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Thirulogachandar V, Govind G, Hensel G, Kale SM, Kuhlmann M, Eschen-Lippold L, Rutten T, Koppolu R, Rajaraman J, Palakolanu SR, Seiler C, Sakuma S, Jayakodi M, Lee J, Kumlehn J, Komatsuda T, Schnurbusch T, Sreenivasulu N. HOMEOBOX2, the paralog of SIX-ROWED SPIKE1/HOMEOBOX1, is dispensable for barley spikelet development. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2900-2916. [PMID: 38366171 DOI: 10.1093/jxb/erae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
The HD-ZIP class I transcription factor Homeobox 1 (HvHOX1), also known as Vulgare Row-type Spike 1 (VRS1) or Six-rowed Spike 1, regulates lateral spikelet fertility in barley (Hordeum vulgare L.). It was shown that HvHOX1 has a high expression only in lateral spikelets, while its paralog HvHOX2 was found to be expressed in different plant organs. Yet, the mechanistic functions of HvHOX1 and HvHOX2 during spikelet development are still fragmentary. Here, we show that compared with HvHOX1, HvHOX2 is more highly conserved across different barley genotypes and Hordeum species, hinting at a possibly vital but still unclarified biological role. Using bimolecular fluorescence complementation, DNA-binding, and transactivation assays, we validate that HvHOX1 and HvHOX2 are bona fide transcriptional activators that may potentially heterodimerize. Accordingly, both genes exhibit similar spatiotemporal expression patterns during spike development and growth, albeit their mRNA levels differ quantitatively. We show that HvHOX1 delays the lateral spikelet meristem differentiation and affects fertility by aborting the reproductive organs. Interestingly, the ancestral relationship of the two genes inferred from their co-expressed gene networks suggested that HvHOX1 and HvHOX2 might play a similar role during barley spikelet development. However, CRISPR-derived mutants of HvHOX1 and HvHOX2 demonstrated the suppressive role of HvHOX1 on lateral spikelets, while the loss of HvHOX2 does not influence spikelet development. Collectively, our study shows that through the suppression of reproductive organs, lateral spikelet fertility is regulated by HvHOX1, whereas HvHOX2 is dispensable for spikelet development in barley.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sandip M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
| | | | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Sudhakar Reddy Palakolanu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Christiane Seiler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Shun Sakuma
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120 Halle, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Plant Genome Research Unit, Tsukuba 3058602, Japan
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Stadt Seeland, Germany
- Research Group Abiotic Stress Genomics, Interdisciplinary Center for Crop Plant Research (IZN), Hoher Weg 8, 06120 Halle (Saale), Germany
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2
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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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3
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Hansson M, Youssef HM, Zakhrabekova S, Stuart D, Svensson JT, Dockter C, Stein N, Waugh R, Lundqvist U, Franckowiak J. A guide to barley mutants. Hereditas 2024; 161:11. [PMID: 38454479 PMCID: PMC10921644 DOI: 10.1186/s41065-023-00304-w] [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: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments. RESULTS Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. CONCLUSION Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.
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Affiliation(s)
- Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
| | - Helmy M Youssef
- Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle, 06120, Germany
| | | | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Jan T Svensson
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, E06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Urrbrae, 5064, Australia
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Jerome Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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4
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Fan C, Xu D, Wang C, Chen Z, Dou T, Qin D, Guo A, Zhao M, Pei H, Zhao M, Zhang R, Wang K, Zhang J, Ni Z, Guo G. Natural variations of HvSRN1 modulate the spike rachis node number in barley. PLANT COMMUNICATIONS 2024; 5:100670. [PMID: 37563835 PMCID: PMC10811343 DOI: 10.1016/j.xplc.2023.100670] [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: 02/17/2023] [Revised: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Grain number, one of the major determinants of yield in Triticeae crops, is largely determined by spikelet number and spike rachis node number (SRN). Here, we identified three quantitative trait loci (QTLs) for SRN using 145 recombinant inbred lines derived from a barley R90/1815D cross. qSRN1, the major-effect QTL, was mapped to chromosome 2H and explained up to 38.77% of SRN variation. Map-based cloning revealed that qSRN1 encodes the RAWUL domain-containing protein HvSRN1. Further analysis revealed that two key SNPs in the HvSRN1 promoter region (∼2 kb upstream of the transcription start site) affect the transcript level of HvSRN1 and contribute to variation in SRN. Similar to its orthologous proteins OsLAX2 and ZmBA2, HvSRN1 showed protein-protein interactions with HvLAX1, suggesting that the LAX2-LAX1 model for spike morphology regulation may be conserved in Poaceae crops. CRISPR-Cas9-induced HvSRN1 mutants showed reduced SRN but increased grain size and weight, demonstrating a trade-off effect. Our results shed light on the role of HvSRN1 variation in regulating the balance between grain number and weight in barley.
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Affiliation(s)
- Chaofeng Fan
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Dongdong Xu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhaoyan Chen
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Tingyu Dou
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Dandan Qin
- Key Laboratory for Crop Molecular Breeding of Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Aikui Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Meng Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Honghong Pei
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Mengwei Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Renxu Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Ke Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China.
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5
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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6
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Zhang Z, Zhao P, Wang X, Wang H, Zhai Z, Zhao X, Xing L, Qi Z, Shang Y. Identification and map-based cloning of long glume mutant gene lgm1 in barley. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:3. [PMID: 38222975 PMCID: PMC10786806 DOI: 10.1007/s11032-024-01448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/03/2024] [Indexed: 01/16/2024]
Abstract
The spikes of gramineous plants are composed of specialized units called spikelets. Two bracts at the spikelet bases are known as glumes. The spikelet glumes in barley are degenerated into threadlike structures. Here, we report a long glume mutant, lgm1, similar in appearance to a lemma with a long awn at the apex. Map-based cloning showed that the mutant lgm1 allele has an approximate 1.27 Mb deletion of in chromosome 2H. The deleted segment contains five putative high-confidence genes, among which HORVU.MOREX.r3.2HG0170820 encodes a C2H2 zinc finger protein, an ortholog of rice NSG1/LRG1 and an important candidate for the Lgm1 allele. Line GA01 with a long glume and short awn was obtained in progenies of crosses involving the lgm1 mutant. Interestingly, lsg1, a mutant with long glumes on lateral spikelets, was obtained in the progenies of the lgm1 mutant. The long glume variant increased the weight of kernels in the lateral spikelets and increased kernel uniformity across the entire spike, greatly improving the potential of six-rowed barley for malting. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01448-x.
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Affiliation(s)
- Zhenlan Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Pengtao Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xiaoyun Wang
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004 Jiangxi China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 Jiangsu China
| | - Zhouping Zhai
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Xiaoguang Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 Jiangsu China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 Jiangsu China
| | - Yi Shang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100 Shaanxi China
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7
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Liu Y, Chen J, Yin C, Wang Z, Wu H, Shen K, Zhang Z, Kang L, Xu S, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Gong Y, Yu X, Sun Z, Ye B, Liu D, Zhang L, Shen L, Hao Y, Ma Y, Lu F, Guo Z. A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biol 2023; 24:196. [PMID: 37641093 PMCID: PMC10463835 DOI: 10.1186/s13059-023-03044-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Lipeng Kang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Song Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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8
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Rozanova IV, Grigoriev YN, Efimov VM, Igoshin AV, Khlestkina EK. Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley. Biomolecules 2023; 13:909. [PMID: 37371489 DOI: 10.3390/biom13060909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.
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Affiliation(s)
- Irina V Rozanova
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Yuriy N Grigoriev
- Siberian Research Institute of Plant Cultivation and Breeding-Branch of Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Krasnoobsk, 630501 Novosibirsk, Russia
| | - Vadim M Efimov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Alexander V Igoshin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Elena K Khlestkina
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
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9
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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. FRONTIERS IN PLANT SCIENCE 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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10
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Hong Y, Zhang M, Xu R. Genetic Localization and Homologous Genes Mining for Barley Grain Size. Int J Mol Sci 2023; 24:ijms24054932. [PMID: 36902360 PMCID: PMC10003025 DOI: 10.3390/ijms24054932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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11
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Sakuma S, Koppolu R. Form follows function in Triticeae inflorescences. BREEDING SCIENCE 2023; 73:46-56. [PMID: 37168815 PMCID: PMC10165339 DOI: 10.1270/jsbbs.22085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/21/2022] [Indexed: 05/13/2023]
Abstract
Grass inflorescences produce grains, which are directly connected to our food. In grass crops, yields are mainly affected by grain number and weight; thus, understanding inflorescence shape is crucially important for cereal crop breeding. In the last two decades, several key genes controlling inflorescence shape have been elucidated, thanks to the availability of rich genetic resources and powerful genomics tools. In this review, we focus on the inflorescence architecture of Triticeae species, including the major cereal crops wheat and barley. We summarize recent advances in our understanding of the genetic basis of spike branching, and spikelet and floret development in the Triticeae. Considering our changing climate and its impacts on cereal crop yields, we also discuss the future orientation of research.
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Affiliation(s)
- Shun Sakuma
- Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
- Corresponding authors (e-mail: and )
| | - Ravi Koppolu
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
- Corresponding authors (e-mail: and )
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12
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de Souza Moraes T, van Es SW, Hernández-Pinzón I, Kirschner GK, van der Wal F, da Silveira SR, Busscher-Lange J, Angenent GC, Moscou M, Immink RGH, van Esse GW. The TCP transcription factor HvTB2 heterodimerizes with VRS5 and controls spike architecture in barley. PLANT REPRODUCTION 2022; 35:205-220. [PMID: 35254529 PMCID: PMC9352630 DOI: 10.1007/s00497-022-00441-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Understanding the molecular network, including protein-protein interactions, of VRS5 provide new routes towards the identification of other key regulators of plant architecture in barley. The TCP transcriptional regulator TEOSINTE BRANCHED 1 (TB1) is a key regulator of plant architecture. In barley, an important cereal crop, HvTB1 (also referred to as VULGARE SIX-ROWED spike (VRS) 5), inhibits the outgrowth of side shoots, or tillers, and grains. Despite its key role in barley development, there is limited knowledge on the molecular network that is utilized by VRS5. In this work, we performed protein-protein interaction studies of VRS5. Our analysis shows that VRS5 potentially interacts with a diverse set of proteins, including other class II TCP's, NF-Y TF, but also chromatin remodelers. Zooming in on the interaction capacity of VRS5 with other TCP TFs shows that VRS5 preferably interacts with other class II TCP TFs in the TB1 clade. Induced mutagenesis through CRISPR-Cas of one of the putative VRS5 interactors, HvTB2 (also referred to as COMPOSITUM 1 and BRANCHED AND INDETERMINATE SPIKELET 1), resulted in plants that have lost their characteristic unbranched spike architecture. More specifically, hvtb2 mutants exhibited branches arising at the main spike, suggesting that HvTB2 acts as inhibitor of branching. Our protein-protein interaction studies of VRS5 resulted in the identification of HvTB2 as putative interactor of VRS5, another key regulator of spike architecture in barley. The study presented here provides a first step to underpin the protein-protein interactome of VRS5 and to identify other, yet unknown, key regulators of barley plant architecture.
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Affiliation(s)
- Tatiana de Souza Moraes
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratório de Biotecnologia Vegetal, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, CEP 13416-000, Brazil
| | - Sam W van Es
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | | | - Gwendolyn K Kirschner
- Institute of Crop Functional Genomics, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Froukje van der Wal
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Sylvia Rodrigues da Silveira
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratório de Biotecnologia Vegetal, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, CEP 13416-000, Brazil
| | - Jacqueline Busscher-Lange
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Gerco C Angenent
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Matthew Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Richard G H Immink
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
| | - G Wilma van Esse
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
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13
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Jiang C, Lei M, Guo Y, Gao G, Shi L, Jin Y, Cai Y, Himmelbach A, Zhou S, He Q, Yao X, Kan J, Haberer G, Duan F, Li L, Liu J, Zhang J, Spannagl M, Liu C, Stein N, Feng Z, Mascher M, Yang P. A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley. PLANT COMMUNICATIONS 2022; 3:100317. [PMID: 35605197 PMCID: PMC9284286 DOI: 10.1016/j.xplc.2022.100317] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/13/2022] [Accepted: 03/11/2022] [Indexed: 05/26/2023]
Abstract
Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525 M3 lines in the barley landrace "Hatiexi" (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miaomiao Lei
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Guangqi Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yanlong Jin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Cai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China; College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuefeng Yao
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jinhong Kan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Georg Haberer
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fengying Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manuel Spannagl
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chunming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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14
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Zhong J, Kong F. The control of compound inflorescences: insights from grasses and legumes. TRENDS IN PLANT SCIENCE 2022; 27:564-576. [PMID: 34973922 DOI: 10.1016/j.tplants.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/16/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
A major challenge in biology is to understand how organisms have increased developmental complexity during evolution. Inflorescences, with remarkable variation in branching systems, are a fitting model to understand architectural complexity. Inflorescences bear flowers that may become fruits and/or seeds, impacting crop productivity and species fitness. Great advances have been achieved in understanding the regulation of complex inflorescences, particularly in economically and ecologically important grasses and legumes. Surprisingly, a synthesis is still lacking regarding the common or distinct principles underlying the regulation of inflorescence complexity. Here, we synthesize the similarities and differences in the regulation of compound inflorescences in grasses and legumes, and propose that the emergence of novel higher-order repetitive modules is key to the evolution of inflorescence complexity.
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Affiliation(s)
- Jinshun Zhong
- School of Life Sciences, South China Agricultural University, Wushan Street 483, Guangzhou 510642, China; Institute for Plant Genetics, Heinrich-Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany; Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany; Cluster of Excellence on Plant Sciences, 'SMART Plants for Tomorrow's Needs', Heinrich-Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany.
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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15
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Koppolu R, Jiang G, Milner SG, Muqaddasi QH, Rutten T, Himmelbach A, Guo Y, Stein N, Mascher M, Schnurbusch T. The barley mutant multiflorus2.b reveals quantitative genetic variation for new spikelet architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:571-590. [PMID: 34773464 PMCID: PMC8866347 DOI: 10.1007/s00122-021-03986-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/26/2021] [Indexed: 05/26/2023]
Abstract
Spikelet indeterminacy and supernumerary spikelet phenotypes in barley multiflorus2.b mutant show polygenic inheritance. Genetic analysis of multiflorus2.b revealed major QTLs for spikelet determinacy and supernumerary spikelet phenotypes on 2H and 6H chromosomes. Understanding the genetic basis of yield forming factors in small grain cereals is of extreme importance, especially in the wake of stagnation of further yield gains in these crops. One such yield forming factor in these cereals is the number of grain-bearing florets produced per spikelet. Wild-type barley (Hordeum vulgare L.) spikelets are determinate structures, and the spikelet axis (rachilla) degenerates after producing single floret. In contrast, the rachilla of wheat (Triticum ssp.) spikelets, which are indeterminate, elongates to produce up to 12 florets. In our study, we characterized the barley spikelet determinacy mutant multiflorus2.b (mul2.b) that produced up to three fertile florets on elongated rachillae of lateral spikelets. Apart from the lateral spikelet indeterminacy (LS-IN), we also characterized the supernumerary spikelet phenotype in the central spikelets (CS-SS) of mul2.b. Through our phenotypic and genetic analyses, we identified two major QTLs on chromosomes 2H and 6H, and two minor QTLs on 3H for the LS-IN phenotype. For, the CS-SS phenotype, we identified one major QTL on 6H, and a minor QTL on 5H chromosomes. Notably, the 6H QTLs for CS-SS and LS-IN phenotypes co-located with each other, potentially indicating that a single genetic factor might regulate both phenotypes. Thus, our in-depth phenotyping combined with genetic analyses revealed the quantitative nature of the LS-IN and CS-SS phenotypes in mul2.b, paving the way for cloning the genes underlying these QTLs in the future.
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Affiliation(s)
- Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany.
| | - Guojing Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Sara G Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
- BASF Agricultural Solutions GmbH, Am Schwabeplan 8, OT Gatersleben, 06466, Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
- Department of Crop Sciences, Center of Integrated Breeding Research (CiBreed), Georg-August-University, 37075, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany.
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.
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16
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Sayed MA, Allam M, Heck QK, Urbanavičiūtė I, Rutten T, Stuart D, Zakhrabekova S, Börner A, Pillen K, Hansson M, Youssef HM. Analyses of MADS-box Genes Suggest HvMADS56 to Regulate Lateral Spikelet Development in Barley. PLANTS (BASEL, SWITZERLAND) 2021; 10:2825. [PMID: 34961296 PMCID: PMC8703372 DOI: 10.3390/plants10122825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022]
Abstract
MADS-box transcription factors are crucial regulators of inflorescence and flower development in plants. Therefore, the recent interest in this family has received much attention in plant breeding programs due to their impact on plant development and inflorescence architecture. The aim of this study was to investigate the role of HvMADS-box genes in lateral spikelet development in barley (Hordeum vulgare L.). A set of 30 spike-contrasting barley lines were phenotypically and genotypically investigated under controlled conditions. We detected clear variations in the spike and spikelet development during the developmental stages among the tested lines. The lateral florets in the deficiens and semi-deficiens lines were more reduced than in two-rowed cultivars except cv. Kristina. Interestingly, cv. Kristina, int-h.43 and int-i.39 exhibited the same behavior as def.5, def.6, semi-def.1, semi-def.8 regarding development and showed reduced lateral florets size. In HOR1555, HOR7191 and HOR7041, the lateral florets continued their development, eventually setting seeds. In contrast, lateral florets in two-rowed barley stopped differentiating after the awn primordia stage giving rise to lateral floret sterility. At harvest, the lines tested showed large variation for all central and lateral spikelet-related traits. Phylogenetic analysis showed that more than half of the 108 MADS-box genes identified are highly conserved and are expressed in different barley tissues. Re-sequence analysis of a subset of these genes showed clear polymorphism in either SNPs or in/del. Variation in HvMADS56 correlated with altered lateral spikelet morphology. This suggests that HvMADS56 plays an important role in lateral spikelet development in barley.
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Affiliation(s)
- Mohammed A. Sayed
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.S.); (T.R.); (A.B.)
- Faculty of Agriculture, Assuit University, Assuit 71526, Egypt;
| | - Mohamed Allam
- Faculty of Agriculture, Assuit University, Assuit 71526, Egypt;
- Department of Agricultural and Forest Sciences, Tuscia University, Via S. C. de Lellis, snc, 01100 Viterbo, Italy;
| | - Quinn Kalby Heck
- Department of Biology, Lund University, Sölvegatan 35B, 22362 Lund, Sweden; (Q.K.H.); (D.S.); (S.Z.); (M.H.)
| | - Ieva Urbanavičiūtė
- Department of Agricultural and Forest Sciences, Tuscia University, Via S. C. de Lellis, snc, 01100 Viterbo, Italy;
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.S.); (T.R.); (A.B.)
| | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35B, 22362 Lund, Sweden; (Q.K.H.); (D.S.); (S.Z.); (M.H.)
| | - Shakhira Zakhrabekova
- Department of Biology, Lund University, Sölvegatan 35B, 22362 Lund, Sweden; (Q.K.H.); (D.S.); (S.Z.); (M.H.)
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.S.); (T.R.); (A.B.)
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35B, 22362 Lund, Sweden; (Q.K.H.); (D.S.); (S.Z.); (M.H.)
| | - Helmy M. Youssef
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany;
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt
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17
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Thirulogachandar V, Koppolu R, Schnurbusch T. Strategies of grain number determination differentiate barley row types. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7754-7768. [PMID: 34460900 DOI: 10.1093/jxb/erab395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Gaining knowledge on fundamental interactions of various yield components is crucial to improve yield potential in small grain cereals. It is well known in barley that increasing grain number greatly improves yield potential; however, the yield components determining grain number and their association in barley row types are less explored. In this study, we assessed different yield components such as potential spikelet number (PSN), spikelet survival (SSL), spikelet number (SN), grain set (GS), and grain survival (GSL), as well as their interactions with grain number by using a selected panel of two- and six-rowed barley types. Also, to analyze the stability of these interactions, we performed the study in the greenhouse and the field. From this study, we found that in two-rowed barley, grain number determination is strongly influenced by PSN rather than SSL and/or GS in both growth conditions. Conversely, in six-rowed barley, grain number is associated with SSL instead of PSN and/or GS. Thus, our study showed that increasing grain number might be possible by augmenting PSN in two-rowed genotypes, while for six-rowed genotypes SSL needs to be improved. We speculate that this disparity of grain number determination in barley row types might be due to the fertility of lateral spikelets. Collectively, this study revealed that grain number in two-rowed barley largely depends on the developmental trait, PSN, while in six-rowed barley, it mainly follows the ability for SSL.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben,Germany
| | - Ravi Koppolu
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben,Germany
| | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben,Germany
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle,Germany
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18
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Huang B, Wu W, Hong Z. Genetic Loci Underlying Awn Morphology in Barley. Genes (Basel) 2021; 12:genes12101613. [PMID: 34681007 PMCID: PMC8535194 DOI: 10.3390/genes12101613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 10/09/2021] [Indexed: 11/28/2022] Open
Abstract
Barley awns are highly active in photosynthesis and account for 30–50% of grain weight in barley. They are diverse in length, ranging from long to awnless, and in shape from straight to hooded or crooked. Their diversity and importance have intrigued geneticists for several decades. A large collection of awnness mutants are available—over a dozen of them have been mapped on chromosomes and a few recently cloned. Different awnness genes interact with each other to produce diverse awn phenotypes. With the availability of the sequenced barley genome and application of new mapping and gene cloning strategies, it will now be possible to identify and clone more awnness genes. A better understanding of the genetic basis of awn diversity will greatly facilitate development of new barley cultivars with improved yield, adaptability and sustainability.
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Affiliation(s)
- Biguang Huang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Collegiate Key Laboratory of Applied Plant Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Weiren Wu
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Z.H.)
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
- Correspondence: (W.W.); (Z.H.)
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19
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Wang JH, Xu ZM, Qiu XB, Li LL, Yu SY, Li T, Tang YY, Pu X, Zhang JY, Zhang HL, Liang JJ, Tang YW, Li W, Long H, Deng GB. Genetic and molecular characterization of determinant of six-rowed spike of barley carrying vrs1.a4. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3225-3236. [PMID: 34132847 DOI: 10.1007/s00122-021-03887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Decisive role of reduced vrs1 transcript abundance in six-rowed spike of barley carrying vrs1.a4 was genetically proved and its potential causes were preliminarily analyzed. Six-rowed spike 1 (vrs1) is the major determinant of the six-rowed spike phenotype of barley (Hordeum vulgare L.). Alleles of Vrs1 have been extensively investigated. Allele vrs1.a4 in six-rowed barley is unique in that it has the same coding sequence as Vrs1.b4 in two-rowed barley. The determinant of row-type in vrs1.a4 carriers has not been experimentally identified. Here, we identified Vrs1.b4 in two-rowed accessions and vrs1.a4 in six-rowed accessions from the Qinghai-Tibet Plateau at high frequency. Genetic analyses revealed a single nuclear gene accounting for row-type alteration in these accessions. Physical mapping identified a 0.08-cM (~ 554-kb) target interval on chromosome 2H, wherein Vrs1 was the most likely candidate gene. Further analysis of Vrs1 expression in offspring of the mapping populations or different Vrs1.b4 and vrs1.a4 lines confirmed that downregulated expression of vrs1.a4 causes six-rowed spike. Regulatory sequence analysis found a single 'TA' dinucleotide deletion in vrs1.a4 carriers within a 'TA' tandem-repeat-enriched region ~ 1 kb upstream of the coding region. DNA methylation levels did not correspond to the expression difference and therefore did not affect Vrs1 expression. More evidence is needed to verify the causal link between the 'TA' deletion and the downregulated Vrs1 expression and hence the six-rowed spike phenotype.
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Affiliation(s)
- Jin-Hui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
- Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhen-Mei Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Xue-Bing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Li-Lan Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Shui-Yang Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Yan-Yan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Juan-Yu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Hai-Li Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Jun-Jun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Ya-Wei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, Tibet, China
| | - Wei Li
- Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
| | - Guang-Bing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
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20
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Liu L, Lindsay PL, Jackson D. Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing. Int J Mol Sci 2021; 22:5167. [PMID: 34068350 PMCID: PMC8153303 DOI: 10.3390/ijms22105167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
Artificial domestication and improvement of the majority of crops began approximately 10,000 years ago, in different parts of the world, to achieve high productivity, good quality, and widespread adaptability. It was initiated from a phenotype-based selection by local farmers and developed to current biotechnology-based breeding to feed over 7 billion people. For most cereal crops, yield relates to grain production, which could be enhanced by increasing grain number and weight. Grain number is typically determined during inflorescence development. Many mutants and genes for inflorescence development have already been characterized in cereal crops. Therefore, optimization of such genes could fine-tune yield-related traits, such as grain number. With the rapidly advancing genome-editing technologies and understanding of yield-related traits, knowledge-driven breeding by design is becoming a reality. This review introduces knowledge about inflorescence yield-related traits in cereal crops, focusing on rice, maize, and wheat. Next, emerging genome-editing technologies and recent studies that apply this technology to engineer crop yield improvement by targeting inflorescence development are reviewed. These approaches promise to usher in a new era of breeding practice.
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Affiliation(s)
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (L.L.); (P.L.L.)
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21
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Thiel J, Koppolu R, Trautewig C, Hertig C, Kale SM, Erbe S, Mascher M, Himmelbach A, Rutten T, Esteban E, Pasha A, Kumlehn J, Provart NJ, Vanderauwera S, Frohberg C, Schnurbusch T. Transcriptional landscapes of floral meristems in barley. SCIENCE ADVANCES 2021; 7:eabf0832. [PMID: 33910893 PMCID: PMC8081368 DOI: 10.1126/sciadv.abf0832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/26/2021] [Indexed: 05/02/2023]
Abstract
Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.
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Affiliation(s)
- J Thiel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - R Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - C Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - C Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S Erbe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - M Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - A Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - T Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - E Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - A Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - J Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - N J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - S Vanderauwera
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - C Frohberg
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - T Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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22
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Levin KA, Boden SA. A new branch of understanding for barley inflorescence development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6869-6871. [PMID: 33382898 PMCID: PMC7774524 DOI: 10.1093/jxb/eraa464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
This article comments on: Shang Y, Yuan L, Di Y, Jia Y, Zhang Z, Li S, Xing L, Qi Z, Wang X, Zhu J, Hua W, Wu X, Zhu M, Li G, Li C. 2020. A CYC/TB1 type TCP transcription factor controls spikelet meristem identity in barley. Journal of Experimental Botany 71, 7118–7131.
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Affiliation(s)
- Kara A Levin
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, Australia
| | - Scott A Boden
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, Australia
- The John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, UK
- Correspondence:
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23
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Shang Y, Yuan L, Di Z, Jia Y, Zhang Z, Li S, Xing L, Qi Z, Wang X, Zhu J, Hua W, Wu X, Zhu M, Li G, Li C. A CYC/TB1-type TCP transcription factor controls spikelet meristem identity in barley. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7118-7131. [PMID: 32915968 DOI: 10.1093/jxb/eraa416] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/09/2020] [Indexed: 05/08/2023]
Abstract
Barley possesses a branchless, spike-shaped inflorescence where determinate spikelets attach directly to the main axis, but the developmental mechanism of spikelet identity remains largely unknown. Here we report the functional analysis of the barley gene BRANCHED AND INDETERMINATE SPIKELET 1 (BDI1), which encodes a TCP transcription factor and plays a crucial role in determining barley inflorescence architecture and spikelet development. The bdi1 mutant exhibited indeterminate spikelet meristems that continued to grow and differentiate after producing a floret meristem; some spikelet meristems at the base of the spike formed two fully developed seeds or converted to branched spikelets, producing a branched inflorescence. Map-based cloning analysis showed that this mutant has a deletion of ~600 kb on chromosome 5H containing three putative genes. Expression analysis and virus-induced gene silencing confirmed that the causative gene, BDI1, encodes a CYC/TB1-type TCP transcription factor and is highly conserved in both wild and cultivated barley. Transcriptome and regulatory network analysis demonstrated that BDI1 may integrate regulation of gene transcription cell wall modification and known trehalose-6-phosphate homeostasis to control spikelet development. Together, our findings reveal that BDI1 represents a key regulator of inflorescence architecture and meristem determinacy in cereal crop plants.
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Affiliation(s)
- Yi Shang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Lu Yuan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Zhaocan Di
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Yong Jia
- Western Barley Genetics Alliance, Murdoch University, Murdoch WA, Australia
| | - Zhenlan Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Xiaoyun Wang
- Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Wei Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Xiaojian Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Minqiu Zhu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/ JCIC-MCP, Nanjing, Jiangsu, China
| | - Gang Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- School of Agriculture, Food, and Wine, University of Adelaide, Waite campus, Urrbrae, South Australia, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, China
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24
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Youssef HM, Allam M, Boussora F, Himmelbach A, Milner SG, Mascher M, Schnurbusch T. Dissecting the Genetic Basis of Lateral and Central Spikelet Development and Grain Traits in Intermedium-Spike Barley ( Hordeum vulgare Convar. Intermedium). PLANTS 2020; 9:plants9121655. [PMID: 33256118 PMCID: PMC7760360 DOI: 10.3390/plants9121655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022]
Abstract
Barley (Hordeum vulgare L.) is one of the major grain crops worldwide and considered as a model plant for temperate cereals. One of the barley row-type groups, named intermedium-barley, was used in our previous study where we reported that other genetic loci rather than vrs1 and Int-c could play a role in lateral spikelet development and even in setting grains. To continue this work, we used phenotypic and genotypic data of 254 intermedium-spike barley accessions aimed at dissecting the genetic basis of development and grain traits of lateral and central spikelet using genome wide association (GWAS) analysis. After genotypic data filtering, 8,653 single-nucleotide polymorphism (SNPs) were used for GWAS analysis. A total of 169 significant associations were identified and we focused only on the subset of associations that exceeded the p < 10−4 threshold. Thirty-three highly significant marker-trait-associations (MTAs), represented in 28 different SNPs on all seven chromosomes for the central and/or lateral spikelet traits; such as kernel length, width, area, weight, unfilled spikelet and 1000-kernel weight, were detected. Highly significant associated markers were anchored physically using barley genome sequencing to identify candidate genes to either contain the SNPs or the closest gene to the SNP position. The results showed that 12 MTAs were specific for lateral spikelet traits, nine MTAs were specific for central spikelet traits and seven MTAs for both central and lateral traits. All together, the GWAS and candidate gene results support our hypothesis that lateral spikelet development could be regulated by loci different from those regulating central spikelet development.
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Affiliation(s)
- Helmy M. Youssef
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- Correspondence: (H.M.Y.); (T.S.); Tel.: 49-3455522683 (H.M.Y.)
| | - Mohamed Allam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Faculty of Agriculture, Assuit University, Assuit 71526, Egypt
| | - Faiza Boussora
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Institute of Arid Lands of Medenine, Route du Djorf km 22.5, Médénine 4100, Tunisia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
| | - Sara G. Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany; (M.A.); (F.B.); (A.H.); (S.G.M.); (M.M.)
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- Correspondence: (H.M.Y.); (T.S.); Tel.: 49-3455522683 (H.M.Y.)
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Pecinka A, Chevalier C, Colas I, Kalantidis K, Varotto S, Krugman T, Michailidis C, Vallés MP, Muñoz A, Pradillo M. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5205-5222. [PMID: 31626285 DOI: 10.1093/jxb/erz457] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.
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Affiliation(s)
- Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of the Region Haná for Agricultural and Biotechnological Research, Olomouc, Czech Republic
| | | | - Isabelle Colas
- James Hutton Institute, Cell and Molecular Science, Pr Waugh's Lab, Invergowrie, Dundee, UK
| | - Kriton Kalantidis
- Department of Biology, University of Crete, and Institute of Molecular Biology Biotechnology, FoRTH, Heraklion, Greece
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment (DAFNAE) University of Padova, Agripolis viale dell'Università, Legnaro (PD), Italy
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Christos Michailidis
- Institute of Experimental Botany, Czech Acad Sci, Praha 6 - Lysolaje, Czech Republic
| | - María-Pilar Vallés
- Department of Genetics and Plant Breeding, Estación Experimental Aula Dei (EEAD), Spanish National Research Council (CSIC), Zaragoza, Spain
| | - Aitor Muñoz
- Department of Plant Molecular Genetics, National Center of Biotechnology/Superior Council of Scientific Research, Autónoma University of Madrid, Madrid, Spain
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
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Walla A, Wilma van Esse G, Kirschner GK, Guo G, Brünje A, Finkemeier I, Simon R, von Korff M. An Acyl-CoA N-Acyltransferase Regulates Meristem Phase Change and Plant Architecture in Barley. PLANT PHYSIOLOGY 2020; 183:1088-1109. [PMID: 32376761 PMCID: PMC7333700 DOI: 10.1104/pp.20.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/19/2020] [Indexed: 05/04/2023]
Abstract
The modification of shoot architecture and increased investment into reproductive structures is key for crop improvement and is achieved through coordinated changes in the development and determinacy of different shoot meristems. A fundamental question is how the development of different shoot meristems is genetically coordinated to optimize the balance between vegetative and reproductive organs. Here we identify the MANY NODED DWARF1 (HvMND1) gene as a major regulator of plant architecture in barley (Hordeum vulgare). The mnd1.a mutant displayed an extended vegetative program with increased phytomer, leaf, and tiller production but a reduction in the number and size of grains. The induction of vegetative structures continued even after the transition to reproductive growth, resulting in a marked increase in longevity. Using mapping by RNA sequencing, we found that the HvMND1 gene encodes an acyl-CoA N-acyltransferase that is predominately expressed in developing axillary meristems and young inflorescences. Exploration of the expression network modulated by HvMND1 revealed differential expression of the developmental microRNAs miR156 and miR172 and several key cell cycle and developmental genes. Our data suggest that HvMND1 plays a significant role in the coordinated regulation of reproductive phase transitions, thereby promoting reproductive growth and whole plant senescence in barley.
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Affiliation(s)
- Agatha Walla
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
| | - G Wilma van Esse
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Laboratory for Molecular Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Gwendolyn K Kirschner
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Annika Brünje
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48149 Münster, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs", 40225 Düsseldorf, Germany
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Natural Genetic Variation Underlying Tiller Development in Barley ( Hordeum vulgare L). G3-GENES GENOMES GENETICS 2020; 10:1197-1212. [PMID: 31996357 PMCID: PMC7144072 DOI: 10.1534/g3.119.400612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In barley (Hordeum vulgare L.), lateral branches called tillers contribute to grain yield and define shoot architecture, but genetic control of tiller number and developmental rate are not well characterized. The primary objectives of this work were to examine relationships between tiller number and other agronomic and morphological traits and identify natural genetic variation associated with tiller number and rate, and related traits. We grew 768 lines from the USDA National Small Grain Collection in the field and collected data over two years for tiller number and rate, and agronomic and morphological traits. Our results confirmed that spike row-type and days to heading are correlated with tiller number, and as much as 28% of tiller number variance was associated with these traits. In addition, negative correlations between tiller number and leaf width and stem diameter were observed, indicating trade-offs between tiller development and other vegetative growth. Thirty-three quantitative trait loci (QTL) were associated with tiller number or rate. Of these, 40% overlapped QTL associated with days to heading and 22% overlapped QTL associated with spike row-type, further supporting that tiller development is associated with these traits. Some QTL associated with tiller number or rate, including the major QTL on chromosome 3H, were not associated with other traits, suggesting that some QTL may be directly related to rate of tiller development or axillary bud number. These results enhance our knowledge of the genetic control of tiller development in barley, which is important for optimizing tiller number and rate for yield improvement.
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Sakuma S, Schnurbusch T. Of floral fortune: tinkering with the grain yield potential of cereal crops. THE NEW PHYTOLOGIST 2020; 225:1873-1882. [PMID: 31509613 DOI: 10.1111/nph.16189] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/28/2019] [Indexed: 05/19/2023]
Abstract
Enhancing the yield potential and stability of small-grain cereals, such as wheat (Triticum sp.), rice (Oryza sativa), and barley (Hordeum vulgare), is a priority for global food security. Over the last several decades, plant breeders have increased grain yield mainly by increasing the number of grains produced in each inflorescence. This trait is determined by the number of spikelets per spike and the number of fertile florets per spikelet. Recent genetic and genomic advances in cereal grass species have identified the molecular determinants of grain number and facilitated the exchange of information across genera. In this review, we focus on the genetic basis of inflorescence architecture in Triticeae crops, highlighting recent insights that have helped to improve grain yield by, for example, reducing the preprogrammed abortion of floral organs. The accumulating information on inflorescence development can be harnessed to enhance grain yield by comparative trait reconstruction and rational design to boost the yield potential of grain crops.
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Affiliation(s)
- Shun Sakuma
- Faculty of Agriculture, Tottori University, Tottori, 680-8553, Japan
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
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29
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Liu H, Li G, Yang X, Kuijer HN, Liang W, Zhang D. Transcriptome profiling reveals phase-specific gene expression in the developing barley inflorescence. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bi X, van Esse W, Mulki MA, Kirschner G, Zhong J, Simon R, von Korff M. CENTRORADIALIS Interacts with FLOWERING LOCUS T-Like Genes to Control Floret Development and Grain Number. PLANT PHYSIOLOGY 2019; 180:1013-1030. [PMID: 31004004 PMCID: PMC6548242 DOI: 10.1104/pp.18.01454] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/08/2019] [Indexed: 05/20/2023]
Abstract
CENTRORADIALIS (CEN) is a key regulator of flowering time and inflorescence architecture in plants. Natural variation in the barley (Hordeum vulgare) homolog HvCEN is important for agricultural range expansion of barley cultivation, but its effects on shoot and spike architecture and consequently yield have not yet been characterized. Here, we evaluated 23 independent hvcen, also termed mat-c, mutants to determine the pleiotropic effects of HvCEN on developmental timing and shoot and spike morphologies of barley under outdoor and controlled conditions. All hvcen mutants flowered early and showed a reduction in spikelet number per spike, tiller number, and yield in the outdoor experiments. Mutations in hvcen accelerated spikelet initiation and reduced axillary bud number in a photoperiod-independent manner but promoted floret development only under long days (LDs). The analysis of a flowering locus t3 (hvft3) hvcen double mutant showed that HvCEN interacts with HvFT3 to control spikelet initiation. Furthermore, early flowering3 (hvelf3) hvcen double mutants with high HvFT1 expression levels under short days suggested that HvCEN interacts with HvFT1 to repress floral development. Global transcriptome profiling in developing shoot apices and inflorescences of mutant and wild-type plants revealed that HvCEN controlled transcripts involved in chromatin remodeling activities, cytokinin and cell cycle regulation and cellular respiration under LDs and short days, whereas HvCEN affected floral homeotic genes only under LDs. Understanding the stage and organ-specific functions of HvCEN and downstream molecular networks will allow the manipulation of different shoot and spike traits and thereby yield.
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Affiliation(s)
- Xiaojing Bi
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Wilma van Esse
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mohamed Aman Mulki
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Gwendolyn Kirschner
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Jinshun Zhong
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
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Abdel-Ghani AH, Sharma R, Wabila C, Dhanagond S, Owais SJ, Duwayri MA, Al-Dalain SA, Klukas C, Chen D, Lübberstedt T, von Wirén N, Graner A, Kilian B, Neumann K. Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage. BMC PLANT BIOLOGY 2019; 19:216. [PMID: 31122195 PMCID: PMC6533710 DOI: 10.1186/s12870-019-1828-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits. RESULTS A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate. CONCLUSIONS This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.
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Affiliation(s)
- Adel H. Abdel-Ghani
- Department of Plant Production, Faculty of Agriculture, Mutah University, Mutah, Karak, 61710 Jordan
| | - Rajiv Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Division of Plant Science, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA UK
| | - Celestine Wabila
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
| | - Sidram Dhanagond
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
| | - Saed J. Owais
- Department of Plant Production, Faculty of Agriculture, Mutah University, Mutah, Karak, 61710 Jordan
| | - Mahmud A. Duwayri
- Department of Horticulture and Agronomy, Faculty of Agriculture, University of Jordan, Amman, Jordan
| | - Saddam A. Al-Dalain
- Al-Shoubak University College, Al-Balqa’ Applied University, Al-, Salt, 19117 Jordan
| | - Christian Klukas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Digitalization in Research & Development (ROM), BASF SE, 67056 Ludwigshafen, Germany
| | - Dijun Chen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt University Berlin, 10115 Berlin, Germany
| | - Thomas Lübberstedt
- Department of Agronomy, Agronomy Hall, Iowa State University, Ames, IA 50011 USA
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle/Saale, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Seeland, Germany
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Wang Q, Sun G, Ren X, Du B, Cheng Y, Wang Y, Li C, Sun D. Dissecting the Genetic Basis of Grain Size and Weight in Barley ( Hordeum vulgare L.) by QTL and Comparative Genetic Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:469. [PMID: 31105718 PMCID: PMC6491919 DOI: 10.3389/fpls.2019.00469] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/28/2019] [Indexed: 05/23/2023]
Abstract
Grain size and weight are crucial components of barley yield and quality and are the target characteristics of domestication and modern breeding. Despite this, little is known about the genetic and molecular mechanisms of grain size and weight in barley. Here, we evaluated nine traits determining grain size and weight, including thousand grain weight (Tgw), grain length (Gl), grain width (Gw), grain length-width ratio (Lwr), grain area (Ga), grain perimeter (Gp), grain diameter (Gd), grain roundness (Gr), and factor form density (Ffd), in a double haploid (DH) population for three consecutive years. Using five mapping methods, we successfully identified 60 reliable QTLs and 27 hotspot regions that distributed on all chromosomes except 6H which controls the nine traits of grain size and weight. Moreover, we also identified 164 barley orthologs of 112 grain size/weight genes from rice, maize, wheat and 38 barley genes that affect grain yield. A total of 45 barley genes or orthologs were identified as potential candidate genes for barley grain size and weight, including 12, 20, 9, and 4 genes or orthologs for barley, rice, maize, and wheat, respectively. Importantly, 20 of them were located in the 14 QTL hotspot regions on chromosome 1H, 2H, 3H, 5H, and 7H, which controls barley grain size and weight. These results indicated that grain size/weight genes of other cereal species might have the same or similar functions in barley. Our findings provide new insights into the understanding of the genetic basis of grain size and weight in barley, and new information to facilitate high-yield breeding in barley. The function of these potential candidate genes identified in this study are worth exploring and studying in detail.
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Affiliation(s)
- Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Department of Biology, Saint Mary’s University, Halifax, NS, Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yun Cheng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yixiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China
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Wabila C, Neumann K, Kilian B, Radchuk V, Graner A. A tiered approach to genome-wide association analysis for the adherence of hulls to the caryopsis of barley seeds reveals footprints of selection. BMC PLANT BIOLOGY 2019; 19:95. [PMID: 30841851 PMCID: PMC6404267 DOI: 10.1186/s12870-019-1694-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/22/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Seeds of domesticated barley are grouped into two distinct types, which differ in morphology. Caryopses covered by adaxial (palea) and abaxial (lemma) hulls that tightly adhere to the pericarp at maturity give rise to hulled seeds whereas caryopses without adhering hulls give rise to naked seeds. The naked caryopsis character is an essential trait regarding the end use of barley. RESULTS To uncover the genetic basis of the trait, a genome-wide association study (GWAS) has been performed in a panel comprising 222 2-rowed and 303 6-rowed spring barley landrace accessions. In addition to the well-described Nud locus on chromosome 7H, three novel loci showed strong associations with the trait: the first locus on 2H was specifically detected in 6-rowed accessions, the second locus on 3H was found in 2-rowed accessions from Eurasia and the third locus on 6H was revealed in 6-rowed accessions from Ethiopia. PCR analysis of naked accessions also confirmed the absence of a 17 kb region harboring the Nud gene on chromosome 7H for all but one naked accession. The latter was characterized by a slightly variant phenotype of the caryopsis. CONCLUSION Our findings provide evidence of the pervasiveness of the 17 kb deletion in spring barley from different geographic regions and at the same time reveal genomic footprints of selection in naked barley, which follow both geographic and morphological patterns.
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Affiliation(s)
- Celestine Wabila
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Present address: Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53113 Bonn, Germany
| | - Volodymyr Radchuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle/Saale, Germany
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Koppolu R, Schnurbusch T. Developmental pathways for shaping spike inflorescence architecture in barley and wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:278-295. [PMID: 30609316 DOI: 10.1111/jipb.12771] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/18/2018] [Indexed: 05/19/2023]
Abstract
Grass species display a wide array of inflorescences ranging from highly branched compound/panicle inflorescences to unbranched spike inflorescences. The unbranched spike is a characteristic feature of the species of tribe Triticeae, including economically important crops, such as wheat and barley. In this review, we describe two important developmental genetic mechanisms regulating spike inflorescence architecture in barley and wheat. These include genetic regulation of (i) row-type pathway specific to Hordeum species and (ii) unbranched spike development in barley and wheat. For a comparative understanding, we describe the branched inflorescence phenotypes of rice and maize along with unbranched Triticeae inflorescences. In the end, we propose a simplified model describing a probable mechanism leading to unbranched spike formation in Triticeae species.
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Affiliation(s)
- Ravi Koppolu
- Independant HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - Thorsten Schnurbusch
- Independant HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, 06120 Halle, Germany
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Zwirek M, Waugh R, McKim SM. Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. THE NEW PHYTOLOGIST 2019; 221:1950-1965. [PMID: 30339269 PMCID: PMC6492131 DOI: 10.1111/nph.15548] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/22/2018] [Indexed: 05/24/2023]
Abstract
Hordeum species develop a central spikelet flanked by two lateral spikelets at each inflorescence node. In 'two-rowed' spikes, the central spikelet alone is fertile and sets grain, while in 'six-rowed' spikes, lateral spikelets can also produce grain. Induced loss-of-function alleles of any of five Six-rowed spike (VRS) genes (VRS1-5) cause complete to intermediate gains of lateral spikelet fertility. Current six-row cultivars contain natural defective vrs1 and vrs5 alleles. Little information is known about VRS mechanism(s). We used comparative developmental, expression and genetic analyses on single and double vrs mutants to learn more about how VRS genes control development and assess their agronomic potential. We show that all VRS genes repress fertility at carpel and awn emergence in developing lateral spikelets. VRS4, VRS3 and VRS5 work through VRS1 to suppress fertility, probably by inducing VRS1 expression. Pairing vrs3, vrs4 or vrs5 alleles increased lateral spikelet fertility, despite the presence of a functional VRS1 allele. The vrs3 allele caused loss of spikelet identity and determinacy, improved grain homogeneity and increased tillering in a vrs4 background, while with vrs5, decreased tiller number and increased grain weight. Interactions amongst VRS genes control spikelet infertility, determinacy and outgrowth, and novel routes to improving six-row grain.
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Affiliation(s)
- Monika Zwirek
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Robbie Waugh
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
- Division of Plant SciencesUniversity of Dundee at The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Sarah M. McKim
- Division of Plant SciencesUniversity of Dundee at The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
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Gauley A, Boden SA. Genetic pathways controlling inflorescence architecture and development in wheat and barley. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:296-309. [PMID: 30325110 PMCID: PMC6900778 DOI: 10.1111/jipb.12732] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/15/2018] [Indexed: 05/18/2023]
Abstract
Modifications of inflorescence architecture have been crucial for the successful domestication of wheat and barley, which are central members of the Triticeae tribe that provide essential grains for the human diet. Investigation of the genes and alleles that underpin domestication-related traits has provided valuable insights into the molecular regulation of inflorescence development of the Triticeae, and further investigation of modified forms of architecture are proving to be equally fruitful. The identified genes are involved in diverse biological processes, including transcriptional regulation, hormone biosynthesis and metabolism, post-transcriptional and post-translational regulation, which alter inflorescence architecture by modifying the development and fertility of lateral organs, called spikelets and florets. Recent advances in sequencing capabilities and the generation of mutant populations are accelerating the identification of genes that influence inflorescence development, which is important given that genetic variation for this trait promises to be a valuable resource for optimizing grain production. This review assesses recent advances in our understanding of the genes controlling inflorescence development in wheat and barley, with the aim of highlighting the importance of improvements in developmental biology for optimizing the agronomic performance of staple crop plants.
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Affiliation(s)
- Adam Gauley
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUnited Kingdom
| | - Scott A. Boden
- Department of Crop GeneticsJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUnited Kingdom
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Dong Z, Alexander M, Chuck G. Understanding Grass Domestication through Maize Mutants. Trends Genet 2019; 35:118-128. [DOI: 10.1016/j.tig.2018.10.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/17/2018] [Accepted: 10/29/2018] [Indexed: 11/28/2022]
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Darrier B, Russell J, Milner SG, Hedley PE, Shaw PD, Macaulay M, Ramsay LD, Halpin C, Mascher M, Fleury DL, Langridge P, Stein N, Waugh R. A Comparison of Mainstream Genotyping Platforms for the Evaluation and Use of Barley Genetic Resources. FRONTIERS IN PLANT SCIENCE 2019; 10:544. [PMID: 31105733 PMCID: PMC6499090 DOI: 10.3389/fpls.2019.00544] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/09/2019] [Indexed: 05/18/2023]
Abstract
We compared the performance of two commonly used genotyping platforms, genotyping-by-sequencing (GBS) and single nucleotide polymorphism-arrays (SNP), to investigate the extent and pattern of genetic variation within a collection of 1,000 diverse barley genotypes selected from the German Federal ex situ GenBank hosted at IPK Gatersleben. Each platform revealed equivalent numbers of robust bi-allelic SNPs (39,733 and 37,930 SNPs for the 50K SNP-array and GBS datasets respectively). A small overlap of 464 SNPs was common to both platforms, indicating that the methodologies we used selectively access informative polymorphism in different portions of the barley genome. Approximately half of the GBS dataset was comprised of SNPs with minor allele frequencies (MAFs) below 1%, illustrating the power of GBS to detect rare alleles in diverse germplasm collections. While desired for certain applications, the highly robust calling of alleles at the same SNPs across multiple populations is an advantage of the SNP-array, allowing direct comparisons of data from related or unrelated studies. Overall MAFs and diversity statistics (π) were higher for the SNP-array data, potentially reflecting the conscious removal of markers with a low MAF in the ascertainment population. A comparison of similarity matrices revealed a positive correlation between both approaches, supporting the validity of using either for entire GenBank characterization. To explore the potential of each dataset for focused genetic analyses we explored the outcomes of their use in genome-wide association scans for row type, growth habit and non-adhering hull, and discriminant analysis of principal components for the drivers of sub-population differentiation. Interpretation of the results from both types of analysis yielded broadly similar conclusions indicating that choice of platform used for such analyses should be determined by the research question being asked, group preferences and their capabilities to extract and interpret the different types of output data easily and quickly. Access to the requisite infrastructure for running, processing, analyzing, querying, storing, and displaying either datatype is an additional consideration. Our investigations reveal that for barley the cost per genotyping assay is less for SNP-arrays than GBS, which translates to a cost per informative datapoint being significantly lower for the SNP-array.
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Affiliation(s)
- Benoit Darrier
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sara G. Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Paul D. Shaw
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Luke D. Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Claire Halpin
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Delphine L. Fleury
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Peter Langridge
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Center of Integrated Breeding Research, Georg-August University, Göttingen, Germany
| | - Robbie Waugh
- School of Agriculture and Wine, The University of Adelaide, Adelaide, SA, Australia
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Robbie Waugh,
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Mulki MA, Bi X, von Korff M. FLOWERING LOCUS T3 Controls Spikelet Initiation But Not Floral Development. PLANT PHYSIOLOGY 2018; 178:1170-1186. [PMID: 30213796 PMCID: PMC6236595 DOI: 10.1104/pp.18.00236] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/30/2018] [Indexed: 05/18/2023]
Abstract
In many angiosperm plants, FLOWERING LOCUS T (FT)-like genes have duplicated and functionally diverged to control different reproductive traits or stages. Barley (Hordeum vulgare) carries several FT-like genes, the functions of which are not well understood. We characterized the role of HvFT3 in the vegetative and reproductive development of barley. Overexpression of HvFT3 accelerated the initiation of spikelet primordia and the early reproductive development of spring barley independently of the photoperiod. However, HvFT3 overexpression did not accelerate floral development, and inflorescences aborted under short days, suggesting that HvFT3 controls spikelet initiation but not floral development. Analysis of a nonfunctional HvFT3 allele supported the specific effects of this gene on spikelet initiation independent of the photoperiod. HvFT3 caused the up-regulation of the winter and spring alleles of the vernalization gene VERNALIZATION1 (VRN-H1) in nonvernalized plants and was therefore dominant over the repressive effects of the vernalization pathway. Global transcriptome analysis in developing main shoot apices of the transgenic lines showed that HvFT3 modified the expression of genes involved in hormone synthesis and response, of floral homeotic genes, and of barley row-type genes SIX-ROWED-SPIKE1 (VRS1), SIX-ROWED-SPIKE4 (VRS4), and INTERMEDIUM C Understanding the specific functions of individual FT-like genes will allow modification of individual phases of preanthesis development and thereby adaptation to different environments and improved yield.
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Affiliation(s)
- Muhammad Aman Mulki
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Xiaojing Bi
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules" 40225 Düsseldorf, Germany
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Trevaskis B. Developmental Pathways Are Blueprints for Designing Successful Crops. FRONTIERS IN PLANT SCIENCE 2018; 9:745. [PMID: 29922318 PMCID: PMC5996307 DOI: 10.3389/fpls.2018.00745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/15/2018] [Indexed: 05/29/2023]
Abstract
Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene-gene or gene-environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted.
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Affiliation(s)
- Ben Trevaskis
- CSIRO Agriculture and Food, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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Walling JG, Zalapa LA, Vinje MA. Evaluation and selection of internal reference genes from two- and six-row U.S. malting barley varieties throughout micromalting for use in RT-qPCR. PLoS One 2018; 13:e0196966. [PMID: 29738567 PMCID: PMC5940201 DOI: 10.1371/journal.pone.0196966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/24/2018] [Indexed: 11/28/2022] Open
Abstract
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a popular method for measuring transcript abundance. The most commonly used method of interpretation is relative quantification and thus necessitates the use of normalization controls (i.e. reference genes) to standardize transcript abundance. The most popular gene targets for RT-qPCR are housekeeping genes because they are thought to maintain a static transcript level among a variety of samples. However, more recent studies have shown, several housekeeping genes are not reliably stable. This is the first study to examine the potential of several reference genes for use in RT-qPCR normalization during barley malting. The process of malting barley mechanizes the imbibition and subsequent germination of barley seeds under controlled conditions. Malt quality is controlled by many pleiotropic genes that are determined by examining the result of physiological changes the barley seed undergoes during the malting process. We compared the stability of 13 reference genes across both two-and six-row malting barleys (Conrad and Legacy, respectfully) throughout the entirety of the malting process. Initially, primer target specificity, amplification efficiency and average Ct values were determined for each of the selected primer pairs. Three statistical programs (geNorm, NormFinder, and BestKeeper) were used to rank the stability of each reference gene. Rankings were similar between the two- and six-row with the exception of BestKeeper’s ranking of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). A consensus ranking among programs was determined using RefFinder. Our results show that Actin (ACT) and Heat Shock Protein 70 (HSP70) were the most stable throughout micromalting, while GAPDH and Cyclophilin (CYP) were the least stable. Two reference genes are necessary for stable transcript normalization according to geNorm and the best two reference genes (ACT and HSP70) provided a sufficient level of stability.
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Affiliation(s)
- Jason G. Walling
- Cereal Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Madison, Wisconsin, United States of America
| | - Leslie A. Zalapa
- Cereal Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Madison, Wisconsin, United States of America
| | - Marcus A. Vinje
- Cereal Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Madison, Wisconsin, United States of America
- * E-mail:
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Sakuma S, Lundqvist U, Kakei Y, Thirulogachandar V, Suzuki T, Hori K, Wu J, Tagiri A, Rutten T, Koppolu R, Shimada Y, Houston K, Thomas WTB, Waugh R, Schnurbusch T, Komatsuda T. Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor. PLANT PHYSIOLOGY 2017; 175:1720-1731. [PMID: 29101279 PMCID: PMC5717734 DOI: 10.1104/pp.17.01149] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/02/2017] [Indexed: 05/17/2023]
Abstract
Increasing grain yield is an endless challenge for cereal crop breeding. In barley (Hordeum vulgare), grain number is controlled mainly by Six-rowed spike 1 (Vrs1), which encodes a homeodomain leucine zipper class I transcription factor. However, little is known about the genetic basis of grain size. Here, we show that extreme suppression of lateral florets contributes to enlarged grains in deficiens barley. Through a combination of fine-mapping and resequencing of deficiens mutants, we have identified that a single amino acid substitution at a putative phosphorylation site in VRS1 is responsible for the deficiens phenotype. deficiens mutant alleles confer an increase in grain size, a reduction in plant height, and a significant increase in thousand grain weight in contemporary cultivated germplasm. Haplotype analysis revealed that barley carrying the deficiens allele (Vrs1.t1) originated from two-rowed types carrying the Vrs1.b2 allele, predominantly found in germplasm from northern Africa. In situ hybridization of histone H4, a marker for cell cycle or proliferation, showed weaker expression in the lateral spikelets compared with central spikelets in deficiens Transcriptome analysis revealed that a number of histone superfamily genes were up-regulated in the deficiens mutant, suggesting that enhanced cell proliferation in the central spikelet may contribute to larger grains. Our data suggest that grain yield can be improved by suppressing the development of specific organs that are not positively involved in sink/source relationships.
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Affiliation(s)
- Shun Sakuma
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305 8602, Japan
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, D-06466 Stadt Seeland, Germany
- Faculty of Agriculture, Tottori University, Tottori 680 8550, Japan
| | | | - Yusuke Kakei
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244 0813, Japan
| | | | - Takako Suzuki
- Agricultural Research Department, Hokkaido Research Organization, Chuo Agricultural Experiment Station, Naganuma, Hokkaido 069 1395, Japan
| | - Kiyosumi Hori
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305 8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305 8518, Japan
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305 8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305 8518, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305 8602, Japan
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, D-06466 Stadt Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, D-06466 Stadt Seeland, Germany
| | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244 0813, Japan
| | - Kelly Houston
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | | | - Robbie Waugh
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Division of Plant Sciences, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, D-06466 Stadt Seeland, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305 8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305 8518, Japan
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