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Sharma V, Ali MF, Kawashima T. Insights into dynamic coenocytic endosperm development: Unraveling molecular, cellular, and growth complexity. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102566. [PMID: 38830335 DOI: 10.1016/j.pbi.2024.102566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
The endosperm, a product of double fertilization, is one of the keys to the evolution and success of angiosperms in conquering the land. While there are differences in endosperm development among flowering plants, the most common form is coenocytic growth, where the endosperm initially undergoes nuclear division without cytokinesis and eventually becomes cellularized. This complex process requires interplay among networks of transcription factors such as MADS-box, auxin response factors (ARFs), and phytohormones. The role of cytoskeletal elements in shaping the coenocytic endosperm and influencing seed growth also becomes evident. This review offers a recent understanding of the molecular and cellular dynamics in coenocytic endosperm development and their contributions to the final seed size.
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Affiliation(s)
- Vijyesh Sharma
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Mohammad Foteh Ali
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA.
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Zhong Y, Chen Y, Pan M, Li X, Hebelstrup K, Cai J, Zhou Q, Dai T, Cao W, Jiang D. Transport and spatio-temporal conversion of sugar facilitate the formation of spatial gradients of starch in wheat caryopses. Commun Biol 2024; 7:928. [PMID: 39090206 PMCID: PMC11294588 DOI: 10.1038/s42003-024-06625-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Wheat grain starch content displays large variations within different pearling fractions, which affecting the processing quality of corresponding flour, while the underlying mechanism on starch gradient formation is unclear. Here, we show that wheat caryopses acquire sugar through the transfer of cells (TCs), inner endosperm (IE), outer endosperm (OE), and finally aleurone (AL) via micro positron emission tomography-computed tomography (PET-CT). To obtain integrated information on spatial transcript distributions, developing caryopses are laser microdissected into AL, OE, IE, and TC. Most genes encoding carbohydrate transporters are upregulated or specifically expressed, and sugar metabolites are more highly enriched in the TC group than in the AL group, in line with the PET-CT results. Genes encoding enzymes in sucrose metabolism, such as sucrose synthase, beta-fructofuranosidase, glucose-1-phosphate adenylyltransferase show significantly lower expression in AL than in OE and IE, indicating that substrate supply is crucial for the formation of starch gradients. Furthermore, the low expressions of gene encoding starch synthase contribute to low starch content in AL. Our results imply that transcriptional regulation represents an important means of impacting starch distribution in wheat grains and suggests breeding targets for enhancing specially pearled wheat with higher quality.
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Affiliation(s)
- Yingxin Zhong
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China
| | - Yuhua Chen
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China
| | - Mingsheng Pan
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China
| | - Xiangnan Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kim Hebelstrup
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Jian Cai
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China
| | - Qin Zhou
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China
| | - Tingbo Dai
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China
| | - Weixing Cao
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Physiology and Ecology in Southern China, Ministry of Agriculture/National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, PR China.
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Ji Y, Hewavithana T, Sharpe AG, Jin L. Understanding grain development in the Poaceae family by comparing conserved and distinctive pathways through omics studies in wheat and maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1393140. [PMID: 39100085 PMCID: PMC11295249 DOI: 10.3389/fpls.2024.1393140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024]
Abstract
The Poaceae family, commonly known as the grass family, encompasses a diverse group of crops that play an essential role in providing food, fodder, biofuels, environmental conservation, and cultural value for both human and environmental well-being. Crops in Poaceae family are deeply intertwined with human societies, economies, and ecosystems, making it one of the most significant plant families in the world. As the major reservoirs of essential nutrients, seed grain of these crops has garnered substantial attention from researchers. Understanding the molecular and genetic processes that controls seed formation, development and maturation can provide insights for improving crop yield, nutritional quality, and stress tolerance. The diversity in photosynthetic pathways between C3 and C4 plants introduces intriguing variations in their physiological and biochemical processes, potentially affecting seed development. In this review, we explore recent studies performed with omics technologies, such as genomics, transcriptomics, proteomics and metabolomics that shed light on the mechanisms underlying seed development in wheat and maize, as representatives of C3 and C4 plants respectively, providing insights into their unique adaptations and strategies for reproductive success.
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Affiliation(s)
- Yuanyuan Ji
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Thulani Hewavithana
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lingling Jin
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
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Khan A, Tian R, Bean SR, Yerka M, Jiao Y. Transcriptome and metabolome analyses reveal regulatory networks associated with nutrition synthesis in sorghum seeds. Commun Biol 2024; 7:841. [PMID: 38987396 PMCID: PMC11237005 DOI: 10.1038/s42003-024-06525-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Cereal seeds are vital for food, feed, and agricultural sustainability because they store and provide essential nutrients to human and animal food and feed systems. Unraveling molecular processes in seed development is crucial for enhancing cereal grain yield and quality. We analyze spatiotemporal transcriptome and metabolome profiles during sorghum seed development in the inbred line 'BTx623'. Morphological and molecular analyses identify the key stages of seed maturation, specifying starch biosynthesis onset at 5 days post-anthesis (dpa) and protein at 10 dpa. Transcriptome profiling from 1 to 25 dpa reveal dynamic gene expression pathways, shifting from cellular growth and embryo development (1-5 dpa) to cell division, fatty acid biosynthesis (5-25 dpa), and seed storage compounds synthesis in the endosperm (5-25 dpa). Network analysis identifies 361 and 207 hub genes linked to starch and protein synthesis in the endosperm, respectively, which will help breeders enhance sorghum grain quality. The availability of this data in the sorghum reference genome line establishes a baseline for future studies as new pangenomes emerge, which will consider copy number and presence-absence variation in functional food traits.
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Affiliation(s)
- Adil Khan
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Ran Tian
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, Center for Grain and Animal Health Research, USDA-ARS, 1515 College Ave, Manhattan, KS, 66502, USA
| | - Melinda Yerka
- Department of Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Yinping Jiao
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
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Zhong Y, Chen Y, Pan M, Wang H, Sun J, Chen Y, Cai J, Zhou Q, Wang X, Jiang D. Insights into the Functional Components in Wheat Grain: Spatial Pattern, Underlying Mechanism and Cultivation Regulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112192. [PMID: 37299171 DOI: 10.3390/plants12112192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/17/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Wheat is a staple crop; its production must achieve both high yield and good quality due to worldwide demands for food security and better quality of life. It has been found that the grain qualities vary greatly within the different layers of wheat kernels. In this paper, the spatial distributions of protein and its components, starch, dietary fiber, and microelements are summarized in detail. The underlying mechanisms regarding the formation of protein and starch, as well as spatial distribution, are discussed from the views of substrate supply and the protein and starch synthesis capacity. The regulating effects of cultivation practices on gradients in composition are identified. Finally, breakthrough solutions for exploring the underlying mechanisms of the spatial gradients of functional components are presented. This paper will provide research perspectives for producing wheat that is both high in yield and of good quality.
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Affiliation(s)
- Yingxin Zhong
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuhua Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingsheng Pan
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hengtong Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayu Sun
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Cai
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qin Zhou
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Jiang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Hertig C, Rutten T, Melzer M, Schippers JHM, Thiel J. Dissection of Developmental Programs and Regulatory Modules Directing Endosperm Transfer Cell and Aleurone Identity in the Syncytial Endosperm of Barley. PLANTS (BASEL, SWITZERLAND) 2023; 12:1594. [PMID: 37111818 PMCID: PMC10142620 DOI: 10.3390/plants12081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Endosperm development in barley starts with the formation of a multinucleate syncytium, followed by cellularization in the ventral part of the syncytium generating endosperm transfer cells (ETCs) as first differentiating subdomain, whereas aleurone (AL) cells will originate from the periphery of the enclosing syncytium. Positional signaling in the syncytial stage determines cell identity in the cereal endosperm. Here, we performed a morphological analysis and employed laser capture microdissection (LCM)-based RNA-seq of the ETC region and the peripheral syncytium at the onset of cellularization to dissect developmental and regulatory programs directing cell specification in the early endosperm. Transcriptome data revealed domain-specific characteristics and identified two-component signaling (TCS) and hormone activities (auxin, ABA, ethylene) with associated transcription factors (TFs) as the main regulatory links for ETC specification. On the contrary, differential hormone signaling (canonical auxin, gibberellins, cytokinin) and interacting TFs control the duration of the syncytial phase and timing of cellularization of AL initials. Domain-specific expression of candidate genes was validated by in situ hybridization and putative protein-protein interactions were confirmed by split-YFP assays. This is the first transcriptome analysis dissecting syncytial subdomains of cereal seeds and provides an essential framework for initial endosperm differentiation in barley, which is likely also valuable for comparative studies with other cereal crops.
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Affiliation(s)
- Christian Hertig
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Twan Rutten
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Jos H. M. Schippers
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Johannes Thiel
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
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Yannam VRR, Lopes M, Guzman C, Soriano JM. Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test. FRONTIERS IN PLANT SCIENCE 2023; 14:1127357. [PMID: 36778676 PMCID: PMC9911887 DOI: 10.3389/fpls.2023.1127357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The release of new wheat varieties is based on two main characteristics, grain yield and quality, to meet the consumer's demand. Identifying the genetic architecture for yield and key quality traits has wide attention for genetic improvement to meet the global requirement. In this sense, the use of landraces represents an impressive source of natural allelic variation. In this study, a genome-wide association analysis (GWAS) with PCA and kinship matrix was performed to detect QTLs in bread wheat for fifteen quality and agronomic traits using 170 diverse landraces from 24 Mediterranean countries in two years of field trials. A total of 53 QTL hotspots containing 165 significant marker-trait associations (MTAs) were located across the genome for quality and agronomical traits except for chromosome 2D. The major specific QTL hotspots for quality traits were QTL_3B.3 (13 MTAs with a mean PVE of 8.2%) and QTL_4A.3 (15 MTAs, mean PVE of 11.0%), and for yield-related traits were QTL_2B.1 (8 MTAs, mean PVE of 7.4%) and QTL_4B.2 (5 MTAs, mean PVE of 10.0%). A search for candidate genes (CG) identified 807 gene models within the QTL hotspots. Ten of these CGs were expressed specifically in grain supporting the role of identified QTLs in Landraces, associated to bread wheat quality traits and grain formation. A cross-validation approach within the collection was performed to calculate the accuracies of genomic prediction for quality and agronomical traits, ranging from -0.03 to 0.64 for quality and 0.46 to 0.65 for agronomic traits. In addition, five prediction equations using the phenotypic data were developed to predict bread loaf volume in landraces. The prediction ability varied from 0.67 to 0.82 depending on the complexity of the traits considered to predict loaf volume.
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Affiliation(s)
- Venkata Rami Reddy Yannam
- Sustainable Field Crops Program, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Marta Lopes
- Sustainable Field Crops Program, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Carlos Guzman
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba, Córdoba, Spain
| | - Jose Miguel Soriano
- Sustainable Field Crops Program, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
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Roy C, Kumar S, Ranjan RD, Kumhar SR, Govindan V. Genomic approaches for improving grain zinc and iron content in wheat. Front Genet 2022; 13:1045955. [PMID: 36437911 PMCID: PMC9683485 DOI: 10.3389/fgene.2022.1045955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/24/2022] [Indexed: 09/29/2023] Open
Abstract
More than three billion people worldwide suffer from iron deficiency associated anemia and an equal number people suffer from zinc deficiency. These conditions are more prevalent in Sub-Saharan Africa and South Asia. In developing countries, children under the age of five with stunted growth and pregnant or lactating women were found to be at high risk of zinc and iron deficiencies. Biofortification, defined as breeding to develop varieties of staple food crops whose grain contains higher levels of micronutrients such as iron and zinc, are one of the most promising, cost-effective and sustainable ways to improve the health in resource-poor households, particularly in rural areas where families consume some part of what they grow. Biofortification through conventional breeding in wheat, particularly for grain zinc and iron, have made significant contributions, transferring important genes and quantitative trait loci (QTLs) from wild and related species into cultivated wheat. Nonetheless, the quantitative, genetically complex nature of iron and zinc levels in wheat grain limits progress through conventional breeding, making it difficult to attain genetic gain both for yield and grain mineral concentrations. Wheat biofortification can be achieved by enhancing mineral uptake, source-to-sink translocation of minerals and their deposition into grains, and the bioavailability of the minerals. A number of QTLs with major and minor effects for those traits have been detected in wheat; introducing the most effective into breeding lines will increase grain zinc and iron concentrations. New approaches to achieve this include marker assisted selection and genomic selection. Faster breeding approaches need to be combined to simultaneously increase grain mineral content and yield in wheat breeding lines.
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Affiliation(s)
- Chandan Roy
- Department of Genetics and Plant Breeding, Agriculture University, Jodhpur, Rajasthan, India
| | - Sudhir Kumar
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Rakesh Deo Ranjan
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Sita Ram Kumhar
- Department of Genetics and Plant Breeding, Agriculture University, Jodhpur, Rajasthan, India
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
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Fang ZT, Kapoor R, Datta A, Liu S, Stull MA, Seitz PG, Johnson CD, Okumoto S. Transcriptome Analysis of Developing Grains from Wheat Cultivars TAM 111 and TAM 112 Reveal Cultivar-Specific Regulatory Networks. Int J Mol Sci 2022; 23:ijms232012660. [PMID: 36293517 PMCID: PMC9604430 DOI: 10.3390/ijms232012660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/20/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Wheat flour's end-use quality is tightly linked to the quantity and composition of storage proteins in the endosperm. TAM 111 and TAM 112 are two popular cultivars grown in the Southern US Great Plains with significantly different protein content. To investigate regulatory differences, transcriptome data were analyzed from developing grains at early- and mid-filling stages. At the mid-filling stage, TAM 111 preferentially upregulated starch metabolism-related pathways compared to TAM 112, whereas amino acid metabolism and transporter-related pathways were over-represented in TAM 112. Elemental analyses also indicated a higher N percentage in TAM 112 at the mid-filling stage. To explore the regulatory variation, weighted correlation gene network was constructed from publicly available RNAseq datasets to identify the modules differentially regulated in TAM 111 and TAM 112. Further, the potential transcription factors (TFs) regulating those modules were identified using graphical least absolute shrinkage and selection operator (GLASSO). Homologs of the OsNF-Y family members with known starch metabolism-related functions showed higher connectivities in TAM 111. Multiple TFs with high connectivity in TAM 112 had predicted functions associated with ABA response in grain. These results will provide novel targets for breeders to explore and further our understanding in mechanisms regulating grain development.
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Affiliation(s)
- Ze-Tian Fang
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843, USA
| | - Rajan Kapoor
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Aniruddha Datta
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research Center, 6500 Amarillo Blvd W, Amarillo, TX 79106, USA
| | - Matthew A. Stull
- Texas A&M AgriLife Genomics and Bioinformatics Service, College Station, TX 77845, USA
| | - Paige G. Seitz
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843, USA
| | - Charles D. Johnson
- Texas A&M AgriLife Genomics and Bioinformatics Service, College Station, TX 77845, USA
| | - Sakiko Okumoto
- Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Texas A&M University, College Station, TX 77843, USA
- Correspondence:
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Saini P, Sheikh I, Saini DK, Mir RR, Dhaliwal HS, Tyagi V. Consensus genomic regions associated with grain protein content in hexaploid and tetraploid wheat. Front Genet 2022; 13:1021180. [PMID: 36246648 PMCID: PMC9554612 DOI: 10.3389/fgene.2022.1021180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
A meta-analysis of QTLs associated with grain protein content (GPC) was conducted in hexaploid and tetraploid wheat to identify robust and stable meta-QTLs (MQTLs). For this purpose, as many as 459 GPC-related QTLs retrieved from 48 linkage-based QTL mapping studies were projected onto the newly developed wheat consensus map. The analysis resulted in the prediction of 57 MQTLs and 7 QTL hotspots located on all wheat chromosomes (except chromosomes 1D and 4D) and the average confidence interval reduced 2.71-fold in the MQTLs and QTL hotspots compared to the initial QTLs. The physical regions occupied by the MQTLs ranged from 140 bp to 224.02 Mb with an average of 15.2 Mb, whereas the physical regions occupied by QTL hotspots ranged from 1.81 Mb to 36.03 Mb with a mean of 8.82 Mb. Nineteen MQTLs and two QTL hotspots were also found to be co-localized with 45 significant SNPs identified in 16 previously published genome-wide association studies in wheat. Candidate gene (CG) investigation within some selected MQTLs led to the identification of 705 gene models which also included 96 high-confidence CGs showing significant expressions in different grain-related tissues and having probable roles in GPC regulation. These significantly expressed CGs mainly involved the genes/gene families encoding for the following proteins: aminotransferases, early nodulin 93, glutamine synthetases, invertase/pectin methylesterase inhibitors, protein BIG GRAIN 1-like, cytochrome P450, glycosyl transferases, hexokinases, small GTPases, UDP-glucuronosyl/UDP-glucosyltransferases, and EamA, SANT/Myb, GNAT, thioredoxin, phytocyanin, and homeobox domains containing proteins. Further, eight genes including GPC-B1, Glu-B1-1b, Glu-1By9, TaBiP1, GSr, TaNAC019-A, TaNAC019-D, and bZIP-TF SPA already known to be associated with GPC were also detected within some of the MQTL regions confirming the efficacy of MQTLs predicted during the current study.
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Affiliation(s)
- Pooja Saini
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Imran Sheikh
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punajb Agricultural University, Ludhiana, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture SKUAST-Kashmir, Srinagar, India
| | - Harcharan Singh Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Vikrant Tyagi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
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Gudi S, Saini DK, Singh G, Halladakeri P, Kumar P, Shamshad M, Tanin MJ, Singh S, Sharma A. Unravelling consensus genomic regions associated with quality traits in wheat using meta-analysis of quantitative trait loci. PLANTA 2022; 255:115. [PMID: 35508739 DOI: 10.1007/s00425-022-03904-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/26/2022] [Indexed: 05/03/2023]
Abstract
Meta-analysis in wheat for three major quality traits identified 110 meta-QTL (MQTL) with reduced confidence interval (CI). Five GWAS validated MQTL (viz., 1A.1, 1B.2, 3B.4, 5B.2, and 6B.2), each involving more than 20 initial QTL and reduced CI (95%) (< 2 cM), were selected for quality breeding programmes. Functional characterization including candidate gene mining and expression analysis discovered 44 high confidence candidate genes associated with quality traits. A meta-analysis of quantitative trait loci (QTL) associated with dough rheology properties, nutritional traits, and processing quality traits was conducted in wheat. For this purpose, as many as 2458 QTL were collected from 50 interval mapping studies published during 2013-2020. Of the total QTL, 1126 QTL were projected onto the consensus map saturated with 249,603 markers which led to the identification of 110 meta-QTL (MQTL). These MQTL exhibited an 18.84-fold reduction in the average CI compared to the average CI of the initial QTL (ranging from 14.87 to 95.55 cM with an average of 40.35 cM). Of the 110, 108 MQTL were physically anchored to the wheat reference genome, including 51 MQTL verified with marker-trait associations (MTAs) reported from earlier genome-wide association studies. Candidate gene (CG) mining allowed the identification of 2533 unique gene models from the MQTL regions. In-silico expression analysis discovered 439 differentially expressed gene models with > 2 transcripts per million expressions in grains and related tissues, which also included 44 high-confidence CGs involved in the various cellular and biochemical processes related to quality traits. Nine functionally characterized wheat genes associated with grain protein content, high-molecular-weight glutenin, and starch synthase enzymes were also found to be co-localized with some of the MQTL. Synteny analysis between wheat and rice MQTL regions identified 23 wheat MQTL syntenic to 16 rice MQTL associated with quality traits. Furthermore, 64 wheat orthologues of 30 known rice genes were detected in 44 MQTL regions. Markers flanking the MQTL identified in the present study can be used for marker-assisted breeding and as fixed effects in the genomic selection models for improving the prediction accuracy during quality breeding. Wheat orthologues of rice genes and other CGs available from MQTLs can be promising targets for further functional validation and to better understand the molecular mechanism underlying the quality traits in wheat.
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Affiliation(s)
- Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Gujarat, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohammad Shamshad
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohammad Jafar Tanin
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Saini DK, Srivastava P, Pal N, Gupta PK. Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1049-1081. [PMID: 34985537 DOI: 10.1007/s00122-021-04018-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/10/2021] [Indexed: 05/03/2023]
Abstract
In wheat, 2852 major QTLs of 8998 QTLs available for yield and related traits were used for meta-analysis; 141 meta-QTLs were identified, which included 13 breeder's MQTLs and 24 ortho-MQTLs; 1202 candidate genes and 50 homologues of genes for yield from other cereals were also identified. Meta-QTL analysis was conducted using 2852 of the 8998 known QTLs, retrieved from 230 reports published during 1999-2020 (including 19 studies on tetraploid wheat) for grain yield (GY) and the following ten component traits: (i) grain weight (GWei), (ii) grain morphology-related traits (GMRTs), (iii) grain number (GN), (iv) spikes-related traits (SRTs), (v) plant height (PH), (vi) tiller number (TN), (vii) harvest index (HI), (viii) biomass yield (BY), (ix) days to heading/flowering and maturity (DTH/F/M), and (x) grain filling duration (GFD). The study resulted in the identification of 141 meta-QTLs (MQTLs), with an average confidence interval (CI) of 1.4 cM as against a CI of > 12.1 cM (8.8 fold reduction) in the QTLs that were used. The corresponding physical length of CI ranged from 0.01 Mb to 661.9 Mb (mean, 31.5 Mb). Seventy-seven (77) of these 141 MQTLs overlapped marker-trait associations (MTAs) reported in genome-wide association studies. Also, 63 MQTLs (each based on at least 10 QTLs) were considered stable and robust, with 13 MQTLs described as breeder's MQTLs (selected based on small CI, large LOD, and high level of phenotypic variation explained). Thirty-five yield-related genes from rice, barley, and maize were also utilized to identify 50 wheat homologues in MQTLs. Further, the use of synteny and collinearity allowed the identification of 24 ortho-MQTLs which were common among the wheat, barley, rice, and maize. The results of the present study should prove useful for wheat breeding and future basic research in cereals including wheat, barley, rice, and maize.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
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13
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Saini DK, Chahal A, Pal N, Srivastava P, Gupta PK. Meta-analysis reveals consensus genomic regions associated with multiple disease resistance in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:11. [PMID: 37309411 PMCID: PMC10248701 DOI: 10.1007/s11032-022-01282-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
In wheat, meta-QTLs (MQTLs) and candidate genes (CGs) were identified for multiple disease resistance (MDR). For this purpose, information was collected from 58 studies for mapping QTLs for resistance to one or more of the five diseases. As many as 493 QTLs were available from these studies, which were distributed in five diseases as follows: septoria tritici blotch (STB) 126 QTLs; septoria nodorum blotch (SNB), 103 QTLs; fusarium head blight (FHB), 184 QTLs; karnal bunt (KB), 66 QTLs; and loose smut (LS), 14 QTLs. Of these 493 QTLs, only 291 QTLs could be projected onto a consensus genetic map, giving 63 MQTLs. The CI of the MQTLs ranged from 0.04 to 15.31 cM with an average of 3.09 cM per MQTL. This is a ~ 4.39 fold reduction from the CI of QTLs, which ranged from 0 to 197.6 cM, with a mean of 13.57 cM. Of 63 MQTLs, 60 were anchored to the reference physical map of wheat (the physical interval of these MQTLs ranged from 0.30 to 726.01 Mb with an average of 74.09 Mb). Thirty-eight (38) of these MQTLs were verified using marker-trait associations (MTAs) derived from genome-wide association studies. As many as 874 CGs were also identified which were further investigated for differential expression using data from five transcriptome studies, resulting in 194 differentially expressed candidate genes (DECGs). Among the DECGs, 85 genes had functions previously reported to be associated with disease resistance. These results should prove useful for fine mapping and cloning of MDR genes and marker-assisted breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01282-z.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttrakhand-263145 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab-141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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Lee Y, Okita TW, Szymanski DB. A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone. THE PLANT CELL 2021; 33:2965-2980. [PMID: 34270775 PMCID: PMC8462808 DOI: 10.1093/plcell/koab182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Multiprotein complexes execute and coordinate diverse cellular processes such as organelle biogenesis, vesicle trafficking, cell signaling, and metabolism. Knowledge about their composition and localization provides useful clues about the mechanisms of cellular homeostasis and system-level control. This is of great biological importance and practical significance in heterotrophic rice (Oryza sativa) endosperm and aleurone-subaleurone tissues, which are a primary source of seed vitamins and stored energy. Dozens of protein complexes have been implicated in the synthesis, transport, and storage of seed proteins, lipids, vitamins, and minerals. Mutations in protein complexes that control RNA transport result in aberrant endosperm with shrunken and floury phenotypes, significantly reducing seed yield and quality. The purpose of this study was to broadly predict protein complex composition in the aleurone-subaleurone layers of developing rice seeds using co-fractionation mass spectrometry. Following orthogonal chromatographic separations of biological replicates, thousands of protein elution profiles were subjected to distance-based clustering to enable large-scale multimerization state measurements and protein complex predictions. The predicted complexes had predicted functions across diverse functional categories, including novel heteromeric RNA binding protein complexes that may influence seed quality. This effective and open-ended proteomics pipeline provides useful clues about system-level posttranslational control during the early stages of rice seed development.
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Affiliation(s)
- Youngwoo Lee
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Thomas W. Okita
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, USA
| | - Daniel B. Szymanski
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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Meziani S, Nadaud I, Tasleem-Tahir A, Nurit E, Benguella R, Branlard G. Wheat aleurone layer: A site enriched with nutrients and bioactive molecules with potential nutritional opportunities for breeding. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Wan Y, Wang Y, Shi Z, Rentsch D, Ward JL, Hassall K, Sparks CA, Huttly AK, Buchner P, Powers S, Shewry PR, Hawkesford MJ. Wheat amino acid transporters highly expressed in grain cells regulate amino acid accumulation in grain. PLoS One 2021; 16:e0246763. [PMID: 33606697 PMCID: PMC7894817 DOI: 10.1371/journal.pone.0246763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/25/2021] [Indexed: 11/18/2022] Open
Abstract
Amino acids are delivered into developing wheat grains to support the accumulation of storage proteins in the starchy endosperm, and transporters play important roles in regulating this process. RNA-seq, RT-qPCR, and promoter-GUS assays showed that three amino acid transporters are differentially expressed in the endosperm transfer cells (TaAAP2), starchy endosperm cells (TaAAP13), and aleurone cells and embryo of the developing grain (TaAAP21), respectively. Yeast complementation revealed that all three transporters can transport a broad spectrum of amino acids. RNAi-mediated suppression of TaAAP13 expression in the starchy endosperm did not reduce the total nitrogen content of the whole grain, but significantly altered the composition and distribution of metabolites in the starchy endosperm, with increasing concentrations of some amino acids (notably glutamine and glycine) from the outer to inner starchy endosperm cells compared with wild type. Overexpression of TaAAP13 under the endosperm-specific HMW-GS (high molecular weight glutenin subunit) promoter significantly increased grain size, grain nitrogen concentration, and thousand grain weight, indicating that the sink strength for nitrogen transport was increased by manipulation of amino acid transporters. However, the total grain number was reduced, suggesting that source nitrogen remobilized from leaves is a limiting factor for productivity. Therefore, simultaneously increasing loading of amino acids into the phloem and delivery to the spike would be required to increase protein content while maintaining grain yield.
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Affiliation(s)
- Yongfang Wan
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Yan Wang
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
- Triticeae Institute, Sichuan Agricultural University, Sichuan, P. R. China
| | - Zhiqiang Shi
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
- National Technology Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology, and Ecology and Production in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Doris Rentsch
- University of Bern, Molecular Plant Physiology, Bern, Switzerland
| | - Jane L. Ward
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Kirsty Hassall
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Caroline A. Sparks
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Alison K. Huttly
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Peter Buchner
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Stephen Powers
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Peter R. Shewry
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Malcolm J. Hawkesford
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
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Kirov I, Dudnikov M, Merkulov P, Shingaliev A, Omarov M, Kolganova E, Sigaeva A, Karlov G, Soloviev A. Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development. PLANTS 2020; 9:plants9121794. [PMID: 33348863 PMCID: PMC7765848 DOI: 10.3390/plants9121794] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 01/22/2023]
Abstract
The intergenic space of plant genomes encodes many functionally important yet unexplored RNAs. The genomic loci encoding these RNAs are often considered “junk”, DNA as they are frequently associated with repeat-rich regions of the genome. The latter makes the annotations of these loci and the assembly of the corresponding transcripts using short RNAseq reads particularly challenging. Here, using long-read Nanopore direct RNA sequencing, we aimed to identify these “junk” RNA molecules, including long non-coding RNAs (lncRNAs) and transposon-derived transcripts expressed during early stages (10 days post anthesis) of seed development of triticale (AABBRR, 2n = 6x = 42), an interspecific hybrid between wheat and rye. Altogether, we found 796 lncRNAs and 20 LTR retrotransposon-related transcripts (RTE-RNAs) expressed at this stage, with most of them being previously unannotated and located in the intergenic as well as intronic regions. Sequence analysis of the lncRNAs provide evidence for the frequent exonization of Class I (retrotransposons) and class II (DNA transposons) transposon sequences and suggest direct influence of “junk” DNA on the structure and origin of lncRNAs. We show that the expression patterns of lncRNAs and RTE-related transcripts have high stage specificity. In turn, almost half of the lncRNAs located in Genomes A and B have the highest expression levels at 10–30 days post anthesis in wheat. Detailed analysis of the protein-coding potential of the RTE-RNAs showed that 75% of them carry open reading frames (ORFs) for a diverse set of GAG proteins, the main component of virus-like particles of LTR retrotransposons. We further experimentally demonstrated that some RTE-RNAs originate from autonomous LTR retrotransposons with ongoing transposition activity during early stages of triticale seed development. Overall, our results provide a framework for further exploration of the newly discovered lncRNAs and RTE-RNAs in functional and genome-wide association studies in triticale and wheat. Our study also demonstrates that Nanopore direct RNA sequencing is an indispensable tool for the elucidation of lncRNA and retrotransposon transcripts.
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Affiliation(s)
- Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
- Correspondence:
| | - Maxim Dudnikov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Pavel Merkulov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
| | - Andrey Shingaliev
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
| | - Murad Omarov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
- Faculty of Computer Science, National Research University Higher School of Economics, Pokrovsky Boulvar, 11, 109028 Moscow, Russia
| | - Elizaveta Kolganova
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
| | - Alexandra Sigaeva
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
| | - Gennady Karlov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
| | - Alexander Soloviev
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, 127550 Moscow, Russia; (M.D.); (P.M.); (A.S.); (M.O.); (E.K.); (A.S.); (G.K.); (A.S.)
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Yuan J, Jiao W, Liu Y, Ye W, Wang X, Liu B, Song Q, Chen ZJ. Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat. BMC Biol 2020; 18:171. [PMID: 33218336 PMCID: PMC7679994 DOI: 10.1186/s12915-020-00909-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background Wheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization, processes which are often accompanied by genetic and epigenetic changes, including DNA methylation. However, the extent and effect of such changes during wheat evolution, particularly from tetraploid-to-hexaploid wheat, are currently elusive. Results Here we report genome-wide DNA methylation landscapes in extracted tetraploid wheat (ETW, AABB), natural hexaploid wheat (NHW, AABBDD), resynthesized hexaploid wheat (RHW, AABBDD), natural tetraploid wheat (NTW, AABB), and diploid (DD). In the endosperm, levels of DNA methylation, especially in CHG (H=A, T, or C) context, were dramatically decreased in the ETW relative to natural hexaploid wheat; hypo-differentially methylated regions (DMRs) (850,832) were 24-fold more than hyper-DMRs (35,111). Interestingly, those demethylated regions in ETW were remethylated in the resynthesized hexaploid wheat after the addition of the D genome. In ETW, hypo-DMRs correlated with gene expression, and TEs were demethylated and activated, which could be silenced in the hexaploid wheat. In NHW, groups of TEs were dispersed in genic regions of three subgenomes, which may regulate the expression of TE-associated genes. Further, hypo-DMRs in ETW were associated with reduced H3K9me2 levels and increased expression of histone variant genes, suggesting concerted epigenetic changes after separation from the hexaploid. Conclusion Genome merger and separation provoke dynamic and reversible changes in chromatin and DNA methylation. These changes correlate with altered gene expression and TE activity, which may provide insights into polyploid genome and wheat evolution.
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Affiliation(s)
- Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yanfeng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchu, 130024, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China.
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China. .,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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Wu TY, Müller M, Gruissem W, Bhullar NK. Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains. RICE (NEW YORK, N.Y.) 2020; 13:62. [PMID: 32894395 PMCID: PMC7477059 DOI: 10.1186/s12284-020-00421-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/20/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. MAIN TEXT Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. CONCLUSION Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.
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Affiliation(s)
- Ting-Ying Wu
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Temasek Life Science Laboratory, 1 Research Link, Singapore, 117604, Singapore
| | - Marlen Müller
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Present address: Roche Glycart AG, Wagistrasse 10, 8952, Schlieren, Switzerland
| | - Wilhelm Gruissem
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland
- Advanced Plant Biotechnology Center, National Chung Hsing University, 145 Xingda Road, Taichung, 40227, Taiwan
| | - Navreet K Bhullar
- Department of Biology, Plant Biotechnology, Institute of Molecular Plant Biology, ETH Zurich, 8092, Zurich, Switzerland.
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Yu X, Wang L, Ran L, Chen X, Sheng J, Yang Y, Wu Y, Chen G, Xiong F. New insights into the mechanism of storage protein biosynthesis in wheat caryopsis under different nitrogen levels. PROTOPLASMA 2020; 257:1289-1308. [PMID: 32405873 DOI: 10.1007/s00709-020-01489-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/12/2020] [Indexed: 06/11/2023]
Abstract
Effect of different nitrogen levels (0, 150, and 300 kg hm-2) at booting stage on storage protein biosynthesis and processing quality of wheat was investigated using microstructural and ultrastructural observation, RNA sequencing, and quality analysis in this study. The results showed that the storage protein genes encoding ω- and γ-gliadin and low molecular weight glutenin subunit were upregulated at N150, and the genes encoding α- or β-gliadin and avenin-like protein were upregulated at N300. Two nitrogen levels induced expression of some interesting regulating genes, such as USE1, STX1B_2_3, SEC23, SEC24, SEC61A, HSP A1_8, HSP20, and HSP90B/TRA1. These regulatory genes were enriched in the KEGG pathway protein export, SNARE interactions in vesicular transport, and protein processing in endoplasmic reticulum. The amount, morphology, and accumulation pattern of protein body in four different endosperm regions in developing caryopsis show different response to N150 and N300, of which N300 had greater influence than N150. N150 and N300 both enhanced the contents of protein components, endosperm fullness, grain hardness, and parameters of processing quality, with the latter showing a greater degree of influence. Contrary to the accumulation pattern of protein body, N300 reduced the ratio of the amount of starch granules to the area ratio of protein body to starch granule. Results suggested that the difference of different nitrogen levels affecting storage protein biosynthesis might be through affecting the expression of the encoding and regulating gene of storage protein.
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Affiliation(s)
- Xurun Yu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Leilei Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Liping Ran
- Guangling College of Yangzhou University, Yangzhou, China
| | - Xinyu Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Jieyue Sheng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yunfei Wu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Gang Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Fei Xiong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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21
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Duan L, Han S, Wang K, Jiang P, Gu Y, Chen L, Mu J, Ye X, Li Y, Yan Y, Li X. Analyzing the action of evolutionarily conserved modules on HMW-GS 1Ax1 promoter activity. PLANT MOLECULAR BIOLOGY 2020; 102:225-237. [PMID: 31820284 DOI: 10.1007/s11103-019-00943-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The specific and high-level expression of 1Ax1 is determined by different promoter regions. HMW-GS synthesis occurs in aleurone layer cells. Heterologous proteins can be stored in protein bodies. High-molecular-weight glutenin subunit (HMW-GS) is highly expressed in the endosperm of wheat and relative species, where their expression level and allelic variation affect the bread-making quality and nutrient quality of flour. However, the mechanism regulating HMW-GS expression remains elusive. In this study, we analyzed the distribution of cis-acting elements in the 2659-bp promoter region of the HMW-GS gene 1Ax1, which can be divided into five element-enriched regions. Fragments derived from progressive 5' deletions were used to drive GUS gene expression in transgenic wheat, which was confirmed in aleurone layer cells, inner starchy endosperm cells, starchy endosperm transfer cells, and aleurone transfer cells by histochemical staining. The promoter region ranging from - 297 to - 1 was responsible for tissue-specific expression, while fragments from - 1724 to - 618 and from - 618 to - 297 were responsible for high-level expression. Under the control of the 1Ax1 promoter, heterologous protein could be stored in the form of protein bodies in inner starchy endosperm cells, even without a special location signal. Our findings not only deepen our understanding of glutenin expression regulation, trafficking, and accumulation but also provide a strategy for the utilization of wheat endosperm as a bioreactor for the production of nutrients and metabolic products.
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Affiliation(s)
- Luning Duan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Shichen Han
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Ke Wang
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Peihong Jiang
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yunsong Gu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Lin Chen
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Junyi Mu
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xingguo Ye
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaxuan Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yueming Yan
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Xiaohui Li
- Key Laboratory of Genetics and Biotechnology, College of Life Science, Capital Normal University, Beijing, 100048, China.
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Sharma S, Kaur G, Kumar A, Meena V, Kaur J, Pandey AK. Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress. BMC Mol Biol 2019; 20:22. [PMID: 31547799 PMCID: PMC6757437 DOI: 10.1186/s12867-019-0139-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/14/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Hexaploid wheat is an important cereal crop that has been targeted to enhance grain micronutrient content including zinc (Zn) and iron (Fe). In this direction, modulating the expression of plant transporters involved in Fe and Zn homeostasis has proven to be one of the promising approaches. The present work was undertaken to identify wheat zinc-induced facilitator-like (ZIFL) family of transporters. The wheat ZIFL genes were characterized for their transcriptional expression response during micronutrient fluctuations and exposure to multiple heavy metals. RESULTS The genome-wide analyses resulted in identification of fifteen putative TaZIFL-like genes, which were distributed only on Chromosome 3, 4 and 5. Wheat ZIFL proteins subjected to the phylogenetic analysis showed the uniform distribution along with rice, Arabidopsis and maize. In-silico analysis of the promoters of the wheat ZIFL genes demonstrated the presence of multiple metal binding sites including those which are involved in Fe and heavy metal homeostasis. Quantitative real-time PCR analysis of wheat ZIFL genes suggested the differential regulation of the transcripts in both roots and shoots under Zn surplus and also during Fe deficiency. Specifically, in roots, TaZIFL2.3, TaZIFL4.1, TaZIFL4.2, TaZIFL5, TaZIFL6.1 and TaZIFL6.2 were significantly up-regulated by both Zn and Fe. This suggested that ZIFL could possibly be regulated by both the nutrient stress in a tissue specific manner. When exposed to heavy metals, TaZIFL4.2 and TaZIFL7.1 show significant up-regulation, whereas TaZIFL5 and TaZIFL6.2 remained almost unaffected. CONCLUSION This is the first report for detailed analysis of wheat ZIFL genes. ZIFL genes also encode for transporter of mugineic acid (TOM) proteins, that are involved in the release of phytosiderophores to enhance Fe/Zn uptake. The detailed expression analysis suggests the varying expression patterns during development of wheat seedlings and also against abiotic/biotic stresses. Overall, this study will lay foundation to prioritize functional assessment of the candidate ZIFL as a putative TOM protein in wheat.
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Affiliation(s)
- Shivani Sharma
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, Mohali, Punjab 140306 India
- University Institute of Engineering and Technology, Panjab University, Sector 25, Chandigarh, Punjab 160015 India
| | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, Mohali, Punjab 140306 India
| | - Anil Kumar
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, Mohali, Punjab 140306 India
| | - Varsha Meena
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, Mohali, Punjab 140306 India
| | - Jaspreet Kaur
- University Institute of Engineering and Technology, Panjab University, Sector 25, Chandigarh, Punjab 160015 India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute (Department of Biotechnology), Sector 81, Knowledge City, Mohali, Punjab 140306 India
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Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family in Triticum aestivum. G3-GENES GENOMES GENETICS 2019; 9:2709-2722. [PMID: 31227524 PMCID: PMC6686943 DOI: 10.1534/g3.119.400444] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The serine protease inhibitor (serpin) gene family is the largest family of protease inhibitors. Serine protease inhibitors have an active, but under-characterized, role in grain development and defense against pathogen attack in cereal crops. By exploiting publicly available genomic, transcriptomic and proteomic data for wheat (Triticum aestivum), we have identified and annotated the entire ’serpinome’ of wheat and constructed a high-quality and robust phylogenetic tree of the gene family, identifying paralogous and homeologous clades from the hexaploid wheat genome, including the Serpin-Z group that have been well characterized in barley. Using publicly available RNAseq data (http://www.wheat-expression.com/), expression profiles of the wheat serpins were explored across a variety of tissues from the developing grain, spikelet and spike. We show that the SERPIN-Z clade, among others, are highly expressed during grain development, and that there is homeologous and paralogous functional redundancy in this gene family. Further to their role in grain development, serpins play an important but under-explored role in response to fungal pathogens. Using 13 RNAseq datasets of wheat tissues infected by fungal pathogens, we identified 37 serpins with a significant disease response. The majority of the disease-responsive serpins were upregulated by Fusarium graminearum, a destructive fungal pathogen that attacks the spike and developing grain of wheat. As serpins are ubiquitous in wheat grain, the genes encoding serpins may be linked to grain development, with their disease response a result of pleiotropy.
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24
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Brinton J, Uauy C. A reductionist approach to dissecting grain weight and yield in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:337-358. [PMID: 30421518 PMCID: PMC6492019 DOI: 10.1111/jipb.12741] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
Grain yield is a highly polygenic trait that is influenced by the environment and integrates events throughout the life cycle of a plant. In wheat, the major grain yield components often present compensatory effects among them, which alongside the polyploid nature of wheat, makes their genetic and physiological study challenging. We propose a reductionist and systematic approach as an initial step to understand the gene networks regulating each individual yield component. Here, we focus on grain weight and discuss the importance of examining individual sub-components, not only to help in their genetic dissection, but also to inform our mechanistic understanding of how they interrelate. This knowledge should allow the development of novel combinations, across homoeologs and between complementary modes of action, thereby advancing towards a more integrated strategy for yield improvement. We argue that this will break barriers in terms of phenotypic variation, enhance our understanding of the physiology of yield, and potentially deliver improved on-farm yield.
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Affiliation(s)
- Jemima Brinton
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
| | - Cristobal Uauy
- John Innes CentreNorwich Research ParkNorwich NR4 7UHUnited Kingdom
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25
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Analysis of the expression of transcription factors and other genes associated with aleurone layer development in wheat endosperm. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2018.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Reeves PA, Richards CM. Biases induced by using geography and environment to guide ex situ conservation. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1098-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Tian B, Talukder SK, Fu J, Fritz AK, Trick HN. Expression of a rice soluble starch synthase gene in transgenic wheat improves the grain yield under heat stress conditions. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2018; 54:216-227. [PMID: 29780215 PMCID: PMC5954006 DOI: 10.1007/s11627-018-9893-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/16/2018] [Indexed: 05/04/2023]
Abstract
Wheat (Triticum aestivum L.) is a temperate cereal with an optimum temperature range of 15-22°C during the grain filling stage. Heat stress is one of the major environmental constraints for wheat production worldwide. Temperatures above 25°C during the grain filling stage significantly reduced wheat yield and quality. This reduction was reported due to the inactivation of the soluble starch synthase, a key heat-labile enzyme in starch transformation of wheat endosperm. To improve wheat productivity under heat stress, the rice soluble starch synthase I, under the control of either a constitutive promoter or an endosperm-specific promoter, was expressed in wheat and the transgenic lines were monitored for expression and the effects on yield-related traits. The results showed that the transgenic wheat events expressed rice soluble starch synthase I at a high level after four generations, and transgenic plants produced grains of greater weight during heat stress. Under heat stress conditions, the thousand kernel weight increased 21-34% in T2 and T3 transgenic plants compared to the non-transgenic control plants. In addition, the photosynthetic duration of transgenic wheat was longer than in non-transgenic controls. This study demonstrated that the engineering of a heat tolerant soluble starch synthase gene can be a potential strategy to improve wheat yield under heat stress conditions.
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Affiliation(s)
- Bin Tian
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506 USA
| | - Shyamal K. Talukder
- Department of Agronomy, 2004 Throckmorton Plant Sciences Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506 USA
- Samuel Roberts Noble Research Institute, LLC, Ardmore, OK 73401 USA
| | - Jianming Fu
- Department of Agronomy, 2004 Throckmorton Plant Sciences Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506 USA
- USDA/ARS/Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Plant Sciences Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506 USA
| | - Allan K. Fritz
- Department of Agronomy, 2004 Throckmorton Plant Sciences Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506 USA
| | - Harold N. Trick
- Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506 USA
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28
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Jiao W, Yuan J, Jiang S, Liu Y, Wang L, Liu M, Zheng D, Ye W, Wang X, Chen ZJ. Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:828-842. [PMID: 29265531 DOI: 10.1111/tpj.13805] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/04/2017] [Indexed: 05/26/2023]
Abstract
Polyploidy occurs in some animals and all flowering plants, including important crops such as wheat. The consequences of polyploidy in crops remain elusive, partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids Sl Sl AA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more non-additively expressed genes in Sl Sl AA than in AADD. In AADD, non-additively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In Sl Sl AA, there was a tendency for expression dominance of Sl over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nucleotide small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in Sl Sl AA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons and gene expression coincide with unstable AADD genomes and stable Sl Sl AA genomes, which could help explain the evolutionary trajectories of wheat allotetraploids formed by different progenitors.
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Affiliation(s)
- Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Shan Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yanfeng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Lili Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Mingming Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Dewei Zheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
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Rangan P, Furtado A, Henry RJ. The transcriptome of the developing grain: a resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat. BMC Genomics 2017; 18:766. [PMID: 29020946 PMCID: PMC5637334 DOI: 10.1186/s12864-017-4154-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat is one of the three major cereals that have been domesticated to feed human populations. The composition of the wheat grain determines the functional properties of wheat including milling efficiency, bread making, and nutritional value. Transcriptome analysis of the developing wheat grain provides key insights into the molecular basis for grain development and quality. RESULTS The transcriptome of 35 genotypes was analysed by RNA-Seq at two development stages (14 and 30 days-post-anthesis, dpa) corresponding to the mid stage of development (stage Z75) and the almost mature seed (stage Z85). At 14dpa, most of the transcripts were associated with the synthesis of the major seed components including storage proteins and starch. At 30dpa, a diverse range of genes were expressed at low levels with a predominance of genes associated with seed defence and stress tolerance. RNA-Seq analysis of changes in expression between 14dpa and 30dpa stages revealed 26,477 transcripts that were significantly differentially expressed at a FDR corrected p-value cut-off at ≤0.01. Functional annotation and gene ontology mapping was performed and KEGG pathway mapping allowed grouping based upon biochemical linkages. This analysis demonstrated that photosynthesis associated with the pericarp was very active at 14dpa but had ceased by 30dpa. Recently reported genes for flour yield in milling and bread quality were found to influence wheat quality largely due to expression patterns at the earlier seed development stage. CONCLUSIONS This study serves as a resource providing an overview of gene expression during wheat grain development at the early (14dpa) and late (30dpa) grain filling stages for use in studies of grain quality and nutritional value and in understanding seed biology.
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Affiliation(s)
- Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia.,Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia.
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30
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Nirmal RC, Furtado A, Rangan P, Henry RJ. Fasciclin-like arabinogalactan protein gene expression is associated with yield of flour in the milling of wheat. Sci Rep 2017; 7:12539. [PMID: 28970511 PMCID: PMC5624953 DOI: 10.1038/s41598-017-12845-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/14/2017] [Indexed: 12/14/2022] Open
Abstract
A large portion of the global wheat crop is milled to produce flour for use in the production of foods such as bread. Pressure to increase food supplies sustainably can be address directly by reducing post-harvest losses during processes such as flour milling. The recovery of flour in the milling of wheat is genetically determined but difficult to assess in wheat breeding due to the requirement for a large sample. Here we report the discovery that human selection for altered expression of putative cell adhesion proteins is associated with wheats that give high yields of flour on milling. Genes encoding fasciclin-like arabinogalactan proteins are expressed at low levels in high milling wheat genotypes at mid grain development. Thirty worldwide wheat genotypes were grouped into good and poor millers based flour yield obtained from laboratory scale milling of mature seeds. Differentially expressed genes were identified by comparing transcript profiles at 14 and 30 days post anthesis obtained from RNA-seq data of all the genotypes. Direct selection for genotypes with appropriate expression of these genes will greatly accelerate wheat breeding and ensure high recoveries of flour from wheat by resulting in grains that break up more easily on milling.
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Affiliation(s)
- Ravi C Nirmal
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Qld, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Qld, Australia
| | - Parimalan Rangan
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, St Lucia, Qld, Australia.
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Yamasaki Y, Gao F, Jordan MC, Ayele BT. Seed maturation associated transcriptional programs and regulatory networks underlying genotypic difference in seed dormancy and size/weight in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:154. [PMID: 28915785 PMCID: PMC5603048 DOI: 10.1186/s12870-017-1104-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 09/08/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Maturation forms one of the critical seed developmental phases and it is characterized mainly by programmed cell death, dormancy and desiccation, however, the transcriptional programs and regulatory networks underlying acquisition of dormancy and deposition of storage reserves during the maturation phase of seed development are poorly understood in wheat. The present study performed comparative spatiotemporal transcriptomic analysis of seed maturation in two wheat genotypes with contrasting seed weight/size and dormancy phenotype. RESULTS The embryo and endosperm tissues of maturing seeds appeared to exhibit genotype-specific temporal shifts in gene expression profile that might contribute to the seed phenotypic variations. Functional annotations of gene clusters suggest that the two tissues exhibit distinct but genotypically overlapping molecular functions. Motif enrichment predicts genotypically distinct abscisic acid (ABA) and gibberellin (GA) regulated transcriptional networks contribute to the contrasting seed weight/size and dormancy phenotypes between the two genotypes. While other ABA responsive element (ABRE) motifs are enriched in both genotypes, the prevalence of G-box-like motif specifically in tissues of the dormant genotype suggests distinct ABA mediated transcriptional mechanisms control the establishment of dormancy during seed maturation. In agreement with this, the bZIP transcription factors that co-express with ABRE enriched embryonic genes differ with genotype. The enrichment of SITEIIATCYTC motif specifically in embryo clusters of maturing seeds irrespective of genotype predicts a tissue specific role for the respective TCP transcription factors with no or minimal contribution to the variations in seed dormancy. CONCLUSION The results of this study advance our understanding of the seed maturation associated molecular mechanisms underlying variation in dormancy and weight/size in wheat seeds, which is a critical step towards the designing of molecular strategies for enhancing seed yield and quality.
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Affiliation(s)
- Yuji Yamasaki
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
| | - Feng Gao
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
| | - Mark C. Jordan
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5 Canada
| | - Belay T. Ayele
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB R3T 2N2 Canada
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32
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Shukla V, Kaur M, Aggarwal S, Bhati KK, Kaur J, Mantri S, Pandey AK. Tissue specific transcript profiling of wheat phosphate transporter genes and its association with phosphate allocation in grains. Sci Rep 2016; 6:39293. [PMID: 27995999 PMCID: PMC5172359 DOI: 10.1038/srep39293] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/21/2016] [Indexed: 11/26/2022] Open
Abstract
Approaches enabling efficient phosphorus utilization in crops are of great importance. In cereal crop like wheat, utilization of inorganic phosphate (Pi) is high and mature grains are the major sink for Pi utilization and storage. Research that addresses the importance of the Pi homeostasis in developing grains is limited. In an attempt to understand the Pi homeostasis in developing wheat grains, we identified twelve new phosphate transporters (PHT), these are phyologentically well distributed along with the members reported from Arabidopsis and rice. Enhanced expression of PHT1-subfamily genes was observed in roots subjected to the Pi starvation suggesting their active role in Pi homeostasis. Differential expression patterns of all the PHT genes during grain filling stages suggested their importance in the filial tissues. Additionally, high accumulation of Pi and total P in aleurone correlates well with the expression of TaPHTs and other phosphate starvation related genes. Tissue specific transcript accumulation of TaPHT1.1, TaPHT1.2, TaPHT1.4 in aleurone; TaPHT3.1 in embryo and TaPHT4.2 in the endosperm was observed. Furthermore, their transcript abundance was affected in low phytate wheat grains. Altogether, this study helps in expanding the knowledge and prioritize the candidate wheat Pi-transporters to modulate the Pi homeostasis in cereal grains.
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Affiliation(s)
- Vishnu Shukla
- National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India), C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali-160071, Punjab, India
| | - Mandeep Kaur
- National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India), C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali-160071, Punjab, India
| | - Sipla Aggarwal
- National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India), C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali-160071, Punjab, India
| | - Kaushal Kumar Bhati
- National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India), C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali-160071, Punjab, India
| | - Jaspreet Kaur
- Department of Biotechnology, University Institute of Engineering and Technology (UIET), Panjab University, Chandigarh, India
| | - Shrikant Mantri
- National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India), C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali-160071, Punjab, India
| | - Ajay K. Pandey
- National Agri-Food Biotechnology Institute (Department of Biotechnology, Government of India), C-127, Industrial Area, S.A.S. Nagar, Phase 8, Mohali-160071, Punjab, India
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Rangan P, Furtado A, Henry RJ. New evidence for grain specific C4 photosynthesis in wheat. Sci Rep 2016; 6:31721. [PMID: 27530078 PMCID: PMC4987656 DOI: 10.1038/srep31721] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/22/2016] [Indexed: 11/30/2022] Open
Abstract
The C4 photosynthetic pathway evolved to allow efficient CO2 capture by plants where effective carbon supply may be limiting as in hot or dry environments, explaining the high growth rates of C4 plants such as maize. Important crops such as wheat and rice are C3 plants resulting in efforts to engineer them to use the C4 pathway. Here we show the presence of a C4 photosynthetic pathway in the developing wheat grain that is absent in the leaves. Genes specific for C4 photosynthesis were identified in the wheat genome and found to be preferentially expressed in the photosynthetic pericarp tissue (cross- and tube-cell layers) of the wheat caryopsis. The chloroplasts exhibit dimorphism that corresponds to chloroplasts of mesophyll- and bundle sheath-cells in leaves of classical C4 plants. Breeding to optimize the relative contributions of C3 and C4 photosynthesis may adapt wheat to climate change, contributing to wheat food security.
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Affiliation(s)
- Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia.,Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi-110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia
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Yu Y, Zhu D, Ma C, Cao H, Wang Y, Xu Y, Zhang W, Yan Y. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.01.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Xie Q, Mayes S, Sparkes DL. Carpel size, grain filling, and morphology determine individual grain weight in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6715-30. [PMID: 26246614 PMCID: PMC4623684 DOI: 10.1093/jxb/erv378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Individual grain weight is a major yield component in wheat. To provide a comprehensive understanding of grain weight determination, the carpel size at anthesis, grain dry matter accumulation, grain water uptake and loss, grain morphological expansion, and final grain weight at different positions within spikelets were investigated in a recombinant inbred line mapping population of bread wheat (Triticum aestivum L.)×spelt (Triticum spelta L.). Carpel size, grain dry matter and water accumulation, and grain dimensions interacted strongly with each other. Furthermore, larger carpels, a faster grain filling rate, earlier and longer grain filling, more grain water, faster grain water absorption and loss rates, and larger grain dimensions were associated with higher grain weight. Frequent quantitative trait locus (QTL) coincidences between these traits were observed, particularly those on chromosomes 2A, 3B, 4A, 5A, 5DL, and 7B, each of which harboured 16-49 QTLs associated with >12 traits. Analysis of the allelic effects of coincident QTLs confirmed their physiological relationships, indicating that the complex but orderly grain filling processes result mainly from pleiotropy or the tight linkages of functionally related genes. After grain filling, distal grains within spikelets were smaller than basal grains, primarily due to later grain filling and a slower initial grain filling rate, followed by synchronous maturation among different grains. Distal grain weight was improved by increased assimilate availability from anthesis. These findings provide deeper insight into grain weight determination in wheat, and the high level of QTL coincidences allows simultaneous improvement of multiple grain filling traits in breeding.
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Affiliation(s)
- Quan Xie
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Sean Mayes
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Debbie L Sparkes
- Division of Plant and Crop Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
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Aggarwal S, Shukla V, Bhati KK, Kaur M, Sharma S, Singh A, Mantri S, Pandey AK. Hormonal Regulation and Expression Profiles of Wheat Genes Involved during Phytic Acid Biosynthesis Pathway. PLANTS 2015; 4:298-319. [PMID: 27135330 PMCID: PMC4844322 DOI: 10.3390/plants4020298] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/26/2015] [Accepted: 06/01/2015] [Indexed: 11/16/2022]
Abstract
Phytic acid (PA) biosynthesis pathway genes were reported from multiple crop species. PA accumulation was enhanced during grain filling and at that time, hormones like Abscisic acid (ABA) and Gibberellic acid (GA3) interplay to control the process of seed development. Regulation of wheat PA pathway genes has not yet been reported in seeds. In an attempt to find the clues for the regulation by hormones, the promoter region of wheat PA pathway genes was analyzed for the presence of cis-elements. Multiple cis-elements of those known to be involved for ABA, GA3, salicylic acid (SA), and cAMP sensing were identified in the promoters of PA pathway genes. Eight genes (TaIMP, TaITPK1-4, TaPLC1, TaIPK2 and TaIPK1) involved in the wheat PA biosynthesis pathway were selected for the expression studies. The temporal expression response was studied in seeds treated with ABA and GA3 using quantitative real time PCR. Our results suggested that exogenous application of ABA induces few PA pathway genes in wheat grains. Comparison of expression profiles for PA pathway for GA3 and ABA suggested the antagonistic regulation of certain genes. Additionally, to reveal stress responses of wheat PA pathway genes, expression was also studied in the presence of SA and cAMP. Results suggested SA specific differential expression of few genes, whereas, overall repression of genes was observed in cAMP treated samples. This study is an effort to understand the regulation of PA biosynthesis genes in wheat.
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Affiliation(s)
- Sipla Aggarwal
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Vishnu Shukla
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Kaushal Kumar Bhati
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Mandeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Shivani Sharma
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Anuradha Singh
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Shrikant Mantri
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, C-127 Industrial Area, S.A.S-Nagar, Phase-8, Mohali, Punjab 160071, India.
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Wang M, Wang S, Xia G. From genome to gene: a new epoch for wheat research? TRENDS IN PLANT SCIENCE 2015; 20:380-387. [PMID: 25887708 DOI: 10.1016/j.tplants.2015.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 06/04/2023]
Abstract
Genetic research for bread wheat (Triticum aestivum), a staple crop around the world, has been impeded by its complex large hexaploid genome that contains a high proportion of repetitive DNA. Recent advances in sequencing technology have now overcome these challenges and led to genome drafts for bread wheat and its progenitors as well as high-resolution transcriptomes. However, the exploitation of these data for identifying agronomically important genes in wheat is lagging behind. We review recent wheat genome sequencing achievements and focus on four aspects of strategies and future hotspots for wheat improvement: positional cloning, 'omics approaches, combining forward and reverse genetics, and epigenetics.
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Affiliation(s)
- Meng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China
| | - Shubin Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China.
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Proteome evolution of wheat (Triticum aestivum L.) aleurone layer at fifteen stages of grain development. J Proteomics 2015; 123:29-41. [DOI: 10.1016/j.jprot.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/11/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022]
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Furtado A, Bundock PC, Banks PM, Fox G, Yin X, Henry RJ. A novel highly differentially expressed gene in wheat endosperm associated with bread quality. Sci Rep 2015; 5:10446. [PMID: 26011437 PMCID: PMC4650634 DOI: 10.1038/srep10446] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 04/13/2015] [Indexed: 11/15/2022] Open
Abstract
Analysis of gene expression in developing wheat seeds was used to identify a gene, wheat bread making (wbm), with highly differential expression (~1000 fold) in the starchy endosperm of genotypes varying in bread making quality. Several alleles differing in the 5’-upstream region (promoter) of this gene were identified, with one present only in genotypes with high levels of wbm expression. RNA-Seq analysis revealed low or no wbm expression in most genotypes but high expression (0.2-0.4% of total gene expression) in genotypes that had good bread loaf volume. The wbm gene is predicted to encode a mature protein of 48 amino acids (including four cysteine residues) not previously identified in association with wheat quality, possibly because of its small size and low frequency in the wheat gene pool. Genotypes with high wbm expression all had good bread making quality but not always good physical dough qualities. The predicted protein was sulphur rich suggesting the possibility of a contribution to bread loaf volume by supporting the crossing linking of proteins in gluten. Improved understanding of the molecular basis of differences in bread making quality may allow more rapid development of high performing genotypes with acceptable end-use properties and facilitate increased wheat production.
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Affiliation(s)
- A Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - P C Bundock
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW-2480, Australia
| | - P M Banks
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - G Fox
- Queensland Alliance for Agriculture and Food Innovation, Centre for Nutrition and Food Science, The University of Queensland, Toowoomba Qld, Australia
| | - X Yin
- Plant Transformation Core Facility, 1-33 Agriculture Building, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
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Pingault L, Choulet F, Alberti A, Glover N, Wincker P, Feuillet C, Paux E. Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome. Genome Biol 2015; 16:29. [PMID: 25853487 PMCID: PMC4355351 DOI: 10.1186/s13059-015-0601-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/28/2015] [Indexed: 12/19/2022] Open
Abstract
Background Because of its size, allohexaploid nature, and high repeat content, the bread wheat genome is a good model to study the impact of the genome structure on gene organization, function, and regulation. However, because of the lack of a reference genome sequence, such studies have long been hampered and our knowledge of the wheat gene space is still limited. The access to the reference sequence of the wheat chromosome 3B provided us with an opportunity to study the wheat transcriptome and its relationships to genome and gene structure at a level that has never been reached before. Results By combining this sequence with RNA-seq data, we construct a fine transcriptome map of the chromosome 3B. More than 8,800 transcription sites are identified, that are distributed throughout the entire chromosome. Expression level, expression breadth, alternative splicing as well as several structural features of genes, including transcript length, number of exons, and cumulative intron length are investigated. Our analysis reveals a non-monotonic relationship between gene expression and structure and leads to the hypothesis that gene structure is determined by its function, whereas gene expression is subject to energetic cost. Moreover, we observe a recombination-based partitioning at the gene structure and function level. Conclusions Our analysis provides new insights into the relationships between gene and genome structure and function. It reveals mechanisms conserved with other plant species as well as superimposed evolutionary forces that shaped the wheat gene space, likely participating in wheat adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0601-9) contains supplementary material, which is available to authorized users.
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Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, Mayer KFX, Olsen OA. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 2014; 345:1250091. [PMID: 25035498 DOI: 10.1126/science.1250091] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.
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Affiliation(s)
- Matthias Pfeifer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Karl G Kugler
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Simen R Sandve
- Department of Plant Sciences/Centre for Integrative Genetics, The Norwegian University of Life Sciences (NMBU), 1432 Åas, Norway
| | - Bujie Zhan
- Department of Plant Sciences/Centre for Integrative Genetics, The Norwegian University of Life Sciences (NMBU), 1432 Åas, Norway
| | - Heidi Rudi
- Department of Plant Sciences/Centre for Integrative Genetics, The Norwegian University of Life Sciences (NMBU), 1432 Åas, Norway
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, NMBU, 1432 Åas, Norway
| | | | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Odd-Arne Olsen
- Department of Plant Sciences/Centre for Integrative Genetics, The Norwegian University of Life Sciences (NMBU), 1432 Åas, Norway.
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Camilios-Neto D, Bonato P, Wassem R, Tadra-Sfeir MZ, Brusamarello-Santos LCC, Valdameri G, Donatti L, Faoro H, Weiss VA, Chubatsu LS, Pedrosa FO, Souza EM. Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. BMC Genomics 2014; 15:378. [PMID: 24886190 PMCID: PMC4042000 DOI: 10.1186/1471-2164-15-378] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/02/2014] [Indexed: 12/20/2022] Open
Abstract
Background The rapid growth of the world’s population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by A. brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB. Results We performed a dual RNA-Seq transcriptional profiling of wheat roots colonized by A. brasilense strain FP2. cDNA libraries from biological replicates of colonized and non-inoculated wheat roots were sequenced and mapped to wheat and A. brasilense reference sequences. The unmapped reads were assembled de novo. Overall, we identified 23,215 wheat expressed ESTs and 702 A. brasilense expressed transcripts. Bacterial colonization caused changes in the expression of 776 wheat ESTs belonging to various functional categories, ranging from transport activity to biological regulation as well as defense mechanism, production of phytohormones and phytochemicals. In addition, genes encoding proteins related to bacterial chemotaxi, biofilm formation and nitrogen fixation were highly expressed in the sub-set of A. brasilense expressed genes. Conclusions PGPB colonization enhanced the expression of plant genes related to nutrient up-take, nitrogen assimilation, DNA replication and regulation of cell division, which is consistent with a higher proportion of colonized root cells in the S-phase. Our data support the use of PGPB as an alternative to improve nutrient acquisition in important crops such as wheat, enhancing plant productivity and sustainability. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-378) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR 81531-990, Brazil.
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Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing. Proc Natl Acad Sci U S A 2014; 111:7582-7. [PMID: 24821765 DOI: 10.1073/pnas.1406383111] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development and seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed, and renewable resources. Little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step toward understanding these networks, we profiled all mRNAs in the maize kernel and endosperm at eight successive stages during the first 12 d after pollination. Analysis of these gene sets identified temporal programs of gene expression, including hundreds of transcription-factor genes. We found a close correlation of the sequentially expressed gene sets with distinct cellular and metabolic programs in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemporal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality.
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Yu Y, Guo G, Lv D, Hu Y, Li J, Li X, Yan Y. Transcriptome analysis during seed germination of elite Chinese bread wheat cultivar Jimai 20. BMC PLANT BIOLOGY 2014; 14:20. [PMID: 24410729 PMCID: PMC3923396 DOI: 10.1186/1471-2229-14-20] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 01/09/2014] [Indexed: 05/26/2023]
Abstract
BACKGROUND Wheat seed germination directly affects wheat yield and quality. Although transcriptome and proteome analyses during seed germination have been reported in some crop plant species, dynamic transcriptome characterization during wheat seed germination has not been conducted. We performed the first comprehensive dynamic transcriptome analysis during different seed germination stages of elite Chinese bread wheat cultivar Jimai 20 using the Affymetrix Wheat Genome Array. RESULTS A total of 61,703 probe sets representing 51,411 transcripts were identified during the five seed germination stages of Jimai 20, of which 2,825 differential expression probe sets corresponding to 2,646 transcripts with different functions were declared by ANOVA and a randomized variance model. The seed germination process included a rapid initial uptake phase (0-12 hours after imbibition [HAI]), a plateau phase (12-24 HAI), and a further water uptake phase (24-48 HAI), corresponding to switches from the degradation of small-molecule sucrose to the metabolism of three major nutrients and to photosynthesis. Hierarchical cluster and MapMan analyses revealed changes in several significant metabolism pathways during seed germination as well as related functional groups. The signal pathway networks constructed with KEGG showed three important genes encoding the phosphofructokinase family protein, with fructose-1, 6-bisphosphatase, and UTP-glucose-1-phosphate uridylyltransferase located at the center, indicating their pivotal roles in the glycolytic pathway, gluconeogenesis, and glycogenesis, respectively. Several significant pathways were selected to establish a metabolic pathway network according to their degree value, which allowed us to find the pathways vital to seed germination. Furthermore, 51 genes involved in transport, signaling pathway, development, lipid metabolism, defense response, nitrogen metabolism, and transcription regulation were analyzed by gene co-expression network with a k-core algorithm to determine which play pivotal roles in germination. Twenty-three meaningful genes were found, and quantitative RT-PCR analysis validated the expression patterns of 12 significant genes. CONCLUSIONS Wheat seed germination comprises three distinct phases and includes complicated regulation networks involving a large number of genes. These genes belong to many functional groups, and their co-regulations guarantee regular germination. Our results provide new insight into metabolic changes during seed germination and interactions between some significant genes.
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Affiliation(s)
- Yonglong Yu
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Guangfang Guo
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Dongwen Lv
- 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
| | - Xiaohui Li
- College of Life Science, Capital Normal University, Beijing 100048, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing 100048, China
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Burton RA, Fincher GB. Evolution and development of cell walls in cereal grains. FRONTIERS IN PLANT SCIENCE 2014; 5:456. [PMID: 25309555 PMCID: PMC4161051 DOI: 10.3389/fpls.2014.00456] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/23/2014] [Indexed: 05/20/2023]
Abstract
The composition of cell walls in cereal grains and other grass species differs markedly from walls in seeds of other plants. In the maternal tissues that surround the embryo and endosperm of the grain, walls contain higher levels of cellulose and in many cases are heavily lignified. This may be contrasted with walls of the endosperm, where the amount of cellulose is relatively low, and the walls are generally not lignified. The low cellulose and lignin contents are possible because the walls of the endosperm perform no load-bearing function in the mature grain and indeed the low levels of these relatively intractable wall components are necessary because they allow rapid degradation of the walls following germination of the grain. The major non-cellulosic components of endosperm walls are usually heteroxylans and (1,3;1,4)-β-glucans, with lower levels of xyloglucans, glucomannans, and pectic polysaccharides. Pectic polysaccharides and xyloglucans are the major non-cellulosic wall constituents in most dicot species, in which (1,3;1,4)-β-glucans are usually absent and heteroxylans are found at relatively low levels. Thus, the "core" non-cellulosic wall polysaccharides in grain of the cereals and other grasses are the heteroxylans and, more specifically, arabinoxylans. The (1,3;1,4)-β-glucans appear in the endosperm of some grass species but are essentially absent from others; they may constitute from zero to more than 45% of the cell walls of the endosperm, depending on the species. It is clear that in some cases these (1,3;1,4)-β-glucans function as a major store of metabolizable glucose in the grain. Cereal grains and their constituent cell wall polysaccharides are centrally important as a source of dietary fiber in human societies and breeders have started to select for high levels of non-cellulosic wall polysaccharides in grain. To meet end-user requirements, it is important that we understand cell wall biology in the grain both during development and following germination.
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Affiliation(s)
| | - Geoffrey B. Fincher
- *Correspondence: Geoffrey B. Fincher, Australian Research Council Centre of Excellence in Plant Cell Walls – School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia e-mail:
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Venglat P, Xiang D, Wang E, Datla R. Genomics of seed development: Challenges and opportunities for genetic improvement of seed traits in crop plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2013.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Affiliation(s)
- R. J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
- E-mail: Tel: +61 7 33460551; Fax: +61 7 33460555
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48
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Structural development of aleurone and its function in common wheat. Mol Biol Rep 2013; 40:6785-92. [DOI: 10.1007/s11033-013-2795-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 09/14/2013] [Indexed: 11/26/2022]
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Lillioja S, Neal AL, Tapsell L, Jacobs DR. Whole grains, type 2 diabetes, coronary heart disease, and hypertension: links to the aleurone preferred over indigestible fiber. Biofactors 2013; 39:242-58. [PMID: 23355358 PMCID: PMC3640698 DOI: 10.1002/biof.1077] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/26/2012] [Indexed: 12/13/2022]
Abstract
Higher whole grain cereal intakes are associated with substantially lower risks of type 2 diabetes, coronary heart disease, and hypertension. These reduced risks have been established in large prospective studies that now include millions of person-years of follow-up. We analyze the results of 11 major prospective studies to provide recommendations about whole grain consumption. The following review establishes the amount of whole grains that should ideally be consumed based on prospective evidence; defines the nature of whole grains; identifies that the whole grain evidence is robust and not due to confounding; and provides a detailed assessment of several potential mechanisms for the effect of whole grains on health. We draw the following conclusions. Firstly, to maintain health, 40 grams or more of whole grains should be consumed daily. This is about a bowl of whole grain breakfast cereal daily, but 80% of the population does not achieve this. Secondly, aleurone in bran is a critical grain component generally overlooked in favor of indigestible fiber. Live aleurone cells constitute 50% of millers' bran. They store minerals, protein, and the antioxidant ferulic acid, and are clearly more than just indigestible fiber. Finally, we suggest potential roles for magnesium, zinc, and ferulic acid in the development of chronic disease. If the results of prospective studies were applied to the life-style practices of modern societies there exists the potential for enormous personal health and public financial benefits.
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Affiliation(s)
- Stephen Lillioja
- Illawarra Health and Medical Research Institute, University of Wollongong, Northfields Avenue, NSW 2522, Australia.
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Widespread, abundant, and diverse TE-associated siRNAs in developing wheat grain. Gene 2013; 522:1-7. [PMID: 23562726 DOI: 10.1016/j.gene.2013.03.101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 01/06/2023]
Abstract
Small RNAs related to RNA interference are key molecules in many developmental processes, in which they can both regulate developmental gene expression and maintain the integrity of the genome and epigenome. In plants, short interfering RNAs (siRNAs) of 24 nt in length are an abundant type of small RNA associated with transposable elements (TEs), other repetitive sequences, and viral defense. One means by which TE-associated siRNAs affect genome integrity is by altering chromatin structure through a process called RNA-directed DNA methylation (RdDM). In this paper, we describe a comparative survey of siRNAs from wheat seedling leaves, seedling roots, young spikelets, and grains at 8 and 15 days after pollination (DAP). We find that the general patterns of siRNA distributions are similar across different TEs and within TEs of the same family regardless of tissue, but the relative abundance of 24-nt siRNAs is highest in developing grains. We also find that TEs that are transcriptionally active in endosperm are associated with the highest siRNA abundance not only in grains, but also in other tissues as well. These results suggest that RdDM is an important feature of developing wheat grain and are consistent with the hypothesis that TE expression in endosperm results in increased TE siRNAs, and that RdDM is a conserved feature of plant seed development.
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