-gliadin genes: structure and EST analysis. Funct Integr Genomics 2009; 9:397-410. [PMID: 19367421 PMCID: PMC2700870 DOI: 10.1007/s10142-009-0122-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Revised: 02/26/2009] [Accepted: 03/08/2009] [Indexed: 10/26/2022]
Abstract
A survey and analysis is made of all available omega-gliadin DNA sequences including omega-gliadin genes within a large genomic clone, previously reported gene sequences, and ESTs identified from the large wheat EST collection. A contiguous portion of the Gli-B3 locus is shown to contain two apparently active omega-gliadin genes, two pseudogenes, and four fragments of the 3' portion of omega-gliadin sequences. Comparison of omega-gliadin sequences allows a phylogenetic picture of their relationships and genomes of origin. Results show three groupings of omega-gliadin active gene sequences assigned to each of the three hexaploid wheat genomes, and a fourth group thus far consisting of pseudogenes assigned to the A-genome. Analysis of omega-gliadin ESTs allows reconstruction of two full-length model sequences encoding the AREL- and ARQL-type proteins from the Gli-A3 and Gli-D3 loci, respectively. There is no DNA evidence of multiple active genes from these two loci. In contrast, ESTs allow identification of at least three to four distinct active genes at the Gli-B3 locus of some cultivars. Additional results include more information on the position of cysteines in some omega-gliadin genes and discussion of problems in studying the omega-gliadin gene family.
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Affiliation(s)
- Olin D Anderson
- Genomics and Gene Discovery Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA.
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47
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Ishikawa G, Nakamura T, Ashida T, Saito M, Nasuda S, Endo TR, Wu J, Matsumoto T. Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:499-514. [PMID: 19057889 DOI: 10.1007/s00122-008-0916-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 10/09/2008] [Indexed: 05/02/2023]
Abstract
PCR-based Landmark Unique Gene (PLUG) markers are EST-PCR markers developed based on the orthologous gene conservation between rice and wheat, and on the intron polymorphisms among the three orthologous genes derived from the A, B and D genomes of wheat. We designed a total of 960 primer sets from wheat ESTs that showed high similarity with 951 single-copy rice genes. When genomic DNA of Chinese Spring wheat was used as a template, 872 primer sets amplified one to five distinct products. Out of these 872 PLUG markers, 531 were assigned to one or more chromosomes by nullisomic-tetrasomic analysis. For each wheat chromosome, the number of loci detected ranged from 32 for chromosome 6A to 73 for chromosome 7D, with an average of 48 loci per chromosome. Several novel synteny perturbations were identified using deletion bin-mapping of markers. Furthermore, we demonstrated that PLUG markers can be used as probes to simultaneously identify BAC clones that contain homoeologous regions from all three genomes.
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Affiliation(s)
- Goro Ishikawa
- Tohoku National Agriculture Research Center, Morioka, Iwate, 020-0198, Japan
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48
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LI GR. Isolation and Sequence Analysis of α-gliadin Genes from Dasypy-rum breviaristatum. ZUOWU XUEBAO 2008. [DOI: 10.3724/sp.j.1006.2008.01097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Huang XQ, Cloutier S. Molecular characterization and genomic organization of low molecular weight glutenin subunit genes at the Glu-3 loci in hexaploid wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:953-66. [PMID: 18305921 DOI: 10.1007/s00122-008-0727-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 02/01/2008] [Indexed: 05/22/2023]
Abstract
In this study, we report on the molecular characterization and genomic organization of the low molecular weight glutenin subunit (LMW-GS) gene family in hexaploid wheat (Triticum aestivum L.). Eighty-two positive BAC clones were identified to contain LMW-GS genes from the hexaploid wheat 'Glenlea' BAC library via filter hybridization and PCR validation. Twelve unique LMW glutenin genes and seven pseudogenes were isolated from these positive BAC clones by primer-template mismatch PCR and subsequent primer walking using hemi-nested touchdown PCR. These genes were sequenced and each consisted of a single-open reading frame (ORF) and untranslated 5' and 3' flanking regions. All 12 LMW glutenin subunits contained eight cysteine residues. The LMW-m-type subunits are the most abundant in hexaploid wheat. Of the 12 LMW-GS, 1, 2 and 9 are i-type, s-type and m-type, respectively. The phylogenetic analysis suggested that the LMW-i type gene showed greater differences to LMW-s and LMW-m-type genes, which, in turn, were more closely related to one another. On the basis of their N-terminal sequences, they were classified into nine groups. Fingerprinting of the 82 BAC clones indicated 30 BAC clones assembled into eight contigs, while the remaining clones were singletons. BAC end sequencing of the 82 clones revealed that long terminal repeat (LTR) retrotransposons were abundant in the Glu-3 regions. The average physical distance between two adjacent LMW-GS genes was estimated to be 81 kb. Most of LMW-GS genes are located in the D: -genome, suggesting that the Glu-D3 locus is much larger than the Glu-B3 locus and Glu-A3 locus. Alignments of sequences indicated that the same type (starting with the same N-terminal sequence) LMW-GS genes were highly conserved in the homologous genomes between hexaploid wheat and its donors such as durum wheat and T. tauschii.
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Affiliation(s)
- Xiu-Qiang Huang
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada
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50
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Zeng J, Dai SF, Zheng YL, Liu DC, Wei YM, Yan ZH. [Isolation and characterization of a low molecular weight glutenin gene from Taenitherum Nevski]. YI CHUAN = HEREDITAS 2008; 30:633-641. [PMID: 18487155 DOI: 10.3724/sp.j.1005.2008.00633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
More and more low-molecular-weight glutenin(LMW glutenin) genes were isolated and characterized from hexaploid wheat (Triticum aestivum L.). However, few homologous genes were obtained from its relative species, which limited our understanding of the relationships among them. Therefore, it is necessary to isolate LMW glutenin homologous genes from wheat wild relative species. Using a pair of specific oligonucleotide PCR primers for Taenitherum genomic DNA, a LMW glutenin gene sequence, with nucleotide sequence in 1 035 bp and deduced amino acid sequence with 343 amino acid residues, was obtained. This sequence was a typical LMW glutenin sequence and characterized by a signal peptide of 21 amino acid residues, a N-terminal conservative domain of 13 amino acid residues, a repetitive domain of short peptide, and a C-terminal conservative domain. Sequence alignment showed the main differences and the relationships between LMW glutenin genes from wheat and Taenitherum. The results presented here give a reference to isolate LMW glutenin gene from Taenitherum, as well as other wheat wild relatives.
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Affiliation(s)
- Jie Zeng
- Triticeae Research Institute, Sichuan Agricultural University, Dujiangyan 611830, China.
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